Daily Papers

Synthetic datasets have successfully been used to probe visual question-answering datasets for their reasoning abilities. CLEVR (johnson2017clevr), for example, tests a range of visual reasoning abilities. The questions in CLEVR focus on comparisons of shapes, colors, and sizes, numerical reasoning, and existence claims. This paper introduces a minimally biased, diagnostic visual question-answering dataset, QLEVR, that goes beyond existential and numerical quantification and focus on more complex quantifiers and their combinations, e.g., asking whether there are more than two red balls that are smaller than at least three blue balls in an image. We describe how the dataset was created and present a first evaluation of state-of-the-art visual question-answering models, showing that QLEVR presents a formidable challenge to our current models. Code and Dataset are available at https://github.com/zechenli03/QLEVR

Visual Dialog is a multimodal task of answering a sequence of questions grounded in an image, using the conversation history as context. It entails challenges in vision, language, reasoning, and grounding. However, studying these subtasks in isolation on large, real datasets is infeasible as it requires prohibitively-expensive complete annotation of the 'state' of all images and dialogs. We develop CLEVR-Dialog, a large diagnostic dataset for studying multi-round reasoning in visual dialog. Specifically, we construct a dialog grammar that is grounded in the scene graphs of the images from the CLEVR dataset. This combination results in a dataset where all aspects of the visual dialog are fully annotated. In total, CLEVR-Dialog contains 5 instances of 10-round dialogs for about 85k CLEVR images, totaling to 4.25M question-answer pairs. We use CLEVR-Dialog to benchmark performance of standard visual dialog models; in particular, on visual coreference resolution (as a function of the coreference distance). This is the first analysis of its kind for visual dialog models that was not possible without this dataset. We hope the findings from CLEVR-Dialog will help inform the development of future models for visual dialog. Our dataset and code are publicly available.

When building artificial intelligence systems that can reason and answer questions about visual data, we need diagnostic tests to analyze our progress and discover shortcomings. Existing benchmarks for visual question answering can help, but have strong biases that models can exploit to correctly answer questions without reasoning. They also conflate multiple sources of error, making it hard to pinpoint model weaknesses. We present a diagnostic dataset that tests a range of visual reasoning abilities. It contains minimal biases and has detailed annotations describing the kind of reasoning each question requires. We use this dataset to analyze a variety of modern visual reasoning systems, providing novel insights into their abilities and limitations.

State-of-the-art visual grounding models can achieve high detection accuracy, but they are not designed to distinguish between all objects versus only certain objects of interest. In natural language, in order to specify a particular object or set of objects of interest, humans use determiners such as "my", "either" and "those". Determiners, as an important word class, are a type of schema in natural language about the reference or quantity of the noun. Existing grounded referencing datasets place much less emphasis on determiners, compared to other word classes such as nouns, verbs and adjectives. This makes it difficult to develop models that understand the full variety and complexity of object referencing. Thus, we have developed and released the DetermiNet dataset , which comprises 250,000 synthetically generated images and captions based on 25 determiners. The task is to predict bounding boxes to identify objects of interest, constrained by the semantics of the given determiner. We find that current state-of-the-art visual grounding models do not perform well on the dataset, highlighting the limitations of existing models on reference and quantification tasks.

The ability to perceive how objects change over time is a crucial ingredient in human intelligence. However, current benchmarks cannot faithfully reflect the temporal understanding abilities of video-language models (VidLMs) due to the existence of static visual shortcuts. To remedy this issue, we present VITATECS, a diagnostic VIdeo-Text dAtaset for the evaluation of TEmporal Concept underStanding. Specifically, we first introduce a fine-grained taxonomy of temporal concepts in natural language in order to diagnose the capability of VidLMs to comprehend different temporal aspects. Furthermore, to disentangle the correlation between static and temporal information, we generate counterfactual video descriptions that differ from the original one only in the specified temporal aspect. We employ a semi-automatic data collection framework using large language models and human-in-the-loop annotation to obtain high-quality counterfactual descriptions efficiently. Evaluation of representative video-language understanding models confirms their deficiency in temporal understanding, revealing the need for greater emphasis on the temporal elements in video-language research.

Despite the successes of recent developments in visual AI, different shortcomings still exist; from missing exact logical reasoning, to abstract generalization abilities, to understanding complex and noisy scenes. Unfortunately, existing benchmarks, were not designed to capture more than a few of these aspects. Whereas deep learning datasets focus on visually complex data but simple visual reasoning tasks, inductive logic datasets involve complex logical learning tasks, however, lack the visual component. To address this, we propose the visual logical learning dataset, V-LoL, that seamlessly combines visual and logical challenges. Notably, we introduce the first instantiation of V-LoL, V-LoL-Trains, -- a visual rendition of a classic benchmark in symbolic AI, the Michalski train problem. By incorporating intricate visual scenes and flexible logical reasoning tasks within a versatile framework, V-LoL-Trains provides a platform for investigating a wide range of visual logical learning challenges. We evaluate a variety of AI systems including traditional symbolic AI, neural AI, as well as neuro-symbolic AI. Our evaluations demonstrate that even state-of-the-art AI faces difficulties in dealing with visual logical learning challenges, highlighting unique advantages and limitations specific to each methodology. Overall, V-LoL opens up new avenues for understanding and enhancing current abilities in visual logical learning for AI systems.

This paper presents a comparison of six machine learning (ML) algorithms: GRU-SVM (Agarap, 2017), Linear Regression, Multilayer Perceptron (MLP), Nearest Neighbor (NN) search, Softmax Regression, and Support Vector Machine (SVM) on the Wisconsin Diagnostic Breast Cancer (WDBC) dataset (Wolberg, Street, & Mangasarian, 1992) by measuring their classification test accuracy and their sensitivity and specificity values. The said dataset consists of features which were computed from digitized images of FNA tests on a breast mass (Wolberg, Street, & Mangasarian, 1992). For the implementation of the ML algorithms, the dataset was partitioned in the following fashion: 70% for training phase, and 30% for the testing phase. The hyper-parameters used for all the classifiers were manually assigned. Results show that all the presented ML algorithms performed well (all exceeded 90% test accuracy) on the classification task. The MLP algorithm stands out among the implemented algorithms with a test accuracy of ~99.04%.

Complex question answering over knowledge base (Complex KBQA) is challenging because it requires various compositional reasoning capabilities, such as multi-hop inference, attribute comparison, set operation. Existing benchmarks have some shortcomings that limit the development of Complex KBQA: 1) they only provide QA pairs without explicit reasoning processes; 2) questions are poor in diversity or scale. To this end, we introduce KQA Pro, a dataset for Complex KBQA including ~120K diverse natural language questions. We introduce a compositional and interpretable programming language KoPL to represent the reasoning process of complex questions. For each question, we provide the corresponding KoPL program and SPARQL query, so that KQA Pro serves for both KBQA and semantic parsing tasks. Experimental results show that SOTA KBQA methods cannot achieve promising results on KQA Pro as on current datasets, which suggests that KQA Pro is challenging and Complex KBQA requires further research efforts. We also treat KQA Pro as a diagnostic dataset for testing multiple reasoning skills, conduct a thorough evaluation of existing models and discuss further directions for Complex KBQA. Our codes and datasets can be obtained from https://github.com/shijx12/KQAPro_Baselines.

Clinical diagnosis is critical in medical practice, typically requiring a continuous and evolving process that includes primary diagnosis, differential diagnosis, and final diagnosis. However, most existing clinical diagnostic tasks are single-step processes, which does not align with the complex multi-step diagnostic procedures found in real-world clinical settings. In this paper, we propose a multi-step diagnostic task and annotate a clinical diagnostic dataset (MSDiagnosis). This dataset includes primary diagnosis, differential diagnosis, and final diagnosis questions. Additionally, we propose a novel and effective framework. This framework combines forward inference, backward inference, reflection, and refinement, enabling the LLM to self-evaluate and adjust its diagnostic results. To assess the effectiveness of our proposed method, we design and conduct extensive experiments. The experimental results demonstrate the effectiveness of the proposed method. We also provide a comprehensive experimental analysis and suggest future research directions for this task.

Recent works have found evidence of gender bias in models of machine translation and coreference resolution using mostly synthetic diagnostic datasets. While these quantify bias in a controlled experiment, they often do so on a small scale and consist mostly of artificial, out-of-distribution sentences. In this work, we find grammatical patterns indicating stereotypical and non-stereotypical gender-role assignments (e.g., female nurses versus male dancers) in corpora from three domains, resulting in a first large-scale gender bias dataset of 108K diverse real-world English sentences. We manually verify the quality of our corpus and use it to evaluate gender bias in various coreference resolution and machine translation models. We find that all tested models tend to over-rely on gender stereotypes when presented with natural inputs, which may be especially harmful when deployed in commercial systems. Finally, we show that our dataset lends itself to finetuning a coreference resolution model, finding it mitigates bias on a held out set. Our dataset and models are publicly available at www.github.com/SLAB-NLP/BUG. We hope they will spur future research into gender bias evaluation mitigation techniques in realistic settings.

Recent diagnostic datasets on compositional generalization, such as SCAN (Lake and Baroni, 2018) and COGS (Kim and Linzen, 2020), expose severe problems in models trained from scratch on these datasets. However, in contrast to this poor performance, state-of-the-art models trained on larger and more general datasets show better generalization ability. In this work, to reconcile this inconsistency, we conduct an empirical analysis by training Transformer models on a variety of training sets with different data factors, including dataset scale, pattern complexity, example difficulty, etc. First, we show that increased dataset complexity can lead to better generalization behavior on multiple different generalization challenges. To further understand this improvement, we show two axes of the benefit from more complex datasets: they provide more diverse examples so compositional understanding becomes more effective, and they also prevent ungeneralizable memorization of the examples due to reduced example repetition frequency. Finally, we explore how training examples of different difficulty levels influence generalization differently. On synthetic datasets, simple examples invoke stronger compositionality than hard examples do. On larger-scale real language datasets, while hard examples become more important potentially to ensure decent data coverage, a balanced mixture of simple and hard examples manages to induce the strongest generalizability. The code and data for this work are available at https://github.com/owenzx/data4comp

End-to-end speech large language models ((LLMs)) extend the capabilities of text-based models to directly process and generate audio tokens. However, this often leads to a decline in reasoning and generation performance compared to text input, a phenomenon referred to as intelligence degradation. To systematically evaluate this gap, we propose S2SBench, a benchmark designed to quantify performance degradation in Speech LLMs. It includes diagnostic datasets targeting sentence continuation and commonsense reasoning under audio input. We further introduce a pairwise evaluation protocol based on perplexity differences between plausible and implausible samples to measure degradation relative to text input. We apply S2SBench to analyze the training process of Baichuan-Audio, which further demonstrates the benchmark's effectiveness. All datasets and evaluation code are available at https://github.com/undobug/S2SBench.

Multimodal language models (MLLMs) are increasingly being implemented in real-world environments, necessitating their ability to interpret 3D spaces and comprehend temporal dynamics. Despite their potential, current top models within our community still fall short in adequately understanding spatial and temporal dimensions. We introduce Coarse Correspondence, a simple, training-free, effective, and general-purpose visual prompting method to elicit 3D and temporal understanding in multimodal LLMs. Our method uses a lightweight tracking model to find object correspondences between frames in a video or between sets of image viewpoints. It selects the most frequent object instances and visualizes them with markers with unique IDs in the image. With this simple approach, we achieve state-of-the-art results on 3D understanding benchmarks including ScanQA (+20.5\%) and a subset of OpenEQA (+9.7\%), and on long-form video benchmarks such as EgoSchema (+6.0\%). We also curate a small diagnostic dataset to evaluate whether MLLMs can reason about space from a described viewpoint other than the camera viewpoint. Again, Coarse Correspondence improves spatial perspective-taking abilities but we highlight that MLLMs struggle with this task. Together, we demonstrate that our simple prompting method can significantly aid downstream tasks that require 3D or temporal reasoning.

Natural language inference (NLI) is an increasingly important task for natural language understanding, which requires one to infer whether a sentence entails another. However, the ability of NLI models to make pragmatic inferences remains understudied. We create an IMPlicature and PRESupposition diagnostic dataset (IMPPRES), consisting of >25k semiautomatically generated sentence pairs illustrating well-studied pragmatic inference types. We use IMPPRES to evaluate whether BERT, InferSent, and BOW NLI models trained on MultiNLI (Williams et al., 2018) learn to make pragmatic inferences. Although MultiNLI appears to contain very few pairs illustrating these inference types, we find that BERT learns to draw pragmatic inferences. It reliably treats scalar implicatures triggered by "some" as entailments. For some presupposition triggers like "only", BERT reliably recognizes the presupposition as an entailment, even when the trigger is embedded under an entailment canceling operator like negation. BOW and InferSent show weaker evidence of pragmatic reasoning. We conclude that NLI training encourages models to learn some, but not all, pragmatic inferences.

High-resolution image (HRI) understanding aims to process images with a large number of pixels, such as pathological images and agricultural aerial images, both of which can exceed 1 million pixels. Vision Large Language Models (VLMs) can allegedly handle HRIs, however, there is a lack of a comprehensive benchmark for VLMs to evaluate HRI understanding. To address this gap, we introduce HRScene, a novel unified benchmark for HRI understanding with rich scenes. HRScene incorporates 25 real-world datasets and 2 synthetic diagnostic datasets with resolutions ranging from 1,024 times 1,024 to 35,503 times 26,627. HRScene is collected and re-annotated by 10 graduate-level annotators, covering 25 scenarios, ranging from microscopic to radiology images, street views, long-range pictures, and telescope images. It includes HRIs of real-world objects, scanned documents, and composite multi-image. The two diagnostic evaluation datasets are synthesized by combining the target image with the gold answer and distracting images in different orders, assessing how well models utilize regions in HRI. We conduct extensive experiments involving 28 VLMs, including Gemini 2.0 Flash and GPT-4o. Experiments on HRScene show that current VLMs achieve an average accuracy of around 50% on real-world tasks, revealing significant gaps in HRI understanding. Results on synthetic datasets reveal that VLMs struggle to effectively utilize HRI regions, showing significant Regional Divergence and lost-in-middle, shedding light on future research.

Observing and analyzing children's social behaviors is crucial for the early diagnosis of Autism Spectrum Disorders (ASD). This work focuses on automatically detecting ASD using computer vision techniques and large language models (LLMs). Existing methods typically rely on supervised learning. However, the scarcity of ASD diagnostic datasets and the lack of interpretability in diagnostic results significantly limits its clinical application. To address these challenges, we introduce a novel unsupervised approach based on script-centric behavior understanding. Our pipeline converts video content into scripts that describe the behavior of characters, leveraging the generalizability of large language models to detect ASD in a zero-shot or few-shot manner. Specifically, we propose a scripts transcription module for multimodal behavior data textualization and a domain prompts module to bridge LLMs. Our method achieves an accuracy of 92.00\% in diagnosing ASD in children with an average age of 24 months, surpassing the performance of supervised learning methods by 3.58\% absolutely. Extensive experiments confirm the effectiveness of our approach and suggest its potential for advancing ASD research through LLMs.

Retrieval-augmented generation (RAG) is a well-suited technique for retrieving privacy-sensitive Electronic Health Records (EHR). It can serve as a key module of the healthcare copilot, helping reduce misdiagnosis for healthcare practitioners and patients. However, the diagnostic accuracy and specificity of existing heuristic-based RAG models used in the medical domain are inadequate, particularly for diseases with similar manifestations. This paper proposes MedRAG, a RAG model enhanced by knowledge graph (KG)-elicited reasoning for the medical domain that retrieves diagnosis and treatment recommendations based on manifestations. MedRAG systematically constructs a comprehensive four-tier hierarchical diagnostic KG encompassing critical diagnostic differences of various diseases. These differences are dynamically integrated with similar EHRs retrieved from an EHR database, and reasoned within a large language model. This process enables more accurate and specific decision support, while also proactively providing follow-up questions to enhance personalized medical decision-making. MedRAG is evaluated on both a public dataset DDXPlus and a private chronic pain diagnostic dataset (CPDD) collected from Tan Tock Seng Hospital, and its performance is compared against various existing RAG methods. Experimental results show that, leveraging the information integration and relational abilities of the KG, our MedRAG provides more specific diagnostic insights and outperforms state-of-the-art models in reducing misdiagnosis rates. Our code will be available at https://github.com/SNOWTEAM2023/MedRAG

Recent works show that pre-trained language models (PTLMs), such as BERT, possess certain commonsense and factual knowledge. They suggest that it is promising to use PTLMs as "neural knowledge bases" via predicting masked words. Surprisingly, we find that this may not work for numerical commonsense knowledge (e.g., a bird usually has two legs). In this paper, we investigate whether and to what extent we can induce numerical commonsense knowledge from PTLMs as well as the robustness of this process. To study this, we introduce a novel probing task with a diagnostic dataset, NumerSense, containing 13.6k masked-word-prediction probes (10.5k for fine-tuning and 3.1k for testing). Our analysis reveals that: (1) BERT and its stronger variant RoBERTa perform poorly on the diagnostic dataset prior to any fine-tuning; (2) fine-tuning with distant supervision brings some improvement; (3) the best supervised model still performs poorly as compared to human performance (54.06% vs 96.3% in accuracy).

