Daily Papers

Capturing long-range dependencies efficiently is essential for visual recognition tasks, yet existing methods face limitations. Convolutional neural networks (CNNs) struggle with restricted receptive fields, while Vision Transformers (ViTs) achieve global context and long-range modeling at a high computational cost. State-space models (SSMs) offer an alternative, but their application in vision remains underexplored. This work introduces vGamba, a hybrid vision backbone that integrates SSMs with attention mechanisms to enhance efficiency and expressiveness. At its core, the Gamba bottleneck block that includes, Gamba Cell, an adaptation of Mamba for 2D spatial structures, alongside a Multi-Head Self-Attention (MHSA) mechanism and a Gated Fusion Module for effective feature representation. The interplay of these components ensures that vGamba leverages the low computational demands of SSMs while maintaining the accuracy of attention mechanisms for modeling long-range dependencies in vision tasks. Additionally, the Fusion module enables seamless interaction between these components. Extensive experiments on classification, detection, and segmentation tasks demonstrate that vGamba achieves a superior trade-off between accuracy and computational efficiency, outperforming several existing models.

We tackle the challenge of efficiently reconstructing a 3D asset from a single image with growing demands for automated 3D content creation pipelines. Previous methods primarily rely on Score Distillation Sampling (SDS) and Neural Radiance Fields (NeRF). Despite their significant success, these approaches encounter practical limitations due to lengthy optimization and considerable memory usage. In this report, we introduce Gamba, an end-to-end amortized 3D reconstruction model from single-view images, emphasizing two main insights: (1) 3D representation: leveraging a large number of 3D Gaussians for an efficient 3D Gaussian splatting process; (2) Backbone design: introducing a Mamba-based sequential network that facilitates context-dependent reasoning and linear scalability with the sequence (token) length, accommodating a substantial number of Gaussians. Gamba incorporates significant advancements in data preprocessing, regularization design, and training methodologies. We assessed Gamba against existing optimization-based and feed-forward 3D generation approaches using the real-world scanned OmniObject3D dataset. Here, Gamba demonstrates competitive generation capabilities, both qualitatively and quantitatively, while achieving remarkable speed, approximately 0.6 second on a single NVIDIA A100 GPU.

Single-nucleus RNA sequencing (snRNA-seq) has significantly advanced our understanding of the disease etiology of neurodegenerative disorders. However, the low quality of specimens derived from postmortem brain tissues, combined with the high variability caused by disease heterogeneity, makes it challenging to integrate snRNA-seq data from multiple sources for precise analyses. To address these challenges, we present scMamba, a pre-trained model designed to improve the quality and utility of snRNA-seq analysis, with a particular focus on neurodegenerative diseases. Inspired by the recent Mamba model, scMamba introduces a novel architecture that incorporates a linear adapter layer, gene embeddings, and bidirectional Mamba blocks, enabling efficient processing of snRNA-seq data while preserving information from the raw input. Notably, scMamba learns generalizable features of cells and genes through pre-training on snRNA-seq data, without relying on dimension reduction or selection of highly variable genes. We demonstrate that scMamba outperforms benchmark methods in various downstream tasks, including cell type annotation, doublet detection, imputation, and the identification of differentially expressed genes.

Mamba, a State Space Model (SSM) that accelerates training by recasting recurrence as a parallel scan, has recently emerged as a linearly-scaling alternative to self-attention. Because of its unidirectional nature, each state in Mamba only has information of its previous states and is blind to states after. Current Mamba-based computer-vision methods typically overcome this by augmenting Mamba's global forward scan with a global backward scan, forming a bi-directional scan to restore a full receptive field. However, this operation doubles the computational load, eroding much of the efficiency advantage that originally Mamba have. To eliminate this extra scans, we introduce LBMamba, a locally bi-directional SSM block that embeds a lightweight locally backward scan inside the forward scan and executes it in per-thread registers. Building on LBMamba, we present LBVim, a backbone that alternates scan directions every two layers to recover a global receptive field without extra backward sweeps. We validate our approach on both natural images and whole slide images (WSIs) and show that it constantly offers a superior performance-throughput trade-off. Under the same throughput, LBVim achieves 0.8% to 1.6% higher top-1 accuracy on the ImageNet-1K classification dataset, 0.6% to 2.7% higher mIoU on the ADE20K semantic segmentation dataset, 0.9% higher APb and 1.1% higher APm on the COCO detection dataset. Our method also boosts the accuracy of four SOTA Mamba models, namely VMamba, LocalVim, PlainMamba and Adventurer, by 0.5% to 3.4%. We integrate LBMamba into the SOTA pathology multiple instance learning (MIL) model, MambaMIL, which is unidirectional. Experiments on 3 public WSI classification datasets show that our method achieves a relative improvement of up to 3.06% better AUC, 3.39% better F1, 1.67% better accuracy. Our code is available at https://github.com/cvlab-stonybrook/LBMamba.

