Daily Papers

The typical Selective State-Space Model (SSM) used in Mamba addresses several limitations of Transformers, such as the quadratic computational complexity with respect to sequence length and the significant memory requirements during inference due to the key-value (KV) cache. However, the increasing size of Mamba models continues to pose challenges for training and deployment, particularly due to their substantial computational demands during both training and inference. In this work, we introduce Bi-Mamba, a scalable and powerful 1-bit Mamba architecture designed to enable more efficient large language models (LLMs), with model sizes of 780M, 1.3B, and 2.7B parameters. Bi-Mamba models are trained from scratch on a standard LLM-scale dataset using an autoregressive distillation loss. Extensive experiments on language modeling benchmarks demonstrate that Bi-Mamba achieves performance comparable to its full-precision (FP16 or BF16) counterparts, while outperforming post-training binarization (PTB) Mamba and binarization-aware training (BAT) Transformer baselines. Moreover, Bi-Mamba drastically reduces memory usage and computational cost compared to the original Mamba. Our work pioneers a new line of linear-complexity LLMs under low-bit representation and provides the way for the design of specialized hardware optimized for efficient 1-bit Mamba-based models. Code and the pre-trained weights are available at https://github.com/Tangshengku/Bi-Mamba.

Single-cell RNA sequencing (scRNA-seq) enables high-resolution analysis of cellular heterogeneity, but its complexity, which is marked by high dimensionality, sparsity, and batch effects, which poses major computational challenges. Transformer-based models have made significant advances in this domain but are often limited by their quadratic complexity and suboptimal handling of long-range dependencies. In this work, we introduce GeneMamba, a scalable and efficient foundation model for single-cell transcriptomics built on state space modeling. Leveraging the Bi-Mamba architecture, GeneMamba captures bidirectional gene context with linear-time complexity, offering substantial computational gains over transformer baselines. The model is pretrained on nearly 30 million cells and incorporates biologically informed objectives, including pathway-aware contrastive loss and rank-based gene encoding. We evaluate GeneMamba across diverse tasks, including multi-batch integration, cell type annotation, and gene-gene correlation, demonstrating strong performance, interpretability, and robustness. These results position GeneMamba as a practical and powerful alternative to transformer-based methods, advancing the development of biologically grounded, scalable tools for large-scale single-cell data analysis.

The analysis of tabular data has traditionally been dominated by gradient-boosted decision trees (GBDTs), known for their proficiency with mixed categorical and numerical features. However, recent deep learning innovations are challenging this dominance. We introduce Mambular, an adaptation of the Mamba architecture optimized for tabular data. We extensively benchmark Mambular against state-of-the-art models, including neural networks and tree-based methods, and demonstrate its competitive performance across diverse datasets. Additionally, we explore various adaptations of Mambular to understand its effectiveness for tabular data. We investigate different pooling strategies, feature interaction mechanisms, and bi-directional processing. Our analysis shows that interpreting features as a sequence and passing them through Mamba layers results in surprisingly performant models. The results highlight Mambulars potential as a versatile and powerful architecture for tabular data analysis, expanding the scope of deep learning applications in this domain. The source code is available at https://github.com/basf/mamba-tabular.

Tooth segmentation is a pivotal step in modern digital dentistry, essential for applications across orthodontic diagnosis and treatment planning. Despite its importance, this process is fraught with challenges due to the high noise and low contrast inherent in 2D and 3D tooth data. Both Convolutional Neural Networks (CNNs) and Transformers has shown promise in medical image segmentation, yet each method has limitations in handling long-range dependencies and computational complexity. To address this issue, this paper introduces T-Mamba, integrating frequency-based features and shared bi-positional encoding into vision mamba to address limitations in efficient global feature modeling. Besides, we design a gate selection unit to integrate two features in spatial domain and one feature in frequency domain adaptively. T-Mamba is the first work to introduce frequency-based features into vision mamba, and its flexibility allows it to process both 2D and 3D tooth data without the need for separate modules. Also, the TED3, a large-scale public tooth 2D dental X-ray dataset, has been presented in this paper. Extensive experiments demonstrate that T-Mamba achieves new SOTA results on a public tooth CBCT dataset and outperforms previous SOTA methods on TED3 dataset. The code and models are publicly available at: https://github.com/isbrycee/T-Mamba.

Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA. Here, we propose an architecture motivated by these challenges that builds off the long-range Mamba block, and extends it to a BiMamba component that supports bi-directionality, and to a MambaDNA block that additionally supports RC equivariance. We use MambaDNA as the basis of Caduceus, the first family of RC equivariant bi-directional long-range DNA language models, and we introduce pre-training and fine-tuning strategies that yield Caduceus DNA foundation models. Caduceus outperforms previous long-range models on downstream benchmarks; on a challenging long-range variant effect prediction task, Caduceus exceeds the performance of 10x larger models that do not leverage bi-directionality or equivariance.

We propose Long-LRM, a generalizable 3D Gaussian reconstruction model that is capable of reconstructing a large scene from a long sequence of input images. Specifically, our model can process 32 source images at 960x540 resolution within only 1.3 seconds on a single A100 80G GPU. Our architecture features a mixture of the recent Mamba2 blocks and the classical transformer blocks which allowed many more tokens to be processed than prior work, enhanced by efficient token merging and Gaussian pruning steps that balance between quality and efficiency. Unlike previous feed-forward models that are limited to processing 1~4 input images and can only reconstruct a small portion of a large scene, Long-LRM reconstructs the entire scene in a single feed-forward step. On large-scale scene datasets such as DL3DV-140 and Tanks and Temples, our method achieves performance comparable to optimization-based approaches while being two orders of magnitude more efficient. Project page: https://arthurhero.github.io/projects/llrm

Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on individual proteins with short context lengths. Such protein LMs cannot extrapolate to longer proteins and protein complexes well. They also fail to account for the underlying biological mechanisms carried out by biomolecular interactions and dynamics i.e., proteins often interact with other proteins, molecules, and pathways in complex biological systems. In this work, we propose LC-PLM based on an alternative protein LM architecture, BiMamba-S, built off selective structured state-space models, to learn high-quality universal protein representations at the amino acid token level using masked language modeling. We also introduce its graph-contextual variant, LC-PLM-G, which contextualizes protein-protein interaction (PPI) graphs for a second stage of training. LC-PLM demonstrates favorable neural scaling laws, better length extrapolation capability, and a 7% to 34% improvement on protein downstream tasks than Transformer-based ESM-2. LC-PLM-G further trained within the context of PPI graphs shows promising results on protein structure and function prediction tasks. Our study demonstrates the benefit of increasing the context size with computationally efficient LM architecture (e.g. structured state space models) in learning universal protein representations and incorporating molecular interaction context contained in biological graphs.

Convolutional neural networks (CNN) and Transformers have made impressive progress in the field of remote sensing change detection (CD). However, both architectures have inherent shortcomings: CNN are constrained by a limited receptive field that may hinder their ability to capture broader spatial contexts, while Transformers are computationally intensive, making them costly to train and deploy on large datasets. Recently, the Mamba architecture, based on state space models, has shown remarkable performance in a series of natural language processing tasks, which can effectively compensate for the shortcomings of the above two architectures. In this paper, we explore for the first time the potential of the Mamba architecture for remote sensing CD tasks. We tailor the corresponding frameworks, called MambaBCD, MambaSCD, and MambaBDA, for binary change detection (BCD), semantic change detection (SCD), and building damage assessment (BDA), respectively. All three frameworks adopt the cutting-edge Visual Mamba architecture as the encoder, which allows full learning of global spatial contextual information from the input images. For the change decoder, which is available in all three architectures, we propose three spatio-temporal relationship modeling mechanisms, which can be naturally combined with the Mamba architecture and fully utilize its attribute to achieve spatio-temporal interaction of multi-temporal features, thereby obtaining accurate change information. On five benchmark datasets, our proposed frameworks outperform current CNN- and Transformer-based approaches without using any complex training strategies or tricks, fully demonstrating the potential of the Mamba architecture in CD tasks. Further experiments show that our architecture is quite robust to degraded data. The source code will be available in https://github.com/ChenHongruixuan/MambaCD