Recently, DALL-E, a multimodal transformer language model, and its variants (including diffusion models) have shown high-quality text-to-image generation capabilities. However, despite the interesting image generation results, there has not been a detailed analysis on how to evaluate such models. In this work, we investigate the visual reasoning capabilities and social biases of different text-to-image models, covering both multimodal transformer language models and diffusion models. First, we measure three visual reasoning skills: object recognition, object counting, and spatial relation understanding. For this, we propose PaintSkills, a compositional diagnostic dataset and evaluation toolkit that measures these skills. In our experiments, there exists a large gap between the performance of recent text-to-image models and the upper bound accuracy in object counting and spatial relation understanding skills. Second, we assess gender and skin tone biases by measuring the variance of the gender/skin tone distribution based on automated and human evaluation. We demonstrate that recent text-to-image models learn specific gender/skin tone biases from web image-text pairs. We hope that our work will help guide future progress in improving text-to-image generation models on visual reasoning skills and learning socially unbiased representations. Code and data: https://github.com/j-min/DallEval

This paper is concerned with learning to solve tasks that require a chain of interdependent steps of relational inference, like answering complex questions about the relationships between objects, or solving puzzles where the smaller elements of a solution mutually constrain each other. We introduce the recurrent relational network, a general purpose module that operates on a graph representation of objects. As a generalization of Santoro et al. [2017]'s relational network, it can augment any neural network model with the capacity to do many-step relational reasoning. We achieve state of the art results on the bAbI textual question-answering dataset with the recurrent relational network, consistently solving 20/20 tasks. As bAbI is not particularly challenging from a relational reasoning point of view, we introduce Pretty-CLEVR, a new diagnostic dataset for relational reasoning. In the Pretty-CLEVR set-up, we can vary the question to control for the number of relational reasoning steps that are required to obtain the answer. Using Pretty-CLEVR, we probe the limitations of multi-layer perceptrons, relational and recurrent relational networks. Finally, we show how recurrent relational networks can learn to solve Sudoku puzzles from supervised training data, a challenging task requiring upwards of 64 steps of relational reasoning. We achieve state-of-the-art results amongst comparable methods by solving 96.6% of the hardest Sudoku puzzles.

Large language models (LLMs), particularly those with reasoning capabilities, have rapidly advanced in recent years, demonstrating significant potential across a wide range of applications. However, their deployment in healthcare, especially in disease reasoning tasks, is hindered by the challenge of acquiring expert-level cognitive data. In this paper, we introduce Citrus, a medical language model that bridges the gap between clinical expertise and AI reasoning by emulating the cognitive processes of medical experts. The model is trained on a large corpus of simulated expert disease reasoning data, synthesized using a novel approach that accurately captures the decision-making pathways of clinicians. This approach enables Citrus to better simulate the complex reasoning processes involved in diagnosing and treating medical conditions.To further address the lack of publicly available datasets for medical reasoning tasks, we release the last-stage training data, including a custom-built medical diagnostic dialogue dataset. This open-source contribution aims to support further research and development in the field. Evaluations using authoritative benchmarks such as MedQA, covering tasks in medical reasoning and language understanding, show that Citrus achieves superior performance compared to other models of similar size. These results highlight Citrus potential to significantly enhance medical decision support systems, providing a more accurate and efficient tool for clinical decision-making.

Medical Visual Question Answering (Med-VQA) holds significant potential for clinical decision support, yet existing efforts primarily focus on 2D imaging with limited task diversity. This paper presents 3D-RAD, a large-scale dataset designed to advance 3D Med-VQA using radiology CT scans. The 3D-RAD dataset encompasses six diverse VQA tasks: anomaly detection, image observation, medical computation, existence detection, static temporal diagnosis, and longitudinal temporal diagnosis. It supports both open- and closed-ended questions while introducing complex reasoning challenges, including computational tasks and multi-stage temporal analysis, to enable comprehensive benchmarking. Extensive evaluations demonstrate that existing vision-language models (VLMs), especially medical VLMs exhibit limited generalization, particularly in multi-temporal tasks, underscoring the challenges of real-world 3D diagnostic reasoning. To drive future advancements, we release a high-quality training set 3D-RAD-T of 136,195 expert-aligned samples, showing that fine-tuning on this dataset could significantly enhance model performance. Our dataset and code, aiming to catalyze multimodal medical AI research and establish a robust foundation for 3D medical visual understanding, are publicly available at https://github.com/Tang-xiaoxiao/3D-RAD.

Lung cancer remains the leading cause of cancer-related mortality worldwide, and early detection through low-dose computed tomography (LDCT) has shown significant promise in reducing death rates. With the growing integration of artificial intelligence (AI) into medical imaging, the development and evaluation of robust AI models require access to large, well-annotated datasets. In this study, we introduce the utility of Duke Lung Cancer Screening (DLCS) Dataset, the largest open-access LDCT dataset with over 2,000 scans and 3,000 expert-verified nodules. We benchmark deep learning models for both 3D nodule detection and lung cancer classification across internal and external datasets including LUNA16, LUNA25, and NLST-3D+. For detection, we develop two MONAI-based RetinaNet models (DLCSDmD and LUNA16-mD), evaluated using the Competition Performance Metric (CPM). For classification, we compare five models, including state-of-the-art pretrained models (Models Genesis, Med3D), a selfsupervised foundation model (FMCB), a randomly initialized ResNet50, and proposed a novel Strategic Warm-Start++ (SWS++) model. SWS++ uses curated candidate patches to pretrain a classification backbone within the same detection pipeline, enabling task-relevant feature learning. Our models demonstrated strong generalizability, with SWS++ achieving comparable or superior performance to existing foundational models across multiple datasets (AUC: 0.71 to 0.90). All code, models, and data are publicly released to promote reproducibility and collaboration. This work establishes a standardized benchmarking resource for lung cancer AI research, supporting future efforts in model development, validation, and clinical translation.

Developing and validating artificial intelligence models in medical imaging requires datasets that are large, granular, and diverse. To date, the majority of publicly available breast imaging datasets lack in one or more of these areas. Models trained on these data may therefore underperform on patient populations or pathologies that have not previously been encountered. The EMory BrEast imaging Dataset (EMBED) addresses these gaps by providing 3650,000 2D and DBT screening and diagnostic mammograms for 116,000 women divided equally between White and African American patients. The dataset also contains 40,000 annotated lesions linked to structured imaging descriptors and 61 ground truth pathologic outcomes grouped into six severity classes. Our goal is to share this dataset with research partners to aid in development and validation of breast AI models that will serve all patients fairly and help decrease bias in medical AI.

Audio-visual understanding is a rapidly evolving field that seeks to integrate and interpret information from both auditory and visual modalities. Despite recent advances in multi-modal learning, existing benchmarks often suffer from strong visual bias -- where answers can be inferred from visual data alone -- and provide only aggregate scores that conflate multiple sources of error. This makes it difficult to determine whether models struggle with visual understanding, audio interpretation, or audio-visual alignment. In this work, we introduce DAVE (Diagnostic Audio Visual Evaluation), a novel benchmark dataset designed to systematically evaluate audio-visual models across controlled challenges. DAVE alleviates existing limitations by (i) ensuring both modalities are necessary to answer correctly and (ii) decoupling evaluation into atomic subcategories. Our detailed analysis of state-of-the-art models reveals specific failure modes and provides targeted insights for improvement. By offering this standardized diagnostic framework, we aim to facilitate more robust development of audio-visual models. The dataset is released: https://github.com/gorjanradevski/dave

Doctors and patients alike increasingly use Large Language Models (LLMs) to diagnose clinical cases. However, unlike domains such as math or coding, where correctness can be objectively defined by the final answer, medical diagnosis requires both the outcome and the reasoning process to be accurate. Currently, widely used medical benchmarks like MedQA and MMLU assess only accuracy in the final answer, overlooking the quality and faithfulness of the clinical reasoning process. To address this limitation, we introduce MedCaseReasoning, the first open-access dataset for evaluating LLMs on their ability to align with clinician-authored diagnostic reasoning. The dataset includes 14,489 diagnostic question-and-answer cases, each paired with detailed reasoning statements derived from open-access medical case reports. We evaluate state-of-the-art reasoning LLMs on MedCaseReasoning and find significant shortcomings in their diagnoses and reasoning: for instance, the top-performing open-source model, DeepSeek-R1, achieves only 48% 10-shot diagnostic accuracy and mentions only 64% of the clinician reasoning statements (recall). However, we demonstrate that fine-tuning LLMs on the reasoning traces derived from MedCaseReasoning significantly improves diagnostic accuracy and clinical reasoning recall by an average relative gain of 29% and 41%, respectively. The open-source dataset, code, and models are available at https://github.com/kevinwu23/Stanford-MedCaseReasoning.

We propose a novel multimodal video benchmark - the Perception Test - to evaluate the perception and reasoning skills of pre-trained multimodal models (e.g. Flamingo, BEiT-3, or GPT-4). Compared to existing benchmarks that focus on computational tasks (e.g. classification, detection or tracking), the Perception Test focuses on skills (Memory, Abstraction, Physics, Semantics) and types of reasoning (descriptive, explanatory, predictive, counterfactual) across video, audio, and text modalities, to provide a comprehensive and efficient evaluation tool. The benchmark probes pre-trained models for their transfer capabilities, in a zero-shot / few-shot or limited finetuning regime. For these purposes, the Perception Test introduces 11.6k real-world videos, 23s average length, designed to show perceptually interesting situations, filmed by around 100 participants worldwide. The videos are densely annotated with six types of labels (multiple-choice and grounded video question-answers, object and point tracks, temporal action and sound segments), enabling both language and non-language evaluations. The fine-tuning and validation splits of the benchmark are publicly available (CC-BY license), in addition to a challenge server with a held-out test split. Human baseline results compared to state-of-the-art video QA models show a significant gap in performance (91.4% vs 43.6%), suggesting that there is significant room for improvement in multimodal video understanding. Dataset, baselines code, and challenge server are available at https://github.com/deepmind/perception_test

Artificial intelligence (AI) systems built on incomplete or biased data will often exhibit problematic outcomes. Current methods of data analysis, particularly before model development, are costly and not standardized. The Dataset Nutrition Label (the Label) is a diagnostic framework that lowers the barrier to standardized data analysis by providing a distilled yet comprehensive overview of dataset "ingredients" before AI model development. Building a Label that can be applied across domains and data types requires that the framework itself be flexible and adaptable; as such, the Label is comprised of diverse qualitative and quantitative modules generated through multiple statistical and probabilistic modelling backends, but displayed in a standardized format. To demonstrate and advance this concept, we generated and published an open source prototype with seven sample modules on the ProPublica Dollars for Docs dataset. The benefits of the Label are manyfold. For data specialists, the Label will drive more robust data analysis practices, provide an efficient way to select the best dataset for their purposes, and increase the overall quality of AI models as a result of more robust training datasets and the ability to check for issues at the time of model development. For those building and publishing datasets, the Label creates an expectation of explanation, which will drive better data collection practices. We also explore the limitations of the Label, including the challenges of generalizing across diverse datasets, and the risk of using "ground truth" data as a comparison dataset. We discuss ways to move forward given the limitations identified. Lastly, we lay out future directions for the Dataset Nutrition Label project, including research and public policy agendas to further advance consideration of the concept.

The scarcity of high-quality, logically sound data is a critical bottleneck for advancing the mathematical reasoning of Large Language Models (LLMs). Our work confronts this challenge by turning decades of automated theorem proving research into a scalable data engine. Rather than relying on error-prone LLMs or complex proof-assistant syntax like Lean and Isabelle, our framework leverages E-prover's saturation capabilities on the vast TPTP axiom library to derive a massive, guaranteed-valid corpus of theorems. Our pipeline is principled and simple: saturate axioms, filter for "interesting" theorems, and generate tasks. With no LLMs in the loop, we eliminate factual errors by construction. This purely symbolic data is then transformed into three difficulty-controlled challenges: entailment verification, premise selection, and proof reconstruction. Our zero-shot experiments on frontier models reveal a clear weakness: performance collapses on tasks requiring deep, structural reasoning. Our framework provides both the diagnostic tool to measure this gap and a scalable source of symbolic training data to address it. We make the code and data publicly available. https://github.com/sileod/reasoning_core https://hf.co/datasets/reasoning-core/rc1

Radiologic diagnostic errors-under-reading errors, inattentional blindness, and communication failures-remain prevalent in clinical practice. These issues often stem from missed localized abnormalities, limited global context, and variability in report language. These challenges are amplified in 3D imaging, where clinicians must examine hundreds of slices per scan. Addressing them requires systems with precise localized detection, global volume-level reasoning, and semantically consistent natural language reporting. However, existing 3D vision-language models are unable to meet all three needs jointly, lacking local-global understanding for spatial reasoning and struggling with the variability and noise of uncurated radiology reports. We present MedVista3D, a multi-scale semantic-enriched vision-language pretraining framework for 3D CT analysis. To enable joint disease detection and holistic interpretation, MedVista3D performs local and global image-text alignment for fine-grained representation learning within full-volume context. To address report variability, we apply language model rewrites and introduce a Radiology Semantic Matching Bank for semantics-aware alignment. MedVista3D achieves state-of-the-art performance on zero-shot disease classification, report retrieval, and medical visual question answering, while transferring well to organ segmentation and prognosis prediction. Code and datasets will be released.

The burgeoning integration of 3D medical imaging into healthcare has led to a substantial increase in the workload of medical professionals. To assist clinicians in their diagnostic processes and alleviate their workload, the development of a robust system for retrieving similar case studies presents a viable solution. While the concept holds great promise, the field of 3D medical text-image retrieval is currently limited by the absence of robust evaluation benchmarks and curated datasets. To remedy this, our study presents a groundbreaking dataset, BIMCV-R (This dataset will be released upon acceptance.), which includes an extensive collection of 8,069 3D CT volumes, encompassing over 2 million slices, paired with their respective radiological reports. Expanding upon the foundational work of our dataset, we craft a retrieval strategy, MedFinder. This approach employs a dual-stream network architecture, harnessing the potential of large language models to advance the field of medical image retrieval beyond existing text-image retrieval solutions. It marks our preliminary step towards developing a system capable of facilitating text-to-image, image-to-text, and keyword-based retrieval tasks.

Although large multimodal models (LMMs) have demonstrated remarkable capabilities in visual scene interpretation and reasoning, their capacity for complex and precise 3-dimensional spatial reasoning remains uncertain. Existing benchmarks focus predominantly on 2D spatial understanding and lack a framework to comprehensively evaluate 6D spatial reasoning across varying complexities. To address this limitation, we present PulseCheck457, a scalable and unbiased synthetic dataset designed with 4 key capability for spatial reasoning: multi-object recognition, 2D location, 3D location, and 3D orientation. We develop a cascading evaluation structure, constructing 7 question types across 5 difficulty levels that range from basic single object recognition to our new proposed complex 6D spatial reasoning tasks. We evaluated various large multimodal models (LMMs) on PulseCheck457, observing a general decline in performance as task complexity increases, particularly in 3D reasoning and 6D spatial tasks. To quantify these challenges, we introduce the Relative Performance Dropping Rate (RPDR), highlighting key weaknesses in 3D reasoning capabilities. Leveraging the unbiased attribute design of our dataset, we also uncover prediction biases across different attributes, with similar patterns observed in real-world image settings.

Artificial intelligence has significantly advanced skin cancer diagnosis by enabling rapid and accurate detection of malignant lesions. In this domain, most publicly available image datasets consist of single, isolated skin lesions positioned at the center of the image. While these lesion-centric datasets have been fundamental for developing diagnostic algorithms, they lack the context of the surrounding skin, which is critical for improving lesion detection. The iToBoS dataset was created to address this challenge. It includes 16,954 images of skin regions from 100 participants, captured using 3D total body photography. Each image roughly corresponds to a 7 times 9 cm section of skin with all suspicious lesions annotated using bounding boxes. Additionally, the dataset provides metadata such as anatomical location, age group, and sun damage score for each image. This dataset aims to facilitate training and benchmarking of algorithms, with the goal of enabling early detection of skin cancer and deployment of this technology in non-clinical environments.