Single cell analysis of human skeletal muscle (SM) tissue cross-sections is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images (segmentation) of SM tissue should be automatic and precise. Biomedical scientists in this field currently rely on custom tools and general machine learning (ML) models, both followed by labour intensive and subjective manual interventions to fine-tune segmentation. We believe that fully automated, precise, reproducible segmentation is possible by training ML models. However, in this important biomedical domain, there are currently no good quality, publicly available annotated imaging datasets available for ML model training. In this paper we release NCL-SM: a high quality bioimaging dataset of 46 human SM tissue cross-sections from both healthy control subjects and from patients with genetically diagnosed muscle pathology. These images include > 50k manually segmented muscle fibres (myofibres). In addition we also curated high quality myofibre segmentations, annotating reasons for rejecting low quality myofibres and low quality regions in SM tissue images, making these annotations completely ready for downstream analysis. This, we believe, will pave the way for development of a fully automatic pipeline that identifies individual myofibres within images of tissue sections and, in particular, also classifies individual myofibres that are fit for further analysis.

Accurate medical image segmentation demands the integration of multi-scale information, spanning from local features to global dependencies. However, it is challenging for existing methods to model long-range global information, where convolutional neural networks (CNNs) are constrained by their local receptive fields, and vision transformers (ViTs) suffer from high quadratic complexity of their attention mechanism. Recently, Mamba-based models have gained great attention for their impressive ability in long sequence modeling. Several studies have demonstrated that these models can outperform popular vision models in various tasks, offering higher accuracy, lower memory consumption, and less computational burden. However, existing Mamba-based models are mostly trained from scratch and do not explore the power of pretraining, which has been proven to be quite effective for data-efficient medical image analysis. This paper introduces a novel Mamba-based model, Swin-UMamba, designed specifically for medical image segmentation tasks, leveraging the advantages of ImageNet-based pretraining. Our experimental results reveal the vital role of ImageNet-based training in enhancing the performance of Mamba-based models. Swin-UMamba demonstrates superior performance with a large margin compared to CNNs, ViTs, and latest Mamba-based models. Notably, on AbdomenMRI, Encoscopy, and Microscopy datasets, Swin-UMamba outperforms its closest counterpart U-Mamba_Enc by an average score of 2.72%.

Identifying cell types and understanding their functional properties is crucial for unraveling the mechanisms underlying perception and cognition. In the retina, functional types can be identified by carefully selected stimuli, but this requires expert domain knowledge and biases the procedure towards previously known cell types. In the visual cortex, it is still unknown what functional types exist and how to identify them. Thus, for unbiased identification of the functional cell types in retina and visual cortex, new approaches are needed. Here we propose an optimization-based clustering approach using deep predictive models to obtain functional clusters of neurons using Most Discriminative Stimuli (MDS). Our approach alternates between stimulus optimization with cluster reassignment akin to an expectation-maximization algorithm. The algorithm recovers functional clusters in mouse retina, marmoset retina and macaque visual area V4. This demonstrates that our approach can successfully find discriminative stimuli across species, stages of the visual system and recording techniques. The resulting most discriminative stimuli can be used to assign functional cell types fast and on the fly, without the need to train complex predictive models or show a large natural scene dataset, paving the way for experiments that were previously limited by experimental time. Crucially, MDS are interpretable: they visualize the distinctive stimulus patterns that most unambiguously identify a specific type of neuron.