State space models (SSMs) with selection mechanisms and hardware-aware architectures, namely Mamba, have recently demonstrated significant promise in long-sequence modeling. Since the self-attention mechanism in transformers has quadratic complexity with image size and increasing computational demands, the researchers are now exploring how to adapt Mamba for computer vision tasks. This paper is the first comprehensive survey aiming to provide an in-depth analysis of Mamba models in the field of computer vision. It begins by exploring the foundational concepts contributing to Mamba's success, including the state space model framework, selection mechanisms, and hardware-aware design. Next, we review these vision mamba models by categorizing them into foundational ones and enhancing them with techniques such as convolution, recurrence, and attention to improve their sophistication. We further delve into the widespread applications of Mamba in vision tasks, which include their use as a backbone in various levels of vision processing. This encompasses general visual tasks, Medical visual tasks (e.g., 2D / 3D segmentation, classification, and image registration, etc.), and Remote Sensing visual tasks. We specially introduce general visual tasks from two levels: High/Mid-level vision (e.g., Object detection, Segmentation, Video classification, etc.) and Low-level vision (e.g., Image super-resolution, Image restoration, Visual generation, etc.). We hope this endeavor will spark additional interest within the community to address current challenges and further apply Mamba models in computer vision.

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.

We present PlainMamba: a simple non-hierarchical state space model (SSM) designed for general visual recognition. The recent Mamba model has shown how SSMs can be highly competitive with other architectures on sequential data and initial attempts have been made to apply it to images. In this paper, we further adapt the selective scanning process of Mamba to the visual domain, enhancing its ability to learn features from two-dimensional images by (i) a continuous 2D scanning process that improves spatial continuity by ensuring adjacency of tokens in the scanning sequence, and (ii) direction-aware updating which enables the model to discern the spatial relations of tokens by encoding directional information. Our architecture is designed to be easy to use and easy to scale, formed by stacking identical PlainMamba blocks, resulting in a model with constant width throughout all layers. The architecture is further simplified by removing the need for special tokens. We evaluate PlainMamba on a variety of visual recognition tasks including image classification, semantic segmentation, object detection, and instance segmentation. Our method achieves performance gains over previous non-hierarchical models and is competitive with hierarchical alternatives. For tasks requiring high-resolution inputs, in particular, PlainMamba requires much less computing while maintaining high performance. Code and models are available at https://github.com/ChenhongyiYang/PlainMamba

In this technical report, we present Falcon Mamba 7B, a new base large language model based on the novel Mamba architecture. Falcon Mamba 7B is trained on 5.8 trillion tokens with carefully selected data mixtures. As a pure Mamba-based model, Falcon Mamba 7B surpasses leading open-weight models based on Transformers, such as Mistral 7B, Llama3.1 8B, and Falcon2 11B. It is on par with Gemma 7B and outperforms models with different architecture designs, such as RecurrentGemma 9B and RWKV-v6 Finch 7B/14B. Currently, Falcon Mamba 7B is the best-performing Mamba model in the literature at this scale, surpassing both existing Mamba and hybrid Mamba-Transformer models, according to the Open LLM Leaderboard. Due to its architecture, Falcon Mamba 7B is significantly faster at inference and requires substantially less memory for long sequence generation. Despite recent studies suggesting that hybrid Mamba-Transformer models outperform pure architecture designs, we demonstrate that even the pure Mamba design can achieve similar, or even superior results compared to the Transformer and hybrid designs. We make the weights of our implementation of Falcon Mamba 7B publicly available on https://huggingface.co/tiiuae/falcon-mamba-7b, under a permissive license.