Automated diagnostic systems (ADS) have shown significant potential in the early detection of polyps during endoscopic examinations, thereby reducing the incidence of colorectal cancer. However, due to high annotation costs and strict privacy concerns, acquiring high-quality endoscopic images poses a considerable challenge in the development of ADS. Despite recent advancements in generating synthetic images for dataset expansion, existing endoscopic image generation algorithms failed to accurately generate the details of polyp boundary regions and typically required medical priors to specify plausible locations and shapes of polyps, which limited the realism and diversity of the generated images. To address these limitations, we present Polyp-Gen, the first full-automatic diffusion-based endoscopic image generation framework. Specifically, we devise a spatial-aware diffusion training scheme with a lesion-guided loss to enhance the structural context of polyp boundary regions. Moreover, to capture medical priors for the localization of potential polyp areas, we introduce a hierarchical retrieval-based sampling strategy to match similar fine-grained spatial features. In this way, our Polyp-Gen can generate realistic and diverse endoscopic images for building reliable ADS. Extensive experiments demonstrate the state-of-the-art generation quality, and the synthetic images can improve the downstream polyp detection task. Additionally, our Polyp-Gen has shown remarkable zero-shot generalizability on other datasets. The source code is available at https://github.com/CUHK-AIM-Group/Polyp-Gen.

We introduce EgoSchema, a very long-form video question-answering dataset, and benchmark to evaluate long video understanding capabilities of modern vision and language systems. Derived from Ego4D, EgoSchema consists of over 5000 human curated multiple choice question answer pairs, spanning over 250 hours of real video data, covering a very broad range of natural human activity and behavior. For each question, EgoSchema requires the correct answer to be selected between five given options based on a three-minute-long video clip. While some prior works have proposed video datasets with long clip lengths, we posit that merely the length of the video clip does not truly capture the temporal difficulty of the video task that is being considered. To remedy this, we introduce temporal certificate sets, a general notion for capturing the intrinsic temporal understanding length associated with a broad range of video understanding tasks & datasets. Based on this metric, we find EgoSchema to have intrinsic temporal lengths over 5.7x longer than the second closest dataset and 10x to 100x longer than any other video understanding dataset. Further, our evaluation of several current state-of-the-art video and language models shows them to be severely lacking in long-term video understanding capabilities. Even models with several billions of parameters achieve QA accuracy less than 33% (random is 20%) on the EgoSchema multi-choice question answering task, while humans achieve about 76% accuracy. We posit that {}, with its long intrinsic temporal structures and diverse complexity, would serve as a valuable evaluation probe for developing effective long-term video understanding systems in the future. Data and Zero-shot model evaluation code are open-sourced for both public and commercial use under the Ego4D license at http://egoschema.github.io

Training of neural networks for automated diagnosis of pigmented skin lesions is hampered by the small size and lack of diversity of available datasets of dermatoscopic images. We tackle this problem by releasing the HAM10000 ("Human Against Machine with 10000 training images") dataset. We collected dermatoscopic images from different populations acquired and stored by different modalities. Given this diversity we had to apply different acquisition and cleaning methods and developed semi-automatic workflows utilizing specifically trained neural networks. The final dataset consists of 10015 dermatoscopic images which are released as a training set for academic machine learning purposes and are publicly available through the ISIC archive. This benchmark dataset can be used for machine learning and for comparisons with human experts. Cases include a representative collection of all important diagnostic categories in the realm of pigmented lesions. More than 50% of lesions have been confirmed by pathology, while the ground truth for the rest of the cases was either follow-up, expert consensus, or confirmation by in-vivo confocal microscopy.

Spatial control is a core capability in controllable image generation. Advancements in layout-guided image generation have shown promising results on in-distribution (ID) datasets with similar spatial configurations. However, it is unclear how these models perform when facing out-of-distribution (OOD) samples with arbitrary, unseen layouts. In this paper, we propose LayoutBench, a diagnostic benchmark for layout-guided image generation that examines four categories of spatial control skills: number, position, size, and shape. We benchmark two recent representative layout-guided image generation methods and observe that the good ID layout control may not generalize well to arbitrary layouts in the wild (e.g., objects at the boundary). Next, we propose IterInpaint, a new baseline that generates foreground and background regions in a step-by-step manner via inpainting, demonstrating stronger generalizability than existing models on OOD layouts in LayoutBench. We perform quantitative and qualitative evaluation and fine-grained analysis on the four LayoutBench skills to pinpoint the weaknesses of existing models. Lastly, we show comprehensive ablation studies on IterInpaint, including training task ratio, crop&paste vs. repaint, and generation order. Project website: https://layoutbench.github.io

The meaningful use of electronic health records (EHR) continues to progress in the digital era with clinical decision support systems augmented by artificial intelligence. A priority in improving provider experience is to overcome information overload and reduce the cognitive burden so fewer medical errors and cognitive biases are introduced during patient care. One major type of medical error is diagnostic error due to systematic or predictable errors in judgment that rely on heuristics. The potential for clinical natural language processing (cNLP) to model diagnostic reasoning in humans with forward reasoning from data to diagnosis and potentially reduce the cognitive burden and medical error has not been investigated. Existing tasks to advance the science in cNLP have largely focused on information extraction and named entity recognition through classification tasks. We introduce a novel suite of tasks coined as Diagnostic Reasoning Benchmarks, DR.BENCH, as a new benchmark for developing and evaluating cNLP models with clinical diagnostic reasoning ability. The suite includes six tasks from ten publicly available datasets addressing clinical text understanding, medical knowledge reasoning, and diagnosis generation. DR.BENCH is the first clinical suite of tasks designed to be a natural language generation framework to evaluate pre-trained language models. Experiments with state-of-the-art pre-trained generative language models using large general domain models and models that were continually trained on a medical corpus demonstrate opportunities for improvement when evaluated in DR. BENCH. We share DR. BENCH as a publicly available GitLab repository with a systematic approach to load and evaluate models for the cNLP community.

We introduce RJUA-QA, a novel medical dataset for question answering (QA) and reasoning with clinical evidence, contributing to bridge the gap between general large language models (LLMs) and medical-specific LLM applications. RJUA-QA is derived from realistic clinical scenarios and aims to facilitate LLMs in generating reliable diagnostic and advice. The dataset contains 2,132 curated Question-Context-Answer pairs, corresponding about 25,000 diagnostic records and clinical cases. The dataset covers 67 common urological disease categories, where the disease coverage exceeds 97.6\% of the population seeking medical services in urology. Each data instance in RJUA-QA comprises: (1) a question mirroring real patient to inquiry about clinical symptoms and medical conditions, (2) a context including comprehensive expert knowledge, serving as a reference for medical examination and diagnosis, (3) a doctor response offering the diagnostic conclusion and suggested examination guidance, (4) a diagnosed clinical disease as the recommended diagnostic outcome, and (5) clinical advice providing recommendations for medical examination. RJUA-QA is the first medical QA dataset for clinical reasoning over the patient inquiries, where expert-level knowledge and experience are required for yielding diagnostic conclusions and medical examination advice. A comprehensive evaluation is conducted to evaluate the performance of both medical-specific and general LLMs on the RJUA-QA dataset.

Chest Xray imaging is a widely used diagnostic tool in modern medicine, and its high utilization creates substantial workloads for radiologists. To alleviate this burden, vision language models are increasingly applied to automate Chest Xray radiology report generation (CXRRRG), aiming for clinically accurate descriptions while reducing manual effort. Conventional approaches, however, typically rely on single images, failing to capture the longitudinal context necessary for producing clinically faithful comparison statements. Recently, growing attention has been directed toward incorporating longitudinal data into CXR RRG, enabling models to leverage historical studies in ways that mirror radiologists diagnostic workflows. Nevertheless, existing surveys primarily address single image CXRRRG and offer limited guidance for longitudinal settings, leaving researchers without a systematic framework for model design. To address this gap, this survey provides the first comprehensive review of longitudinal radiology report generation (LRRG). Specifically, we examine dataset construction strategies, report generation architectures alongside longitudinally tailored designs, and evaluation protocols encompassing both longitudinal specific measures and widely used benchmarks. We further summarize LRRG methods performance, alongside analyses of different ablation studies, which collectively highlight the critical role of longitudinal information and architectural design choices in improving model performance. Finally, we summarize five major limitations of current research and outline promising directions for future development, aiming to lay a foundation for advancing this emerging field.

Image captioning, situated at the intersection of computer vision and natural language processing, requires a sophisticated understanding of both visual scenes and linguistic structure. While modern approaches are dominated by large-scale Transformer architectures, this paper documents a systematic, iterative development of foundational image captioning models, progressing from a simple CNN-LSTM encoder-decoder to a competitive attention-based system. This paper presents a series of five models, beginning with Genesis and concluding with Nexus, an advanced model featuring an EfficientNetV2B3 backbone and a dynamic attention mechanism. The experiments chart the impact of architectural enhancements and demonstrate a key finding within the classic CNN-LSTM paradigm: merely upgrading the visual backbone without a corresponding attention mechanism can degrade performance, as the single-vector bottleneck cannot transmit the richer visual detail. This insight validates the architectural shift to attention. Trained on the MS COCO 2017 dataset, the final model, Nexus, achieves a BLEU-4 score of 31.4, surpassing several foundational benchmarks and validating the iterative design process. This work provides a clear, replicable blueprint for understanding the core architectural principles that underpin modern vision-language tasks.

Breast cancer remains a leading cause of cancer-related mortality worldwide, making early detection and accurate treatment response monitoring critical priorities. We present BreastDCEDL, a curated, deep learning-ready dataset comprising pre-treatment 3D Dynamic Contrast-Enhanced MRI (DCE-MRI) scans from 2,070 breast cancer patients drawn from the I-SPY1, I-SPY2, and Duke cohorts, all sourced from The Cancer Imaging Archive. The raw DICOM imaging data were rigorously converted into standardized 3D NIfTI volumes with preserved signal integrity, accompanied by unified tumor annotations and harmonized clinical metadata including pathologic complete response (pCR), hormone receptor (HR), and HER2 status. Although DCE-MRI provides essential diagnostic information and deep learning offers tremendous potential for analyzing such complex data, progress has been limited by lack of accessible, public, multicenter datasets. BreastDCEDL addresses this gap by enabling development of advanced models, including state-of-the-art transformer architectures that require substantial training data. To demonstrate its capacity for robust modeling, we developed the first transformer-based model for breast DCE-MRI, leveraging Vision Transformer (ViT) architecture trained on RGB-fused images from three contrast phases (pre-contrast, early post-contrast, and late post-contrast). Our ViT model achieved state-of-the-art pCR prediction performance in HR+/HER2- patients (AUC 0.94, accuracy 0.93). BreastDCEDL includes predefined benchmark splits, offering a framework for reproducible research and enabling clinically meaningful modeling in breast cancer imaging.

Skin lesion datasets provide essential information for understanding various skin conditions and developing effective diagnostic tools. They aid the artificial intelligence-based early detection of skin cancer, facilitate treatment planning, and contribute to medical education and research. Published large datasets have partially coverage the subclassifications of the skin lesions. This limitation highlights the need for more expansive and varied datasets to reduce false predictions and help improve the failure analysis for skin lesions. This study presents a diverse dataset comprising 12,345 dermatoscopic images with 38 subclasses of skin lesions collected in Turkiye which comprises different skin types in the transition zone between Europe and Asia. Each subgroup contains high-resolution photos and expert annotations, providing a strong and reliable basis for future research. The detailed analysis of each subgroup provided in this study facilitates targeted research endeavors and enhances the depth of understanding regarding the skin lesions. This dataset distinguishes itself through a diverse structure with 5 super classes, 15 main classes, 38 subclasses and its 12,345 high-resolution dermatoscopic images.

Current vision-language models (VLMs) in medicine are primarily designed for categorical question answering (e.g., "Is this normal or abnormal?") or qualitative descriptive tasks. However, clinical decision-making often relies on quantitative assessments, such as measuring the size of a tumor or the angle of a joint, from which physicians draw their own diagnostic conclusions. This quantitative reasoning capability remains underexplored and poorly supported in existing VLMs. In this work, we introduce MedVision, a large-scale dataset and benchmark specifically designed to evaluate and improve VLMs on quantitative medical image analysis. MedVision spans 22 public datasets covering diverse anatomies and modalities, with 30.8 million image-annotation pairs. We focus on three representative quantitative tasks: (1) detection of anatomical structures and abnormalities, (2) tumor/lesion (T/L) size estimation, and (3) angle/distance (A/D) measurement. Our benchmarks show that current off-the-shelf VLMs perform poorly on these tasks. However, with supervised fine-tuning on MedVision, we significantly enhance their performance across detection, T/L estimation, and A/D measurement, demonstrating reduced error rates and improved precision. This work provides a foundation for developing VLMs with robust quantitative reasoning capabilities in medical imaging. Code and data are available at https://medvision-vlm.github.io.

Coronary artery disease (CAD) remains the leading cause of death globally and invasive coronary angiography (ICA) is considered the gold standard of anatomical imaging evaluation when CAD is suspected. However, risk evaluation based on ICA has several limitations, such as visual assessment of stenosis severity, which has significant interobserver variability. This motivates to development of a lesion classification system that can support specialists in their clinical procedures. Although deep learning classification methods are well-developed in other areas of medical imaging, ICA image classification is still at an early stage. One of the most important reasons is the lack of available and high-quality open-access datasets. In this paper, we reported a new annotated ICA images dataset, CADICA, to provide the research community with a comprehensive and rigorous dataset of coronary angiography consisting of a set of acquired patient videos and associated disease-related metadata. This dataset can be used by clinicians to train their skills in angiographic assessment of CAD severity and by computer scientists to create computer-aided diagnostic systems to help in such assessment. In addition, baseline classification methods are proposed and analyzed, validating the functionality of CADICA and giving the scientific community a starting point to improve CAD detection.

Alignment is no longer a luxury, it is a necessity. As large language models (LLMs) enter high-stakes domains like education, healthcare, governance, and law, their behavior must reliably reflect human-aligned values and safety constraints. Yet current evaluations rely heavily on behavioral proxies such as refusal rates, G-Eval scores, and toxicity classifiers, all of which have critical blind spots. Aligned models are often vulnerable to jailbreaking, stochasticity of generation, and alignment faking. To address this issue, we introduce the Alignment Quality Index (AQI). This novel geometric and prompt-invariant metric empirically assesses LLM alignment by analyzing the separation of safe and unsafe activations in latent space. By combining measures such as the Davies-Bouldin Score (DBS), Dunn Index (DI), Xie-Beni Index (XBI), and Calinski-Harabasz Index (CHI) across various formulations, AQI captures clustering quality to detect hidden misalignments and jailbreak risks, even when outputs appear compliant. AQI also serves as an early warning signal for alignment faking, offering a robust, decoding invariant tool for behavior agnostic safety auditing. Additionally, we propose the LITMUS dataset to facilitate robust evaluation under these challenging conditions. Empirical tests on LITMUS across different models trained under DPO, GRPO, and RLHF conditions demonstrate AQI's correlation with external judges and ability to reveal vulnerabilities missed by refusal metrics. We make our implementation publicly available to foster future research in this area.

PlantVillageVQA is a large-scale visual question answering (VQA) dataset derived from the widely used PlantVillage image corpus. It was designed to advance the development and evaluation of vision-language models for agricultural decision-making and analysis. The PlantVillageVQA dataset comprises 193,609 high-quality question-answer (QA) pairs grounded over 55,448 images spanning 14 crop species and 38 disease conditions. Questions are organised into 3 levels of cognitive complexity and 9 distinct categories. Each question category was phrased manually following expert guidance and generated via an automated two-stage pipeline: (1) template-based QA synthesis from image metadata and (2) multi-stage linguistic re-engineering. The dataset was iteratively reviewed by domain experts for scientific accuracy and relevancy. The final dataset was evaluated using three state-of-the-art models for quality assessment. Our objective remains to provide a publicly available, standardised and expert-verified database to enhance diagnostic accuracy for plant disease identifications and advance scientific research in the agricultural domain. Our dataset will be open-sourced at https://huggingface.co/datasets/SyedNazmusSakib/PlantVillageVQA.

Pancreatic NEuroendocrine Tumors (pNETs) are very rare endocrine neoplasms that account for less than 5% of all pancreatic malignancies, with an incidence of only 1-1.5 cases per 100,000. Early detection of pNETs is critical for improving patient survival, but the rarity of pNETs makes segmenting them from CT a very challenging problem. So far, there has not been a dataset specifically for pNETs available to researchers. To address this issue, we propose a pNETs dataset, a well-annotated Contrast-Enhanced Computed Tomography (CECT) dataset focused exclusively on Pancreatic Neuroendocrine Tumors, containing data from 469 patients. This is the first dataset solely dedicated to pNETs, distinguishing it from previous collections. Additionally, we provide the baseline detection networks with a new slice-wise weight loss function designed for the UNet-based model, improving the overall pNET segmentation performance. We hope that our dataset can enhance the understanding and diagnosis of pNET Tumors within the medical community, facilitate the development of more accurate diagnostic tools, and ultimately improve patient outcomes and advance the field of oncology.

Multimodal large language models (MLLMs) have shown great potential in general domains but perform poorly in some specific domains due to a lack of domain-specific data, such as image-text data or vedio-text data. In some specific domains, there is abundant graphic and textual data scattered around, but lacks standardized arrangement. In the field of medical ultrasound, there are ultrasonic diagnostic books, ultrasonic clinical guidelines, ultrasonic diagnostic reports, and so on. However, these ultrasonic materials are often saved in the forms of PDF, images, etc., and cannot be directly used for the training of MLLMs. This paper proposes a novel image-text reasoning supervised fine-tuning data generation pipeline to create specific domain quadruplets (image, question, thinking trace, and answer) from domain-specific materials. A medical ultrasound domain dataset ReMUD is established, containing over 45,000 reasoning and non-reasoning supervised fine-tuning Question Answering (QA) and Visual Question Answering (VQA) data. The ReMUD-7B model, fine-tuned on Qwen2.5-VL-7B-Instruct, outperforms general-domain MLLMs in medical ultrasound field. To facilitate research, the ReMUD dataset, data generation codebase, and ReMUD-7B parameters will be released at https://github.com/ShiDaizi/ReMUD, addressing the data shortage issue in specific domain MLLMs.

With the rapid development of computational pathology, many AI-assisted diagnostic tasks have emerged. Cellular nuclei segmentation can segment various types of cells for downstream analysis, but it relies on predefined categories and lacks flexibility. Moreover, pathology visual question answering can perform image-level understanding but lacks region-level detection capability. To address this, we propose a new benchmark called Pathology Visual Grounding (PathVG), which aims to detect regions based on expressions with different attributes. To evaluate PathVG, we create a new dataset named RefPath which contains 27,610 images with 33,500 language-grounded boxes. Compared to visual grounding in other domains, PathVG presents pathological images at multi-scale and contains expressions with pathological knowledge. In the experimental study, we found that the biggest challenge was the implicit information underlying the pathological expressions. Based on this, we proposed Pathology Knowledge-enhanced Network (PKNet) as the baseline model for PathVG. PKNet leverages the knowledge-enhancement capabilities of Large Language Models (LLMs) to convert pathological terms with implicit information into explicit visual features, and fuses knowledge features with expression features through the designed Knowledge Fusion Module (KFM). The proposed method achieves state-of-the-art performance on the PathVG benchmark.

Large vision-language models (LVLMs) have shown great promise in medical applications, particularly in visual question answering (MedVQA) and diagnosis from medical images. However, existing datasets and models often fail to consider critical aspects of medical diagnostics, such as the integration of historical records and the analysis of disease progression over time. In this paper, we introduce MMXU (Multimodal and MultiX-ray Understanding), a novel dataset for MedVQA that focuses on identifying changes in specific regions between two patient visits. Unlike previous datasets that primarily address single-image questions, MMXU enables multi-image questions, incorporating both current and historical patient data. We demonstrate the limitations of current LVLMs in identifying disease progression on MMXU-test, even those that perform well on traditional benchmarks. To address this, we propose a MedRecord-Augmented Generation (MAG) approach, incorporating both global and regional historical records. Our experiments show that integrating historical records significantly enhances diagnostic accuracy by at least 20\%, bridging the gap between current LVLMs and human expert performance. Additionally, we fine-tune models with MAG on MMXU-dev, which demonstrates notable improvements. We hope this work could illuminate the avenue of advancing the use of LVLMs in medical diagnostics by emphasizing the importance of historical context in interpreting medical images. Our dataset is released at https://github.com/linjiemu/MMXU{https://github.com/linjiemu/MMXU}.

Recently, Computer-Aided Diagnosis (CAD) systems have emerged as indispensable tools in clinical diagnostic workflows, significantly alleviating the burden on radiologists. Nevertheless, despite their integration into clinical settings, CAD systems encounter limitations. Specifically, while CAD systems can achieve high performance in the detection of lung nodules, they face challenges in accurately predicting multiple cancer types. This limitation can be attributed to the scarcity of publicly available datasets annotated with expert-level cancer type information. This research aims to bridge this gap by providing publicly accessible datasets and reliable tools for medical diagnosis, facilitating a finer categorization of different types of lung diseases so as to offer precise treatment recommendations. To achieve this objective, we curated a diverse dataset of lung Computed Tomography (CT) images, comprising 330 annotated nodules (nodules are labeled as bounding boxes) from 95 distinct patients. The quality of the dataset was evaluated using a variety of classical classification and detection models, and these promising results demonstrate that the dataset has a feasible application and further facilitate intelligent auxiliary diagnosis.

Scalp disorders are highly prevalent worldwide, yet remain underdiagnosed due to limited access to expert evaluation and the high cost of annotation. Although AI-based approaches hold great promise, their practical deployment is hindered by challenges such as severe data imbalance and the absence of pixel-level segmentation labels. To address these issues, we propose ScalpVision, an AI-driven system for the holistic diagnosis of scalp diseases. In ScalpVision, effective hair segmentation is achieved using pseudo image-label pairs and an innovative prompting method in the absence of traditional hair masking labels. Additionally, ScalpVision introduces DiffuseIT-M, a generative model adopted for dataset augmentation while maintaining hair information, facilitating improved predictions of scalp disease severity. Our experimental results affirm ScalpVision's efficiency in diagnosing a variety of scalp conditions, showcasing its potential as a valuable tool in dermatological care. Our code is available at https://github.com/winston1214/ScalpVision.

This work has been carried out to improve the dearth of high-quality EEG datasets used for schizophrenia diagnostic tools development and studies from populations of developing and underdeveloped regions of the world. To this aim, the presented dataset contains international 10/20 system EEG recordings from West African subjects of Nigerian origin in restful states, mental arithmetic task execution states and while passively reacting to auditory stimuli, the first of its kind from the region and continent. The subjects are divided into patients and healthy controls and recorded from 37 patients and 22 healthy control subjects identified by the Mini International Schizophrenia Interview (MINI) and also assessed by the Positive and Negative Symptoms Scale (PANSS) and the World Health Organization Disability Assessment Schedule (WHODAS). All patients are admitted schizophrenia patients of the Mental Health Ward, Medical Outpatient Department of the Obafemi Awolowo University Teaching Hospital Complex (OAUTHC, Ile-Ife) and its subsidiary Wesley Guild Hospital Unit (OAUTHC, Ilesa). Controls are drawn from students and clinicians who volunteered to participate in the study at the Mental Health Ward of OAUTHC and the Wesley Guild Hospital Unit. This dataset is the first version of the Nigerian schizophrenia dataset (NSzED) and can be used by the neuroscience and computational psychiatry research community studying the diagnosis and prognosis of schizophrenia using the electroencephalogram signal modality.

Large Language Models (LLMs) have not only exhibited exceptional performance across various tasks, but also demonstrated sparks of intelligence. Recent studies have focused on assessing their capabilities on human exams and revealed their impressive competence in different domains. However, cognitive research on the overall knowledge structure of LLMs is still lacking. In this paper, based on educational diagnostic assessment method, we conduct an evaluation using MoocRadar, a meticulously annotated human test dataset based on Bloom Taxonomy. We aim to reveal the knowledge structures of LLMs and gain insights of their cognitive capabilities. This research emphasizes the significance of investigating LLMs' knowledge and understanding the disparate cognitive patterns of LLMs. By shedding light on models' knowledge, researchers can advance development and utilization of LLMs in a more informed and effective manner.

Given the clinical notes written in electronic health records (EHRs), it is challenging to predict the diagnostic codes which is formulated as a multi-label classification task. The large set of labels, the hierarchical dependency, and the imbalanced data make this prediction task extremely hard. Most existing work built a binary prediction for each label independently, ignoring the dependencies between labels. To address this problem, we propose a two-stage framework to improve automatic ICD coding by capturing the label correlation. Specifically, we train a label set distribution estimator to rescore the probability of each label set candidate generated by a base predictor. This paper is the first attempt at learning the label set distribution as a reranking module for medical code prediction. In the experiments, our proposed framework is able to improve upon best-performing predictors on the benchmark MIMIC datasets. The source code of this project is available at https://github.com/MiuLab/ICD-Correlation.

Feature vectors provided by pre-trained deep artificial neural networks have become a dominant source for image representation in recent literature. Their contribution to the performance of image analysis can be improved through finetuning. As an ultimate solution, one might even train a deep network from scratch with the domain-relevant images, a highly desirable option which is generally impeded in pathology by lack of labeled images and the computational expense. In this study, we propose a new network, namely KimiaNet, that employs the topology of the DenseNet with four dense blocks, fine-tuned and trained with histopathology images in different configurations. We used more than 240,000 image patches with 1000x1000 pixels acquired at 20x magnification through our proposed "highcellularity mosaic" approach to enable the usage of weak labels of 7,126 whole slide images of formalin-fixed paraffin-embedded human pathology samples publicly available through the The Cancer Genome Atlas (TCGA) repository. We tested KimiaNet using three public datasets, namely TCGA, endometrial cancer images, and colorectal cancer images by evaluating the performance of search and classification when corresponding features of different networks are used for image representation. As well, we designed and trained multiple convolutional batch-normalized ReLU (CBR) networks. The results show that KimiaNet provides superior results compared to the original DenseNet and smaller CBR networks when used as feature extractor to represent histopathology images.

Recent advancements in Digital Pathology (DP), particularly through artificial intelligence and Foundation Models, have underscored the importance of large-scale, diverse, and richly annotated datasets. Despite their critical role, publicly available Whole Slide Image (WSI) datasets often lack sufficient scale, tissue diversity, and comprehensive clinical metadata, limiting the robustness and generalizability of AI models. In response, we introduce the HISTAI dataset, a large, multimodal, open-access WSI collection comprising over 60,000 slides from various tissue types. Each case in the HISTAI dataset is accompanied by extensive clinical metadata, including diagnosis, demographic information, detailed pathological annotations, and standardized diagnostic coding. The dataset aims to fill gaps identified in existing resources, promoting innovation, reproducibility, and the development of clinically relevant computational pathology solutions. The dataset can be accessed at https://github.com/HistAI/HISTAI.

The emergence of vision-language models has transformed medical AI, enabling unprecedented advances in diagnostic capability and clinical applications. However, progress in dermatology has lagged behind other medical domains due to the lack of standard image-text pairs. Existing dermatological datasets are limited in both scale and depth, offering only single-label annotations across a narrow range of diseases instead of rich textual descriptions, and lacking the crucial clinical context needed for real-world applications. To address these limitations, we present Derm1M, the first large-scale vision-language dataset for dermatology, comprising 1,029,761 image-text pairs. Built from diverse educational resources and structured around a standard ontology collaboratively developed by experts, Derm1M provides comprehensive coverage for over 390 skin conditions across four hierarchical levels and 130 clinical concepts with rich contextual information such as medical history, symptoms, and skin tone. To demonstrate Derm1M potential in advancing both AI research and clinical application, we pretrained a series of CLIP-like models, collectively called DermLIP, on this dataset. The DermLIP family significantly outperforms state-of-the-art foundation models on eight diverse datasets across multiple tasks, including zero-shot skin disease classification, clinical and artifacts concept identification, few-shot/full-shot learning, and cross-modal retrieval. Our dataset and code will be public.

Rare diseases, including Inborn Errors of Metabolism (IEM), pose significant diagnostic challenges. Case reports serve as key but computationally underutilized resources to inform diagnosis. Clinical dense information extraction refers to organizing medical information into structured predefined categories. Large Language Models (LLMs) may enable scalable information extraction from case reports but are rarely evaluated for this task. We introduce CaseReportBench, an expert-annotated dataset for dense information extraction of case reports, focusing on IEMs. Using this dataset, we assess various models and prompting strategies, introducing novel approaches such as category-specific prompting and subheading-filtered data integration. Zero-shot chain-of-thought prompting offers little advantage over standard zero-shot prompting. Category-specific prompting improves alignment with the benchmark. The open-source model Qwen2.5-7B outperforms GPT-4o for this task. Our clinician evaluations show that LLMs can extract clinically relevant details from case reports, supporting rare disease diagnosis and management. We also highlight areas for improvement, such as LLMs' limitations in recognizing negative findings important for differential diagnosis. This work advances LLM-driven clinical natural language processing and paves the way for scalable medical AI applications.

This paper presents a large publicly available multi-center lumbar spine magnetic resonance imaging (MRI) dataset with reference segmentations of vertebrae, intervertebral discs (IVDs), and spinal canal. The dataset includes 447 sagittal T1 and T2 MRI series from 218 patients with a history of low back pain. It was collected from four different hospitals and was divided into a training (179 patients) and validation (39 patients) set. An iterative data annotation approach was used by training a segmentation algorithm on a small part of the dataset, enabling semi-automatic segmentation of the remaining images. The algorithm provided an initial segmentation, which was subsequently reviewed, manually corrected, and added to the training data. We provide reference performance values for this baseline algorithm and nnU-Net, which performed comparably. We set up a continuous segmentation challenge to allow for a fair comparison of different segmentation algorithms. This study may encourage wider collaboration in the field of spine segmentation, and improve the diagnostic value of lumbar spine MRI.

The advancement of artificial intelligence in oral healthcare relies on the availability of large-scale multimodal datasets that capture the complexity of clinical practice. In this paper, we present a comprehensive multimodal dataset, comprising 8775 dental checkups from 4800 patients collected over eight years (2018-2025), with patients ranging from 10 to 90 years of age. The dataset includes 50000 intraoral images, 8056 radiographs, and detailed textual records, including diagnoses, treatment plans, and follow-up notes. The data were collected under standard ethical guidelines and annotated for benchmarking. To demonstrate its utility, we fine-tuned state-of-the-art large vision-language models, Qwen-VL 3B and 7B, and evaluated them on two tasks: classification of six oro-dental anomalies and generation of complete diagnostic reports from multimodal inputs. We compared the fine-tuned models with their base counterparts and GPT-4o. The fine-tuned models achieved substantial gains over these baselines, validating the dataset and underscoring its effectiveness in advancing AI-driven oro-dental healthcare solutions. The dataset is publicly available, providing an essential resource for future research in AI dentistry.

Electrocardiogram (ECG) plays a foundational role in modern cardiovascular care, enabling non-invasive diagnosis of arrhythmias, myocardial ischemia, and conduction disorders. While machine learning has achieved expert-level performance in ECG interpretation, the development of clinically deployable multimodal AI systems remains constrained, primarily due to the lack of publicly available datasets that simultaneously incorporate raw signals, diagnostic images, and interpretation text. Most existing ECG datasets provide only single-modality data or, at most, dual modalities, making it difficult to build models that can understand and integrate diverse ECG information in real-world settings. To address this gap, we introduce MEETI (MIMIC-IV-Ext ECG-Text-Image), the first large-scale ECG dataset that synchronizes raw waveform data, high-resolution plotted images, and detailed textual interpretations generated by large language models. In addition, MEETI includes beat-level quantitative ECG parameters extracted from each lead, offering structured parameters that support fine-grained analysis and model interpretability. Each MEETI record is aligned across four components: (1) the raw ECG waveform, (2) the corresponding plotted image, (3) extracted feature parameters, and (4) detailed interpretation text. This alignment is achieved using consistent, unique identifiers. This unified structure supports transformer-based multimodal learning and supports fine-grained, interpretable reasoning about cardiac health. By bridging the gap between traditional signal analysis, image-based interpretation, and language-driven understanding, MEETI established a robust foundation for the next generation of explainable, multimodal cardiovascular AI. It offers the research community a comprehensive benchmark for developing and evaluating ECG-based AI systems.

Root canal (RC) treatment is a highly delicate and technically complex procedure in clinical practice, heavily influenced by the clinicians' experience and subjective judgment. Deep learning has made significant advancements in the field of computer-aided diagnosis (CAD) because it can provide more objective and accurate diagnostic results. However, its application in RC treatment is still relatively rare, mainly due to the lack of public datasets in this field. To address this issue, in this paper, we established a First Molar Root Canal segmentation dataset called FMRC-2025. Additionally, to alleviate the workload of manual annotation for dentists and fully leverage the unlabeled data, we designed a Cross-Frequency Collaborative training semi-supervised learning (SSL) Network called CFC-Net. It consists of two components: (1) Cross-Frequency Collaborative Mean Teacher (CFC-MT), which introduces two specialized students (SS) and one comprehensive teacher (CT) for collaborative multi-frequency training. The CT and SS are trained on different frequency components while fully integrating multi-frequency knowledge through cross and full frequency consistency supervisions. (2) Uncertainty-guided Cross-Frequency Mix (UCF-Mix) mechanism enables the network to generate high-confidence pseudo-labels while learning to integrate multi-frequency information and maintaining the structural integrity of the targets. Extensive experiments on FMRC-2025 and three public dental datasets demonstrate that CFC-MT is effective for RC segmentation and can also exhibit strong generalizability on other dental segmentation tasks, outperforming state-of-the-art SSL medical image segmentation methods. Codes and dataset will be released.

Recent advancements in medical imaging and artificial intelligence (AI) have greatly enhanced diagnostic capabilities, but the development of effective deep learning (DL) models is still constrained by the lack of high-quality annotated datasets. The traditional manual annotation process by medical experts is time- and resource-intensive, limiting the scalability of these datasets. In this work, we introduce a robust and versatile framework that combines AI and crowdsourcing to improve both the quality and quantity of medical image datasets across different modalities. Our approach utilises a user-friendly online platform that enables a diverse group of crowd annotators to label medical images efficiently. By integrating the MedSAM segmentation AI with this platform, we accelerate the annotation process while maintaining expert-level quality through an algorithm that merges crowd-labelled images. Additionally, we employ pix2pixGAN, a generative AI model, to expand the training dataset with synthetic images that capture realistic morphological features. These methods are combined into a cohesive framework designed to produce an enhanced dataset, which can serve as a universal pre-processing pipeline to boost the training of any medical deep learning segmentation model. Our results demonstrate that this framework significantly improves model performance, especially when training data is limited.

Quantitative evaluation has increased dramatically among recent video inpainting work, but the video and mask content used to gauge performance has received relatively little attention. Although attributes such as camera and background scene motion inherently change the difficulty of the task and affect methods differently, existing evaluation schemes fail to control for them, thereby providing minimal insight into inpainting failure modes. To address this gap, we propose the Diagnostic Evaluation of Video Inpainting on Landscapes (DEVIL) benchmark, which consists of two contributions: (i) a novel dataset of videos and masks labeled according to several key inpainting failure modes, and (ii) an evaluation scheme that samples slices of the dataset characterized by a fixed content attribute, and scores performance on each slice according to reconstruction, realism, and temporal consistency quality. By revealing systematic changes in performance induced by particular characteristics of the input content, our challenging benchmark enables more insightful analysis into video inpainting methods and serves as an invaluable diagnostic tool for the field. Our code and data are available at https://github.com/MichiganCOG/devil .

Medical vision-language models (VLMs) have shown promise as clinical assistants across various medical fields. However, specialized dermatology VLM capable of delivering professional and detailed diagnostic analysis remains underdeveloped, primarily due to less specialized text descriptions in current dermatology multimodal datasets. To address this issue, we propose MM-Skin, the first large-scale multimodal dermatology dataset that encompasses 3 imaging modalities, including clinical, dermoscopic, and pathological and nearly 10k high-quality image-text pairs collected from professional textbooks. In addition, we generate over 27k diverse, instruction-following vision question answering (VQA) samples (9 times the size of current largest dermatology VQA dataset). Leveraging public datasets and MM-Skin, we developed SkinVL, a dermatology-specific VLM designed for precise and nuanced skin disease interpretation. Comprehensive benchmark evaluations of SkinVL on VQA, supervised fine-tuning (SFT) and zero-shot classification tasks across 8 datasets, reveal its exceptional performance for skin diseases in comparison to both general and medical VLM models. The introduction of MM-Skin and SkinVL offers a meaningful contribution to advancing the development of clinical dermatology VLM assistants. MM-Skin is available at https://github.com/ZwQ803/MM-Skin

Traditional Chinese medicine (TCM) tongue diagnosis, while clinically valuable, faces standardization challenges due to subjective interpretation and inconsistent imaging protocols, compounded by the lack of large-scale, annotated datasets for AI development. To address this gap, we present the first specialized dataset for AI-driven TCM tongue diagnosis, comprising 6,719 high-quality images captured under standardized conditions and annotated with 20 pathological symptom categories (averaging 2.54 clinically validated labels per image, all verified by licensed TCM practitioners). The dataset supports multiple annotation formats (COCO, TXT, XML) for broad usability and has been benchmarked using nine deep learning models (YOLOv5/v7/v8 variants, SSD, and MobileNetV2) to demonstrate its utility for AI development. This resource provides a critical foundation for advancing reliable computational tools in TCM, bridging the data shortage that has hindered progress in the field, and facilitating the integration of AI into both research and clinical practice through standardized, high-quality diagnostic data.

With the rapid development of COVID-19 into a global pandemic, there is an ever more urgent need for cheap, fast and reliable tools that can assist physicians in diagnosing COVID-19. Medical imaging such as CT can take a key role in complementing conventional diagnostic tools from molecular biology, and, using deep learning techniques, several automatic systems were demonstrated promising performances using CT or X-ray data. Here, we advocate a more prominent role of point-of-care ultrasound imaging to guide COVID-19 detection. Ultrasound is non-invasive and ubiquitous in medical facilities around the globe. Our contribution is threefold. First, we gather a lung ultrasound (POCUS) dataset consisting of 1103 images (654 COVID-19, 277 bacterial pneumonia and 172 healthy controls), sampled from 64 videos. This dataset was assembled from various online sources, processed specifically for deep learning models and is intended to serve as a starting point for an open-access initiative. Second, we train a deep convolutional neural network (POCOVID-Net) on this 3-class dataset and achieve an accuracy of 89% and, by a majority vote, a video accuracy of 92% . For detecting COVID-19 in particular, the model performs with a sensitivity of 0.96, a specificity of 0.79 and F1-score of 0.92 in a 5-fold cross validation. Third, we provide an open-access web service (POCOVIDScreen) that is available at: https://pocovidscreen.org. The website deploys the predictive model, allowing to perform predictions on ultrasound lung images. In addition, it grants medical staff the option to (bulk) upload their own screenings in order to contribute to the growing public database of pathological lung ultrasound images. Dataset and code are available from: https://github.com/jannisborn/covid19_pocus_ultrasound. NOTE: This preprint is superseded by our paper in Applied Sciences: https://doi.org/10.3390/app11020672

Recent progress in Large Vision-Language Models (LVLMs) has enabled promising applications in medical tasks, such as report generation and visual question answering. However, existing benchmarks focus mainly on the final diagnostic answer, offering limited insight into whether models engage in clinically meaningful reasoning. To address this, we present CheXStruct and CXReasonBench, a structured pipeline and benchmark built on the publicly available MIMIC-CXR-JPG dataset. CheXStruct automatically derives a sequence of intermediate reasoning steps directly from chest X-rays, such as segmenting anatomical regions, deriving anatomical landmarks and diagnostic measurements, computing diagnostic indices, and applying clinical thresholds. CXReasonBench leverages this pipeline to evaluate whether models can perform clinically valid reasoning steps and to what extent they can learn from structured guidance, enabling fine-grained and transparent assessment of diagnostic reasoning. The benchmark comprises 18,988 QA pairs across 12 diagnostic tasks and 1,200 cases, each paired with up to 4 visual inputs, and supports multi-path, multi-stage evaluation including visual grounding via anatomical region selection and diagnostic measurements. Even the strongest of 10 evaluated LVLMs struggle with structured reasoning and generalization, often failing to link abstract knowledge with anatomically grounded visual interpretation. The code is available at https://github.com/ttumyche/CXReasonBench

Deep learning in medical imaging has the potential to minimize the risk of diagnostic errors, reduce radiologist workload, and accelerate diagnosis. Training such deep learning models requires large and accurate datasets, with annotations for all training samples. However, in the medical imaging domain, annotated datasets for specific tasks are often small due to the high complexity of annotations, limited access, or the rarity of diseases. To address this challenge, deep learning models can be pre-trained on large image datasets without annotations using methods from the field of self-supervised learning. After pre-training, small annotated datasets are sufficient to fine-tune the models for a specific task. The most popular self-supervised pre-training approaches in medical imaging are based on contrastive learning. However, recent studies in natural image processing indicate a strong potential for masked autoencoder approaches. Our work compares state-of-the-art contrastive learning methods with the recently introduced masked autoencoder approach "SparK" for convolutional neural networks (CNNs) on medical images. Therefore we pre-train on a large unannotated CT image dataset and fine-tune on several CT classification tasks. Due to the challenge of obtaining sufficient annotated training data in medical imaging, it is of particular interest to evaluate how the self-supervised pre-training methods perform when fine-tuning on small datasets. By experimenting with gradually reducing the training dataset size for fine-tuning, we find that the reduction has different effects depending on the type of pre-training chosen. The SparK pre-training method is more robust to the training dataset size than the contrastive methods. Based on our results, we propose the SparK pre-training for medical imaging tasks with only small annotated datasets.

Recent advances in large vision-language models (LVLMs) have demonstrated strong performance on general-purpose medical tasks. However, their effectiveness in specialized domains such as dentistry remains underexplored. In particular, panoramic X-rays, a widely used imaging modality in oral radiology, pose interpretative challenges due to dense anatomical structures and subtle pathological cues, which are not captured by existing medical benchmarks or instruction datasets. To this end, we introduce MMOral, the first large-scale multimodal instruction dataset and benchmark tailored for panoramic X-ray interpretation. MMOral consists of 20,563 annotated images paired with 1.3 million instruction-following instances across diverse task types, including attribute extraction, report generation, visual question answering, and image-grounded dialogue. In addition, we present MMOral-Bench, a comprehensive evaluation suite covering five key diagnostic dimensions in dentistry. We evaluate 64 LVLMs on MMOral-Bench and find that even the best-performing model, i.e., GPT-4o, only achieves 41.45% accuracy, revealing significant limitations of current models in this domain. To promote the progress of this specific domain, we also propose OralGPT, which conducts supervised fine-tuning (SFT) upon Qwen2.5-VL-7B with our meticulously curated MMOral instruction dataset. Remarkably, a single epoch of SFT yields substantial performance enhancements for LVLMs, e.g., OralGPT demonstrates a 24.73% improvement. Both MMOral and OralGPT hold significant potential as a critical foundation for intelligent dentistry and enable more clinically impactful multimodal AI systems in the dental field. The dataset, model, benchmark, and evaluation suite are available at https://github.com/isbrycee/OralGPT.

Multimodal large language models (MLLMs) have made significant strides, yet they face challenges in the medical domain due to limited specialized knowledge. While recent medical MLLMs demonstrate strong performance in lab settings, they often struggle in real-world applications, highlighting a substantial gap between research and practice. In this paper, we seek to address this gap at various stages of the end-to-end learning pipeline, including data collection, model fine-tuning, and evaluation. At the data collection stage, we introduce SemiHVision, a dataset that combines human annotations with automated augmentation techniques to improve both medical knowledge representation and diagnostic reasoning. For model fine-tuning, we trained PMC-Cambrian-8B-AN over 2400 H100 GPU hours, resulting in performance that surpasses public medical models like HuatuoGPT-Vision-34B (79.0% vs. 66.7%) and private general models like Claude3-Opus (55.7%) on traditional benchmarks such as SLAKE and VQA-RAD. In the evaluation phase, we observed that traditional benchmarks cannot accurately reflect realistic clinical task capabilities. To overcome this limitation and provide more targeted guidance for model evaluation, we introduce the JAMA Clinical Challenge, a novel benchmark specifically designed to evaluate diagnostic reasoning. On this benchmark, PMC-Cambrian-AN achieves state-of-the-art performance with a GPT-4 score of 1.29, significantly outperforming HuatuoGPT-Vision-34B (1.13) and Claude3-Opus (1.17), demonstrating its superior diagnostic reasoning abilities.

This technical report delves into the application of GPT-4 Vision (GPT-4V) in the nuanced realm of COVID-19 image classification, leveraging the transformative potential of in-context learning to enhance diagnostic processes.

Machine learning (ML) approaches have demonstrated promising results in a wide range of healthcare applications. Data plays a crucial role in developing ML-based healthcare systems that directly affect people's lives. Many of the ethical issues surrounding the use of ML in healthcare stem from structural inequalities underlying the way we collect, use, and handle data. Developing guidelines to improve documentation practices regarding the creation, use, and maintenance of ML healthcare datasets is therefore of critical importance. In this work, we introduce Healthsheet, a contextualized adaptation of the original datasheet questionnaire ~gebru2018datasheets for health-specific applications. Through a series of semi-structured interviews, we adapt the datasheets for healthcare data documentation. As part of the Healthsheet development process and to understand the obstacles researchers face in creating datasheets, we worked with three publicly-available healthcare datasets as our case studies, each with different types of structured data: Electronic health Records (EHR), clinical trial study data, and smartphone-based performance outcome measures. Our findings from the interviewee study and case studies show 1) that datasheets should be contextualized for healthcare, 2) that despite incentives to adopt accountability practices such as datasheets, there is a lack of consistency in the broader use of these practices 3) how the ML for health community views datasheets and particularly Healthsheets as diagnostic tool to surface the limitations and strength of datasets and 4) the relative importance of different fields in the datasheet to healthcare concerns.

The advancements in data acquisition, storage, and processing techniques have resulted in the rapid growth of heterogeneous medical data. Integrating radiological scans, histopathology images, and molecular information with clinical data is essential for developing a holistic understanding of the disease and optimizing treatment. The need for integrating data from multiple sources is further pronounced in complex diseases such as cancer for enabling precision medicine and personalized treatments. This work proposes Multimodal Integration of Oncology Data System (MINDS) - a flexible, scalable, and cost-effective metadata framework for efficiently fusing disparate data from public sources such as the Cancer Research Data Commons (CRDC) into an interconnected, patient-centric framework. MINDS offers an interface for exploring relationships across data types and building cohorts for developing large-scale multimodal machine learning models. By harmonizing multimodal data, MINDS aims to potentially empower researchers with greater analytical ability to uncover diagnostic and prognostic insights and enable evidence-based personalized care. MINDS tracks granular end-to-end data provenance, ensuring reproducibility and transparency. The cloud-native architecture of MINDS can handle exponential data growth in a secure, cost-optimized manner while ensuring substantial storage optimization, replication avoidance, and dynamic access capabilities. Auto-scaling, access controls, and other mechanisms guarantee pipelines' scalability and security. MINDS overcomes the limitations of existing biomedical data silos via an interoperable metadata-driven approach that represents a pivotal step toward the future of oncology data integration.

In this paper, we introduce a novel Multi-Modal Contrastive Pre-training Framework that synergistically combines X-rays, electrocardiograms (ECGs), and radiology/cardiology reports. Our approach leverages transformers to encode these diverse modalities into a unified representation space, aiming to enhance diagnostic accuracy and facilitate comprehensive patient assessments. We utilize LoRA-Peft to significantly reduce trainable parameters in the LLM and incorporate recent linear attention dropping strategy in the Vision Transformer(ViT) for smoother attention. Furthermore, we provide novel multimodal attention explanations and retrieval for our model. To the best of our knowledge, we are the first to propose an integrated model that combines X-ray, ECG, and Radiology/Cardiology Report with this approach. By utilizing contrastive loss, MoRE effectively aligns modality-specific features into a coherent embedding, which supports various downstream tasks such as zero-shot classification and multimodal retrieval. Employing our proposed methodology, we achieve state-of-the-art (SOTA) on the Mimic-IV, CheXpert, Edema Severity, and PtbXl downstream datasets, surpassing existing multimodal approaches. Our proposed framework shows significant improvements in capturing intricate inter-modal relationships and its robustness in medical diagnosis that establishes a framework for future research in multimodal learning in the healthcare sector.

There has been a rapidly growing interest in Automatic Symptom Detection (ASD) and Automatic Diagnosis (AD) systems in the machine learning research literature, aiming to assist doctors in telemedicine services. These systems are designed to interact with patients, collect evidence about their symptoms and relevant antecedents, and possibly make predictions about the underlying diseases. Doctors would review the interactions, including the evidence and the predictions, collect if necessary additional information from patients, before deciding on next steps. Despite recent progress in this area, an important piece of doctors' interactions with patients is missing in the design of these systems, namely the differential diagnosis. Its absence is largely due to the lack of datasets that include such information for models to train on. In this work, we present a large-scale synthetic dataset of roughly 1.3 million patients that includes a differential diagnosis, along with the ground truth pathology, symptoms and antecedents for each patient. Unlike existing datasets which only contain binary symptoms and antecedents, this dataset also contains categorical and multi-choice symptoms and antecedents useful for efficient data collection. Moreover, some symptoms are organized in a hierarchy, making it possible to design systems able to interact with patients in a logical way. As a proof-of-concept, we extend two existing AD and ASD systems to incorporate the differential diagnosis, and provide empirical evidence that using differentials as training signals is essential for the efficiency of such systems or for helping doctors better understand the reasoning of those systems.

Pre-trained neural language models give high performance on natural language inference (NLI) tasks. But whether they actually understand the meaning of the processed sequences remains unclear. We propose a new diagnostics test suite which allows to assess whether a dataset constitutes a good testbed for evaluating the models' meaning understanding capabilities. We specifically apply controlled corruption transformations to widely used benchmarks (MNLI and ANLI), which involve removing entire word classes and often lead to non-sensical sentence pairs. If model accuracy on the corrupted data remains high, then the dataset is likely to contain statistical biases and artefacts that guide prediction. Inversely, a large decrease in model accuracy indicates that the original dataset provides a proper challenge to the models' reasoning capabilities. Hence, our proposed controls can serve as a crash test for developing high quality data for NLI tasks.

As the global burden of Alzheimer's disease (AD) continues to grow, early and accurate detection has become increasingly critical, especially in regions with limited access to advanced diagnostic tools. We propose BRAINS (Biomedical Retrieval-Augmented Intelligence for Neurodegeneration Screening) to address this challenge. This novel system harnesses the powerful reasoning capabilities of Large Language Models (LLMs) for Alzheimer's detection and monitoring. BRAINS features a dual-module architecture: a cognitive diagnostic module and a case-retrieval module. The Diagnostic Module utilizes LLMs fine-tuned on cognitive and neuroimaging datasets -- including MMSE, CDR scores, and brain volume metrics -- to perform structured assessments of Alzheimer's risk. Meanwhile, the Case Retrieval Module encodes patient profiles into latent representations and retrieves similar cases from a curated knowledge base. These auxiliary cases are fused with the input profile via a Case Fusion Layer to enhance contextual understanding. The combined representation is then processed with clinical prompts for inference. Evaluations on real-world datasets demonstrate BRAINS effectiveness in classifying disease severity and identifying early signs of cognitive decline. This system not only shows strong potential as an assistive tool for scalable, explainable, and early-stage Alzheimer's disease detection, but also offers hope for future applications in the field.

Background: Cancer remains one of the leading causes of morbidity and mortality worldwide. Comprehensive datasets that combine histopathological images with genetic and survival data across various tumour sites are essential for advancing computational pathology and personalised medicine. Results: We present SurGen, a dataset comprising 1,020 H&E-stained whole slide images (WSIs) from 843 colorectal cancer cases. The dataset includes detailed annotations for key genetic mutations (KRAS, NRAS, BRAF) and mismatch repair status, as well as survival data for 426 cases. To demonstrate SurGen's practical utility, we conducted a proof-of-concept machine learning experiment predicting mismatch repair status from the WSIs, achieving a test AUROC of 0.8316. These preliminary results underscore the dataset's potential to facilitate research in biomarker discovery, prognostic modelling, and advanced machine learning applications in colorectal cancer. Conclusions: SurGen offers a valuable resource for the scientific community, enabling studies that require high-quality WSIs linked with comprehensive clinical and genetic information on colorectal cancer. Our initial findings affirm the dataset's capacity to advance diagnostic precision and foster the development of personalised treatment strategies in colorectal oncology. Data available online at https://doi.org/10.6019/S-BIAD1285.

Large Language Models (LLMs) excel in reasoning and generation across domains, but still struggle with identifying and diagnosing complex errors. This stems mainly from training objectives that prioritize correct answers, limiting exposure to and learning from errors. While recent studies have begun to address this by introducing error signals, most rely on shallow, static errors, restricting improvement in deep diagnostic ability. To overcome this, we propose Hide and Seek Game (HSG), a dynamic adversarial framework for error generation and diagnosis, and evaluate it on mathematical problem-solving. HSG involves two adversarial roles: Sneaky, which "hides" by generating subtle, deceptive reasoning errors, and Diagnosis, which "seeks" to accurately detect them. Through adversarial co-evolution, both error stealth and diagnostic precision are enhanced. Experiments on several math reasoning tasks show that HSG significantly boosts error diagnosis, achieving 16.8\%--31.4\% higher accuracy than baselines like GPT-4o. We also release a challenging dataset of deceptive errors and diagnostic annotations as a benchmark for future research.

In disentangling the heterogeneity observed in psychopathology, personality of the patients is considered crucial. While it has been demonstrated that personality traits are reflected in the language used by a patient, we hypothesize that this enables automatic inference of the personality type directly from speech utterances, potentially more accurately than through a traditional questionnaire-based approach explicitly designed for personality classification. To validate this hypothesis, we adopt natural language processing (NLP) and standard machine learning tools for classification. We test this on a dataset of recorded clinical diagnostic interviews (CDI) on a sample of 79 patients diagnosed with major depressive disorder (MDD) -- a condition for which differentiated treatment based on personality styles has been advocated -- and classified into anaclitic and introjective personality styles. We start by analyzing the interviews to see which linguistic features are associated with each style, in order to gain a better understanding of the styles. Then, we develop automatic classifiers based on (a) standardized questionnaire responses; (b) basic text features, i.e., TF-IDF scores of words and word sequences; (c) more advanced text features, using LIWC (linguistic inquiry and word count) and context-aware features using BERT (bidirectional encoder representations from transformers); (d) audio features. We find that automated classification with language-derived features (i.e., based on LIWC) significantly outperforms questionnaire-based classification models. Furthermore, the best performance is achieved by combining LIWC with the questionnaire features. This suggests that more work should be put into developing linguistically based automated techniques for characterizing personality, however questionnaires still to some extent complement such methods.

The emergence of vision-language models (VLMs) has opened new possibilities for clinical reasoning and has shown promising performance in dermatological diagnosis. However, their trustworthiness and clinical utility are often limited by three major factors: (1) Data heterogeneity, where diverse datasets lack consistent diagnostic labels and clinical concept annotations; (2) Absence of grounded diagnostic rationales, leading to a scarcity of reliable reasoning supervision; and (3) Limited scalability and generalization, as models trained on small, densely annotated datasets struggle to transfer nuanced reasoning to large, sparsely-annotated ones. To address these limitations, we propose SkinR1, a novel dermatological VLM that combines deep, textbook-based reasoning with the broad generalization capabilities of reinforcement learning (RL). SkinR1 systematically resolves the key challenges through a unified, end-to-end framework. First, we design a textbook-based reasoning generator that synthesizes high-fidelity, hierarchy-aware, and differential-diagnosis (DDx)-informed trajectories, providing reliable expert-level supervision. Second, we leverage the constructed trajectories for supervised fine-tuning (SFT) empowering the model with grounded reasoning ability. Third, we develop a novel RL paradigm that, by incorporating the hierarchical structure of diseases, effectively transfers these grounded reasoning patterns to large-scale, sparse data. Extensive experiments on multiple dermatology datasets demonstrate that SkinR1 achieves superior diagnostic accuracy. The ablation study demonstrates the importance of the reasoning foundation instilled by SFT.

Deep learning-based electrocardiogram (ECG) classification has shown impressive performance but clinical adoption has been slowed by the lack of transparent and faithful explanations. Post hoc methods such as saliency maps may fail to reflect a model's true decision process. Prototype-based reasoning offers a more transparent alternative by grounding decisions in similarity to learned representations of real ECG segments, enabling faithful, case-based explanations. We introduce ProtoECGNet, a prototype-based deep learning model for interpretable, multi-label ECG classification. ProtoECGNet employs a structured, multi-branch architecture that reflects clinical interpretation workflows: it integrates a 1D CNN with global prototypes for rhythm classification, a 2D CNN with time-localized prototypes for morphology-based reasoning, and a 2D CNN with global prototypes for diffuse abnormalities. Each branch is trained with a prototype loss designed for multi-label learning, combining clustering, separation, diversity, and a novel contrastive loss that encourages appropriate separation between prototypes of unrelated classes while allowing clustering for frequently co-occurring diagnoses. We evaluate ProtoECGNet on all 71 diagnostic labels from the PTB-XL dataset, demonstrating competitive performance relative to state-of-the-art black-box models while providing structured, case-based explanations. To assess prototype quality, we conduct a structured clinician review of the final model's projected prototypes, finding that they are rated as representative and clear. ProtoECGNet shows that prototype learning can be effectively scaled to complex, multi-label time-series classification, offering a practical path toward transparent and trustworthy deep learning models for clinical decision support.

Developing models with robust group fairness properties is paramount, particularly in ethically sensitive domains such as medical diagnosis. Recent approaches to achieving fairness in machine learning require a substantial amount of training data and depend on model retraining, which may not be practical in real-world scenarios. To mitigate these challenges, we propose Bias-based Weight Masking Fine-Tuning (BMFT), a novel post-processing method that enhances the fairness of a trained model in significantly fewer epochs without requiring access to the original training data. BMFT produces a mask over model parameters, which efficiently identifies the weights contributing the most towards biased predictions. Furthermore, we propose a two-step debiasing strategy, wherein the feature extractor undergoes initial fine-tuning on the identified bias-influenced weights, succeeded by a fine-tuning phase on a reinitialised classification layer to uphold discriminative performance. Extensive experiments across four dermatological datasets and two sensitive attributes demonstrate that BMFT outperforms existing state-of-the-art (SOTA) techniques in both diagnostic accuracy and fairness metrics. Our findings underscore the efficacy and robustness of BMFT in advancing fairness across various out-of-distribution (OOD) settings. Our code is available at: https://github.com/vios-s/BMFT

This large scale study focuses on quantifying what X-rays diagnostic prediction tasks generalize well across multiple different datasets. We present evidence that the issue of generalization is not due to a shift in the images but instead a shift in the labels. We study the cross-domain performance, agreement between models, and model representations. We find interesting discrepancies between performance and agreement where models which both achieve good performance disagree in their predictions as well as models which agree yet achieve poor performance. We also test for concept similarity by regularizing a network to group tasks across multiple datasets together and observe variation across the tasks. All code is made available online and data is publicly available: https://github.com/mlmed/torchxrayvision

Multimodal Large Language Models (MLLMs) have exhibited immense potential across numerous medical specialties; yet, dentistry remains underexplored, in part due to limited domain-specific data, scarce dental expert annotations, insufficient modality-specific modeling, and challenges in reliability. In this paper, we present OralGPT-Omni, the first dental-specialized MLLM designed for comprehensive and trustworthy analysis across diverse dental imaging modalities and clinical tasks. To explicitly capture dentists' diagnostic reasoning, we construct TRACE-CoT, a clinically grounded chain-of-thought dataset that mirrors dental radiologists' decision-making processes. This reasoning supervision, combined with our proposed four-stage training paradigm, substantially strengthens the model's capacity for dental image understanding and analysis. In parallel, we introduce MMOral-Uni, the first unified multimodal benchmark for dental image analysis. It comprises 2,809 open-ended question-answer pairs spanning five modalities and five tasks, offering a comprehensive evaluation suite to date for MLLMs in digital dentistry. OralGPT-Omni achieves an overall score of 51.84 on the MMOral-Uni benchmark and 45.31 on the MMOral-OPG benchmark, dramatically outperforming the scores of GPT-5. Our work promotes intelligent dentistry and paves the way for future advances in dental image analysis. All code, benchmark, and models will be made publicly available.

Vision-Language Models (VLMs) have demonstrated impressive capabilities in understanding visual content, but their reliability in safety-critical contexts remains under-explored. We introduce VERI (Visual Emergency Recognition Dataset), a carefully designed diagnostic benchmark of 200 images (100 contrastive pairs). Each emergency scene is matched with a visually similar but safe counterpart through multi-stage human verification and iterative refinement. Using a two-stage protocol - risk identification and emergency response - we evaluate 14 VLMs (2B-124B parameters) across medical emergencies, accidents, and natural disasters. Our analysis reveals a systematic overreaction problem: models excel at identifying real emergencies (70-100 percent success rate) but suffer from an alarming rate of false alarms, misidentifying 31-96 percent of safe situations as dangerous, with 10 scenarios failed by all models regardless of scale. This "better-safe-than-sorry" bias manifests primarily through contextual overinterpretation (88-93 percent of errors), challenging VLMs' reliability for safety applications. These findings highlight persistent limitations that are not resolved by increasing model scale, motivating targeted approaches for improving contextual safety assessment in visually misleading scenarios.

Recent advances in reasoning with large language models (LLMs)has shown remarkable reasoning capabilities in domains such as mathematics and coding, yet their application to clinical diagnosis remains underexplored. Here, we introduce ClinicalGPT-R1, a reasoning enhanced generalist large language model for disease diagnosis. Trained on a dataset of 20,000 real-world clinical records, ClinicalGPT-R1 leverages diverse training strategies to enhance diagnostic reasoning. To benchmark performance, we curated MedBench-Hard, a challenging dataset spanning seven major medical specialties and representative diseases. Experimental results demonstrate that ClinicalGPT-R1 outperforms GPT-4o in Chinese diagnostic tasks and achieves comparable performance to GPT-4 in English settings. This comparative study effectively validates the superior performance of ClinicalGPT-R1 in disease diagnosis tasks. Resources are available at https://github.com/medfound/medfound.

This research introduces a novel AI techniques as Mixture-of-Experts Transformers with Group Relative Policy Optimization (GRPO) for voice health care applications on voice pathology detection. With the architectural innovations, we adopt advanced training paradigms inspired by reinforcement learning, namely Proximal Policy Optimization (PPO) and Group-wise Regularized Policy Optimization (GRPO), to enhance model stability and performance. Experiments conducted on a synthetically generated voice pathology dataset demonstrate that our proposed models significantly improve diagnostic accuracy, F1 score, and ROC-AUC compared to conventional approaches. These findings underscore the potential of integrating transformer architectures with novel training strategies to advance automated voice pathology detection and ultimately contribute to more effective healthcare delivery. The code we used to train and evaluate our models is available at https://github.com/enkhtogtokh/voicegrpo

The rise of large language models (LLMs) has driven significant progress in medical applications, including traditional Chinese medicine (TCM). However, current medical LLMs struggle with TCM diagnosis and syndrome differentiation due to substantial differences between TCM and modern medical theory, and the scarcity of specialized, high-quality corpora. This paper addresses these challenges by proposing BianCang, a TCM-specific LLM, using a two-stage training process that first injects domain-specific knowledge and then aligns it through targeted stimulation. To enhance diagnostic and differentiation capabilities, we constructed pre-training corpora, instruction-aligned datasets based on real hospital records, and the ChP-TCM dataset derived from the Pharmacopoeia of the People's Republic of China. We compiled extensive TCM and medical corpora for continuous pre-training and supervised fine-tuning, building a comprehensive dataset to refine the model's understanding of TCM. Evaluations across 11 test sets involving 29 models and 4 tasks demonstrate the effectiveness of BianCang, offering valuable insights for future research. Code, datasets, and models are available at https://github.com/QLU-NLP/BianCang.

Audio-Visual Question Answering (AVQA) is a complex multi-modal reasoning task, demanding intelligent systems to accurately respond to natural language queries based on audio-video input pairs. Nevertheless, prevalent AVQA approaches are prone to overlearning dataset biases, resulting in poor robustness. Furthermore, current datasets may not provide a precise diagnostic for these methods. To tackle these challenges, firstly, we propose a novel dataset, MUSIC-AVQA-R, crafted in two steps: rephrasing questions within the test split of a public dataset (MUSIC-AVQA) and subsequently introducing distribution shifts to split questions. The former leads to a large, diverse test space, while the latter results in a comprehensive robustness evaluation on rare, frequent, and overall questions. Secondly, we propose a robust architecture that utilizes a multifaceted cycle collaborative debiasing strategy to overcome bias learning. Experimental results show that this architecture achieves state-of-the-art performance on MUSIC-AVQA-R, notably obtaining a significant improvement of 9.32%. Extensive ablation experiments are conducted on the two datasets mentioned to analyze the component effectiveness within the debiasing strategy. Additionally, we highlight the limited robustness of existing multi-modal QA methods through the evaluation on our dataset. We also conduct experiments combining various baselines with our proposed strategy on two datasets to verify its plug-and-play capability. Our dataset and code are available at https://github.com/reml-group/MUSIC-AVQA-R.

The gigapixel scale of whole slide images (WSIs) poses a challenge for histopathology multi-modal chatbots, requiring a global WSI analysis for diagnosis, compounding evidence from different WSI patches. Current visual instruction datasets, generated through large language models, focus on creating question/answer pairs for individual image patches, which may lack diagnostic capacity on their own in histopathology, further complicated by the absence of spatial grounding in histopathology image captions. To bridge this gap, we introduce Quilt-Instruct, a large-scale dataset of 107,131 histopathology-specific instruction question/answer pairs, that is collected by leveraging educational histopathology videos from YouTube, which provides spatial localization of captions by automatically extracting narrators' cursor movements. In addition, we provide contextual reasoning by extracting diagnosis and supporting facts from the entire video content to guide the extrapolative reasoning of GPT-4. Using Quilt-Instruct, we train Quilt-LLaVA, which can reason beyond the given single image patch, enabling diagnostic reasoning and the capability of spatial awareness. To evaluate Quilt-LLaVA, we propose a comprehensive evaluation dataset created from 985 images and 1283 human-generated question-answers. We also thoroughly evaluate Quilt-LLaVA using public histopathology datasets, where Quilt-LLaVA significantly outperforms SOTA by over 10% on relative GPT-4 score and 4% and 9% on open and closed set VQA. Our code, data, and model are publicly available at quilt-llava.github.io.

Optical Coherence Tomography Angiography (OCTA) and its derived en-face projections provide high-resolution visualization of the retinal and choroidal vasculature, which is critical for the rapid and accurate diagnosis of retinal diseases. However, acquiring high-quality OCTA images is challenging due to motion sensitivity and the high costs associated with software modifications for conventional OCT devices. Moreover, current deep learning methods for OCT-to-OCTA translation often overlook the vascular differences across retinal layers and struggle to reconstruct the intricate, dense vascular details necessary for reliable diagnosis. To overcome these limitations, we propose XOCT, a novel deep learning framework that integrates Cross-Dimensional Supervision (CDS) with a Multi-Scale Feature Fusion (MSFF) network for layer-aware vascular reconstruction. Our CDS module leverages 2D layer-wise en-face projections, generated via segmentation-weighted z-axis averaging, as supervisory signals to compel the network to learn distinct representations for each retinal layer through fine-grained, targeted guidance. Meanwhile, the MSFF module enhances vessel delineation through multi-scale feature extraction combined with a channel reweighting strategy, effectively capturing vascular details at multiple spatial scales. Our experiments on the OCTA-500 dataset demonstrate XOCT's improvements, especially for the en-face projections which are significant for clinical evaluation of retinal pathologies, underscoring its potential to enhance OCTA accessibility, reliability, and diagnostic value for ophthalmic disease detection and monitoring. The code is available at https://github.com/uci-cbcl/XOCT.

Language models have shown promising performance on the task of translating natural language questions into SQL queries (Text-to-SQL). However, most of the state-of-the-art (SOTA) approaches rely on powerful yet closed-source large language models (LLMs), such as ChatGPT and GPT-4, which may have the limitations of unclear model architectures, data privacy risks, and expensive inference overheads. To address the limitations, we introduce CodeS, a series of pre-trained language models with parameters ranging from 1B to 15B, specifically designed for the text-to-SQL task. CodeS is a fully open-source language model, which achieves superior accuracy with much smaller parameter sizes. This paper studies the research challenges in building CodeS. To enhance the SQL generation abilities of CodeS, we adopt an incremental pre-training approach using a specifically curated SQL-centric corpus. Based on this, we address the challenges of schema linking and rapid domain adaptation through strategic prompt construction and a bi-directional data augmentation technique. We conduct comprehensive evaluations on multiple datasets, including the widely used Spider benchmark, the newly released BIRD benchmark, robustness-diagnostic benchmarks such as Spider-DK, Spider-Syn, Spider-Realistic, and Dr.Spider, as well as two real-world datasets created for financial and academic applications. The experimental results show that our CodeS achieves new SOTA accuracy and robustness on nearly all challenging text-to-SQL benchmarks.

This study investigates the integration of diverse patient data sources into multimodal language models for automated chest X-ray (CXR) report generation. Traditionally, CXR report generation relies solely on CXR images and limited radiology data, overlooking valuable information from patient health records, particularly from emergency departments. Utilising the MIMIC-CXR and MIMIC-IV-ED datasets, we incorporate detailed patient information such as aperiodic vital signs, medications, and clinical history to enhance diagnostic accuracy. We introduce a novel approach to transform these heterogeneous data sources into embeddings that prompt a multimodal language model, significantly enhancing the diagnostic accuracy of generated radiology reports. Our comprehensive evaluation demonstrates the benefits of using a broader set of patient data, underscoring the potential for enhanced diagnostic capabilities and better patient outcomes through the integration of multimodal data in CXR report generation.

Forensic pathology is critical in determining the cause and manner of death through post-mortem examinations, both macroscopic and microscopic. The field, however, grapples with issues such as outcome variability, laborious processes, and a scarcity of trained professionals. This paper presents SongCi, an innovative visual-language model (VLM) designed specifically for forensic pathology. SongCi utilizes advanced prototypical cross-modal self-supervised contrastive learning to enhance the accuracy, efficiency, and generalizability of forensic analyses. It was pre-trained and evaluated on a comprehensive multi-center dataset, which includes over 16 million high-resolution image patches, 2,228 vision-language pairs of post-mortem whole slide images (WSIs), and corresponding gross key findings, along with 471 distinct diagnostic outcomes. Our findings indicate that SongCi surpasses existing multi-modal AI models in many forensic pathology tasks, performs comparably to experienced forensic pathologists and significantly better than less experienced ones, and provides detailed multi-modal explainability, offering critical assistance in forensic investigations. To the best of our knowledge, SongCi is the first VLM specifically developed for forensic pathological analysis and the first large-vocabulary computational pathology (CPath) model that directly processes gigapixel WSIs in forensic science.

Machine learning has brought striking advances in multilingual natural language processing capabilities over the past year. For example, the latest techniques have improved the state-of-the-art performance on the XTREME multilingual benchmark by more than 13 points. While a sizeable gap to human-level performance remains, improvements have been easier to achieve in some tasks than in others. This paper analyzes the current state of cross-lingual transfer learning and summarizes some lessons learned. In order to catalyze meaningful progress, we extend XTREME to XTREME-R, which consists of an improved set of ten natural language understanding tasks, including challenging language-agnostic retrieval tasks, and covers 50 typologically diverse languages. In addition, we provide a massively multilingual diagnostic suite (MultiCheckList) and fine-grained multi-dataset evaluation capabilities through an interactive public leaderboard to gain a better understanding of such models. The leaderboard and code for XTREME-R will be made available at https://sites.research.google/xtreme and https://github.com/google-research/xtreme respectively.

Recent advances in vision language models (VLMs) have enabled broad progress in the general medical field. However, pathology still remains a more challenging subdomain, with current pathology specific VLMs exhibiting limitations in both diagnostic accuracy and reasoning plausibility. Such shortcomings are largely attributable to the nature of current pathology datasets, which are primarily composed of image description pairs that lack the depth and structured diagnostic paradigms employed by real world pathologists. In this study, we leverage pathology textbooks and real world pathology experts to construct high-quality, reasoning-oriented datasets. Building on this, we introduce Patho-R1, a multimodal RL-based pathology Reasoner, trained through a three-stage pipeline: (1) continued pretraining on 3.5 million image-text pairs for knowledge infusion; (2) supervised fine-tuning on 500k high-quality Chain-of-Thought samples for reasoning incentivizing; (3) reinforcement learning using Group Relative Policy Optimization and Decoupled Clip and Dynamic sAmpling Policy Optimization strategies for multimodal reasoning quality refinement. To further assess the alignment quality of our dataset, we propose PathoCLIP, trained on the same figure-caption corpus used for continued pretraining. Comprehensive experimental results demonstrate that both PathoCLIP and Patho-R1 achieve robust performance across a wide range of pathology-related tasks, including zero-shot classification, cross-modal retrieval, Visual Question Answering, and Multiple Choice Question. Our project is available at the Patho-R1 repository: https://github.com/Wenchuan-Zhang/Patho-R1.

Detecting media bias is crucial, specifically in the South Asian region. Despite this, annotated datasets and computational studies for Bangla political bias research remain scarce. Crucially because, political stance detection in Bangla news requires understanding of linguistic cues, cultural context, subtle biases, rhetorical strategies, code-switching, implicit sentiment, and socio-political background. To address this, we introduce the first benchmark dataset of 200 politically significant and highly debated Bangla news articles, labeled for government-leaning, government-critique, and neutral stances, alongside diagnostic analyses for evaluating large language models (LLMs). Our comprehensive evaluation of 28 proprietary and open-source LLMs shows strong performance in detecting government-critique content (F1 up to 0.83) but substantial difficulty with neutral articles (F1 as low as 0.00). Models also tend to over-predict government-leaning stances, often misinterpreting ambiguous narratives. This dataset and its associated diagnostics provide a foundation for advancing stance detection in Bangla media research and offer insights for improving LLM performance in low-resource languages.

Large Language Models (LLMs) have been widely applied in various professional fields. By fine-tuning the models using domain specific question and answer datasets, the professional domain knowledge and Q\&A abilities of these models have significantly improved, for example, medical professional LLMs that use fine-tuning of doctor-patient Q\&A data exhibit extraordinary disease diagnostic abilities. However, we observed that despite improvements in specific domain knowledge, the performance of medical LLM in long-context understanding has significantly declined, especially compared to general language models with similar parameters. The purpose of this study is to investigate the phenomenon of reduced performance in understanding long-context in medical LLM. We designed a series of experiments to conduct open-book professional knowledge exams on all models to evaluate their ability to read long-context. By adjusting the proportion and quantity of general data and medical data in the process of fine-tuning, we can determine the best data composition to optimize the professional model and achieve a balance between long-context performance and specific domain knowledge.

Understanding visual scenes is fundamental to human intelligence. While discriminative models have significantly advanced computer vision, they often struggle with compositional understanding. In contrast, recent generative text-to-image diffusion models excel at synthesizing complex scenes, suggesting inherent compositional capabilities. Building on this, zero-shot diffusion classifiers have been proposed to repurpose diffusion models for discriminative tasks. While prior work offered promising results in discriminative compositional scenarios, these results remain preliminary due to a small number of benchmarks and a relatively shallow analysis of conditions under which the models succeed. To address this, we present a comprehensive study of the discriminative capabilities of diffusion classifiers on a wide range of compositional tasks. Specifically, our study covers three diffusion models (SD 1.5, 2.0, and, for the first time, 3-m) spanning 10 datasets and over 30 tasks. Further, we shed light on the role that target dataset domains play in respective performance; to isolate the domain effects, we introduce a new diagnostic benchmark Self-Bench comprised of images created by diffusion models themselves. Finally, we explore the importance of timestep weighting and uncover a relationship between domain gap and timestep sensitivity, particularly for SD3-m. To sum up, diffusion classifiers understand compositionality, but conditions apply! Code and dataset are available at https://github.com/eugene6923/Diffusion-Classifiers-Compositionality.

Medical vision-language models (VLMs) excel at image-text understanding but typically rely on a single-pass reasoning that neglects localized visual cues. In clinical practice, however, human experts iteratively scan, focus, and refine the regions of interest before reaching a final diagnosis. To narrow this machine-human perception gap, we introduce ViTAR, a novel VLM framework that emulates the iterative reasoning process of human experts through a cognitive chain of "think-act-rethink-answer". ViTAR treats medical images as interactive objects, enabling models to engage multi-step visual reasoning. To support this approach, we curate a high-quality instruction dataset comprising 1K interactive examples that encode expert-like diagnostic behaviors. In addition, a 16K visual question answering training data has been curated towards fine-grained visual diagnosis. We introduce a two-stage training strategy that begins with supervised fine-tuning to guide cognitive trajectories, followed by the reinforcement learning to optimize decision-making. Extensive evaluations demonstrate that ViTAR outperforms strong state-of-the-art models. Visual attention analysis reveals that from the "think" to "rethink" rounds, ViTAR increasingly anchors visual grounding to clinically critical regions and maintains high attention allocation to visual tokens during reasoning, providing mechanistic insight into its improved performance. These findings demonstrate that embedding expert-style iterative thinking chains into VLMs enhances both performance and trustworthiness of medical AI.

Medical eye-tracking data is an important information source for understanding how radiologists visually interpret medical images. This information not only improves the accuracy of deep learning models for X-ray analysis but also their interpretability, enhancing transparency in decision-making. However, the current eye-tracking data is dispersed, unprocessed, and ambiguous, making it difficult to derive meaningful insights. Therefore, there is a need to create a new dataset with more focus and purposeful eyetracking data, improving its utility for diagnostic applications. In this work, we propose a refinement method inspired by the target-present visual search challenge: there is a specific finding and fixations are guided to locate it. After refining the existing eye-tracking datasets, we transform them into a curated visual search dataset, called GazeSearch, specifically for radiology findings, where each fixation sequence is purposefully aligned to the task of locating a particular finding. Subsequently, we introduce a scan path prediction baseline, called ChestSearch, specifically tailored to GazeSearch. Finally, we employ the newly introduced GazeSearch as a benchmark to evaluate the performance of current state-of-the-art methods, offering a comprehensive assessment for visual search in the medical imaging domain. Code is available at https://github.com/UARK-AICV/GazeSearch.

Current Large Language Models (LLMs) exhibit significant limitations, notably in structured, interpretable, and verifiable medical reasoning, alongside practical deployment challenges related to computational resources and data privacy. This report focused on the development of WiNGPT-3.0, the 32-billion parameter LLMs, engineered with the objective of enhancing its capacity for medical reasoning and exploring its potential for effective integration within healthcare IT infrastructures. The broader aim is to advance towards clinically applicable models. The approach involved a multi-stage training pipeline tailored for general, medical, and clinical reasoning. This pipeline incorporated supervised fine-tuning (SFT) and reinforcement learning (RL), leveraging curated Long Chain-of-Thought (CoT) datasets, auxiliary reward models, and an evidence-based diagnostic chain simulation. WiNGPT-3.0 demonstrated strong performance: specific model variants achieved scores of 66.6 on MedCalc and 87.1 on MedQA-USMLE. Furthermore, targeted training improved performance on a clinical reasoning task from a baseline score of 58.1 to 62.5. These findings suggest that reinforcement learning, even when applied with a limited dataset of only a few thousand examples, can enhance medical reasoning accuracy. Crucially, this demonstration of RL's efficacy with limited data and computation paves the way for more trustworthy and practically deployable LLMs within clinical workflows and health information infrastructures.

In this study, we present seg2med, an advanced medical image synthesis framework that uses Denoising Diffusion Probabilistic Models (DDPM) to generate high-quality synthetic medical images conditioned on anatomical masks from TotalSegmentator. The framework synthesizes CT and MR images from segmentation masks derived from real patient data and XCAT digital phantoms, achieving a Structural Similarity Index Measure (SSIM) of 0.94 +/- 0.02 for CT and 0.89 +/- 0.04 for MR images compared to ground-truth images of real patients. It also achieves a Feature Similarity Index Measure (FSIM) of 0.78 +/- 0.04 for CT images from XCAT. The generative quality is further supported by a Fr\'echet Inception Distance (FID) of 3.62 for CT image generation. Additionally, seg2med can generate paired CT and MR images with consistent anatomical structures and convert images between CT and MR modalities, achieving SSIM values of 0.91 +/- 0.03 for MR-to-CT and 0.77 +/- 0.04 for CT-to-MR conversion. Despite the limitations of incomplete anatomical details in segmentation masks, the framework shows strong performance in cross-modality synthesis and multimodal imaging. seg2med also demonstrates high anatomical fidelity in CT synthesis, achieving a mean Dice coefficient greater than 0.90 for 11 abdominal organs and greater than 0.80 for 34 organs out of 59 in 58 test cases. The highest Dice of 0.96 +/- 0.01 was recorded for the right scapula. Leveraging the TotalSegmentator toolkit, seg2med enables segmentation mask generation across diverse datasets, supporting applications in clinical imaging, data augmentation, multimodal synthesis, and diagnostic algorithm development.

Machine Learning Force Fields (MLFFs) are a promising alternative to expensive ab initio quantum mechanical molecular simulations. Given the diversity of chemical spaces that are of interest and the cost of generating new data, it is important to understand how MLFFs generalize beyond their training distributions. In order to characterize and better understand distribution shifts in MLFFs, we conduct diagnostic experiments on chemical datasets, revealing common shifts that pose significant challenges, even for large foundation models trained on extensive data. Based on these observations, we hypothesize that current supervised training methods inadequately regularize MLFFs, resulting in overfitting and learning poor representations of out-of-distribution systems. We then propose two new methods as initial steps for mitigating distribution shifts for MLFFs. Our methods focus on test-time refinement strategies that incur minimal computational cost and do not use expensive ab initio reference labels. The first strategy, based on spectral graph theory, modifies the edges of test graphs to align with graph structures seen during training. Our second strategy improves representations for out-of-distribution systems at test-time by taking gradient steps using an auxiliary objective, such as a cheap physical prior. Our test-time refinement strategies significantly reduce errors on out-of-distribution systems, suggesting that MLFFs are capable of and can move towards modeling diverse chemical spaces, but are not being effectively trained to do so. Our experiments establish clear benchmarks for evaluating the generalization capabilities of the next generation of MLFFs. Our code is available at https://tkreiman.github.io/projects/mlff_distribution_shifts/.

Foundation models are reshaping computational pathology by enabling transfer learning, where models pre-trained on vast datasets can be adapted for downstream diagnostic, prognostic, and therapeutic response tasks. Despite these advances, foundation models are still limited in their ability to encode the entire gigapixel whole-slide images without additional training and often lack complementary multimodal data. Here, we introduce Threads, a slide-level foundation model capable of generating universal representations of whole-slide images of any size. Threads was pre-trained using a multimodal learning approach on a diverse cohort of 47,171 hematoxylin and eosin (H&E)-stained tissue sections, paired with corresponding genomic and transcriptomic profiles - the largest such paired dataset to be used for foundation model development to date. This unique training paradigm enables Threads to capture the tissue's underlying molecular composition, yielding powerful representations applicable to a wide array of downstream tasks. In extensive benchmarking across 54 oncology tasks, including clinical subtyping, grading, mutation prediction, immunohistochemistry status determination, treatment response prediction, and survival prediction, Threads outperformed all baselines while demonstrating remarkable generalizability and label efficiency. It is particularly well suited for predicting rare events, further emphasizing its clinical utility. We intend to make the model publicly available for the broader community.

As deep learning models gain attraction in medical data, ensuring transparent and trustworthy decision-making is essential. In skin cancer diagnosis, while advancements in lesion detection and classification have improved accuracy, the black-box nature of these methods poses challenges in understanding their decision processes, leading to trust issues among physicians. This study leverages the CLIP (Contrastive Language-Image Pretraining) model, trained on different skin lesion datasets, to capture meaningful relationships between visual features and diagnostic criteria terms. To further enhance transparency, we propose a method called MedGrad E-CLIP, which builds on gradient-based E-CLIP by incorporating a weighted entropy mechanism designed for complex medical imaging like skin lesions. This approach highlights critical image regions linked to specific diagnostic descriptions. The developed integrated pipeline not only classifies skin lesions by matching corresponding descriptions but also adds an essential layer of explainability developed especially for medical data. By visually explaining how different features in an image relates to diagnostic criteria, this approach demonstrates the potential of advanced vision-language models in medical image analysis, ultimately improving transparency, robustness, and trust in AI-driven diagnostic systems.

Speech patterns have been identified as potential diagnostic markers for neuropsychiatric conditions. However, most studies only compare a single clinical group to healthy controls, whereas clinical practice often requires differentiating between multiple potential diagnoses (multiclass settings). To address this, we assembled a dataset of repeated recordings from 420 participants (67 with major depressive disorder, 106 with schizophrenia and 46 with autism, as well as matched controls), and tested the performance of a range of conventional machine learning models and advanced Transformer models on both binary and multiclass classification, based on voice and text features. While binary models performed comparably to previous research (F1 scores between 0.54-0.75 for autism spectrum disorder, ASD; 0.67-0.92 for major depressive disorder, MDD; and 0.71-0.83 for schizophrenia); when differentiating between multiple diagnostic groups performance decreased markedly (F1 scores between 0.35-0.44 for ASD, 0.57-0.75 for MDD, 0.15-0.66 for schizophrenia, and 0.38-0.52 macro F1). Combining voice and text-based models yielded increased performance, suggesting that they capture complementary diagnostic information. Our results indicate that models trained on binary classification may learn to rely on markers of generic differences between clinical and non-clinical populations, or markers of clinical features that overlap across conditions, rather than identifying markers specific to individual conditions. We provide recommendations for future research in the field, suggesting increased focus on developing larger transdiagnostic datasets that include more fine-grained clinical features, and that can support the development of models that better capture the complexity of neuropsychiatric conditions and naturalistic diagnostic assessment.

Neural architecture search (NAS) has achieved breakthrough success in a great number of applications in the past few years. It could be time to take a step back and analyze the good and bad aspects in the field of NAS. A variety of algorithms search architectures under different search space. These searched architectures are trained using different setups, e.g., hyper-parameters, data augmentation, regularization. This raises a comparability problem when comparing the performance of various NAS algorithms. NAS-Bench-101 has shown success to alleviate this problem. In this work, we propose an extension to NAS-Bench-101: NAS-Bench-201 with a different search space, results on multiple datasets, and more diagnostic information. NAS-Bench-201 has a fixed search space and provides a unified benchmark for almost any up-to-date NAS algorithms. The design of our search space is inspired from the one used in the most popular cell-based searching algorithms, where a cell is represented as a DAG. Each edge here is associated with an operation selected from a predefined operation set. For it to be applicable for all NAS algorithms, the search space defined in NAS-Bench-201 includes all possible architectures generated by 4 nodes and 5 associated operation options, which results in 15,625 candidates in total. The training log and the performance for each architecture candidate are provided for three datasets. This allows researchers to avoid unnecessary repetitive training for selected candidate and focus solely on the search algorithm itself. The training time saved for every candidate also largely improves the efficiency of many methods. We provide additional diagnostic information such as fine-grained loss and accuracy, which can give inspirations to new designs of NAS algorithms. In further support, we have analyzed it from many aspects and benchmarked 10 recent NAS algorithms.

Large language models have demonstrated remarkable proficiency in long and complex reasoning tasks. However, they frequently exhibit a problematic reliance on familiar reasoning patterns, a phenomenon we term reasoning rigidity. Despite explicit instructions from users, these models often override clearly stated conditions and default to habitual reasoning trajectories, leading to incorrect conclusions. This behavior presents significant challenges, particularly in domains such as mathematics and logic puzzle, where precise adherence to specified constraints is critical. To systematically investigate reasoning rigidity, a behavior largely unexplored in prior work, we introduce a expert-curated diagnostic set, . Our dataset includes specially modified variants of existing mathematical benchmarks, namely AIME and MATH500, as well as well-known puzzles deliberately redesigned to require deviation from familiar reasoning strategies. Using this dataset, we identify recurring contamination patterns that occur when models default to ingrained reasoning. Specifically, we categorize this contamination into three distinctive modes: (i) Interpretation Overload, (ii) Input Distrust, and (iii) Partial Instruction Attention, each causing models to ignore or distort provided instructions. We publicly release our diagnostic set to facilitate future research on mitigating reasoning rigidity in language models.

Recent advances in reasoning-enhanced large language models (LLMs) and multimodal LLMs (MLLMs) have significantly improved performance in complex tasks, yet medical AI models often overlook the structured reasoning processes inherent in clinical practice. In this work, we present ChestX-Reasoner, a radiology diagnosis MLLM designed to leverage process supervision mined directly from clinical reports, reflecting the step-by-step reasoning followed by radiologists. We construct a large dataset by extracting and refining reasoning chains from routine radiology reports. Our two-stage training framework combines supervised fine-tuning and reinforcement learning guided by process rewards to better align model reasoning with clinical standards. We introduce RadRBench-CXR, a comprehensive benchmark featuring 59K visual question answering samples with 301K clinically validated reasoning steps, and propose RadRScore, a metric evaluating reasoning factuality, completeness, and effectiveness. ChestX-Reasoner outperforms existing medical and general-domain MLLMs in both diagnostic accuracy and reasoning ability, achieving 16%, 5.9%, and 18% improvements in reasoning ability compared to the best medical MLLM, the best general MLLM, and its base model, respectively, as well as 3.3%, 24%, and 27% improvements in outcome accuracy. All resources are open-sourced to facilitate further research in medical reasoning MLLMs.

To create culturally inclusive vision-language models (VLMs), the foremost requirement is developing a test benchmark that can diagnose the models' ability to respond to questions reflecting cultural elements. This paper addresses the necessity for such benchmarks, noting that existing research has relied on human annotators' manual efforts, which impedes diversity and efficiency. We propose a semi-automated pipeline for constructing cultural VLM benchmarks to enhance diversity and efficiency. This pipeline leverages human-VLM collaboration, where VLMs generate questions based on guidelines, human-annotated examples, and image-wise relevant knowledge, which are then reviewed by native speakers for quality and cultural relevance. The effectiveness of our adaptable pipeline is demonstrated through a specific application: creating a dataset tailored to Korean culture, dubbed K-Viscuit. The resulting benchmark features two types of questions: Type 1 questions measure visual recognition abilities, while Type 2 assess fine-grained visual reasoning skills. This ensures a thorough diagnosis of VLM models across various aspects. Our evaluation using K-Viscuit revealed that open-source models notably lag behind proprietary models in understanding Korean culture, highlighting areas for improvement. We provided diverse analyses of VLM performance across different cultural aspects. Besides, we explored the potential of incorporating external knowledge retrieval to enhance the generation process, suggesting future directions for improving cultural interpretation ability of VLMs. Our dataset and code will be made publicly available.

Rare diseases collectively affect over 300 million individuals worldwide, yet timely and accurate diagnosis remains a pervasive challenge. This is largely due to their clinical heterogeneity, low individual prevalence, and the limited familiarity most clinicians have with rare conditions. Here, we introduce DeepRare, the first rare disease diagnosis agentic system powered by a large language model (LLM), capable of processing heterogeneous clinical inputs. The system generates ranked diagnostic hypotheses for rare diseases, each accompanied by a transparent chain of reasoning that links intermediate analytic steps to verifiable medical evidence. DeepRare comprises three key components: a central host with a long-term memory module; specialized agent servers responsible for domain-specific analytical tasks integrating over 40 specialized tools and web-scale, up-to-date medical knowledge sources, ensuring access to the most current clinical information. This modular and scalable design enables complex diagnostic reasoning while maintaining traceability and adaptability. We evaluate DeepRare on eight datasets. The system demonstrates exceptional diagnostic performance among 2,919 diseases, achieving 100% accuracy for 1013 diseases. In HPO-based evaluations, DeepRare significantly outperforms other 15 methods, like traditional bioinformatics diagnostic tools, LLMs, and other agentic systems, achieving an average Recall@1 score of 57.18% and surpassing the second-best method (Reasoning LLM) by a substantial margin of 23.79 percentage points. For multi-modal input scenarios, DeepRare achieves 70.60% at Recall@1 compared to Exomiser's 53.20% in 109 cases. Manual verification of reasoning chains by clinical experts achieves 95.40% agreements. Furthermore, the DeepRare system has been implemented as a user-friendly web application http://raredx.cn/doctor.

As advances in large language models (LLMs) and multimodal techniques continue to mature, the development of general-purpose multimodal large language models (MLLMs) has surged, offering significant applications in interpreting natural images. However, the field of pathology has largely remained untapped, particularly in gathering high-quality data and designing comprehensive model frameworks. To bridge the gap in pathology MLLMs, we present PathAsst, a multimodal generative foundation AI assistant to revolutionize diagnostic and predictive analytics in pathology. The development of PathAsst involves three pivotal steps: data acquisition, CLIP model adaptation, and the training of PathAsst's multimodal generative capabilities. Firstly, we collect over 207K high-quality pathology image-text pairs from authoritative sources. Leveraging the advanced power of ChatGPT, we generate over 180K instruction-following samples. Furthermore, we devise additional instruction-following data specifically tailored for invoking eight pathology-specific sub-models we prepared, allowing the PathAsst to effectively collaborate with these models, enhancing its diagnostic ability. Secondly, by leveraging the collected data, we construct PathCLIP, a pathology-dedicated CLIP, to enhance PathAsst's capabilities in interpreting pathology images. Finally, we integrate PathCLIP with the Vicuna-13b and utilize pathology-specific instruction-tuning data to enhance the multimodal generation capacity of PathAsst and bolster its synergistic interactions with sub-models. The experimental results of PathAsst show the potential of harnessing AI-powered generative foundation model to improve pathology diagnosis and treatment processes.

The rapid development of Large Language Models (LLMs) and the emergence of novel abilities with scale have necessitated the construction of holistic, diverse and challenging benchmarks such as HELM and BIG-bench. However, at the moment, most of these benchmarks focus only on performance in English and evaluations that include Southeast Asian (SEA) languages are few in number. We therefore propose BHASA, a holistic linguistic and cultural evaluation suite for LLMs in SEA languages. It comprises three components: (1) a NLP benchmark covering eight tasks across Natural Language Understanding (NLU), Generation (NLG) and Reasoning (NLR) tasks, (2) LINDSEA, a linguistic diagnostic toolkit that spans the gamut of linguistic phenomena including syntax, semantics and pragmatics, and (3) a cultural diagnostics dataset that probes for both cultural representation and sensitivity. For this preliminary effort, we implement the NLP benchmark only for Indonesian, Vietnamese, Thai and Tamil, and we only include Indonesian and Tamil for LINDSEA and the cultural diagnostics dataset. As GPT-4 is purportedly one of the best-performing multilingual LLMs at the moment, we use it as a yardstick to gauge the capabilities of LLMs in the context of SEA languages. Our initial experiments on GPT-4 with BHASA find it lacking in various aspects of linguistic capabilities, cultural representation and sensitivity in the targeted SEA languages. BHASA is a work in progress and will continue to be improved and expanded in the future. The repository for this paper can be found at: https://github.com/aisingapore/BHASA

Compared to single-turn dialogue, multi-turn dialogue involving multiple images better aligns with the needs of real-world human-AI interactions. Additionally, as training data, it provides richer contextual reasoning information, thereby guiding the model to achieve better performance. However, existing vision-language models (VLMs) primarily rely on single-turn dialogue training and evaluation benchmarks. In this paper, following the characteristics of human dialogue, such as focused topics and concise, clear content, we present MMCR (Multimodal Multi-turn Contextual Reasoning), a novel dataset comprising: (1) MMCR-310k -- the largest multi-image multi-turn instruction tuning dataset with 310K contextual dialogues, each covering 1-4 images and 4 or 8 dialogue turns; and (2) MMCR-Bench -- a diagnostic benchmark featuring dialogues, spanning 8 domains (Humanities, Natural, Science, Education, etc.) and 40 sub-topics. Extensive evaluations demonstrate that models fine-tuned with MMCR-310k achieve 5.2\% higher contextual accuracy on MMCR-Bench, while showing consistent improvements on existing benchmarks (+1.1\% on AI2D, +1.2\% on MMMU and MMVet). MMCR and prompt engineering will be released publicly.

Background: Health datasets from clinical sources do not reflect the breadth and diversity of disease in the real world, impacting research, medical education, and artificial intelligence (AI) tool development. Dermatology is a suitable area to develop and test a new and scalable method to create representative health datasets. Methods: We used Google Search advertisements to invite contributions to an open access dataset of images of dermatology conditions, demographic and symptom information. With informed contributor consent, we describe and release this dataset containing 10,408 images from 5,033 contributions from internet users in the United States over 8 months starting March 2023. The dataset includes dermatologist condition labels as well as estimated Fitzpatrick Skin Type (eFST) and Monk Skin Tone (eMST) labels for the images. Results: We received a median of 22 submissions/day (IQR 14-30). Female (66.72%) and younger (52% < age 40) contributors had a higher representation in the dataset compared to the US population, and 32.6% of contributors reported a non-White racial or ethnic identity. Over 97.5% of contributions were genuine images of skin conditions. Dermatologist confidence in assigning a differential diagnosis increased with the number of available variables, and showed a weaker correlation with image sharpness (Spearman's P values <0.001 and 0.01 respectively). Most contributions were short-duration (54% with onset < 7 days ago ) and 89% were allergic, infectious, or inflammatory conditions. eFST and eMST distributions reflected the geographical origin of the dataset. The dataset is available at github.com/google-research-datasets/scin . Conclusion: Search ads are effective at crowdsourcing images of health conditions. The SCIN dataset bridges important gaps in the availability of representative images of common skin conditions.