Daily Papers

Structure-based drug discovery, encompassing the tasks of protein-ligand docking and pocket-aware 3D drug design, represents a core challenge in drug discovery. However, no existing work can deal with both tasks to effectively leverage the duality between them, and current methods for each task are hindered by challenges in modeling 3D information and the limitations of available data. To address these issues, we propose 3DMolFormer, a unified dual-channel transformer-based framework applicable to both docking and 3D drug design tasks, which exploits their duality by utilizing docking functionalities within the drug design process. Specifically, we represent 3D pocket-ligand complexes using parallel sequences of discrete tokens and continuous numbers, and we design a corresponding dual-channel transformer model to handle this format, thereby overcoming the challenges of 3D information modeling. Additionally, we alleviate data limitations through large-scale pre-training on a mixed dataset, followed by supervised and reinforcement learning fine-tuning techniques respectively tailored for the two tasks. Experimental results demonstrate that 3DMolFormer outperforms previous approaches in both protein-ligand docking and pocket-aware 3D drug design, highlighting its promising application in structure-based drug discovery. The code is available at: https://github.com/HXYfighter/3DMolFormer .

Large transformer models have demonstrated remarkable success. Post-training quantization (PTQ), which requires only a small dataset for calibration and avoids end-to-end retraining, is a promising solution for compressing these large models. Regrettably, existing PTQ methods typically exhibit non-trivial performance loss. We find that the performance bottleneck stems from over-consideration of hardware compatibility in the quantization process, compelling them to reluctantly employ simple quantizers, albeit at the expense of accuracy. With the above insights, we propose RepQuant, a novel PTQ framework with quantization-inference decoupling paradigm to address the above issues. RepQuant employs complex quantizers in the quantization process and simplified quantizers in the inference process, and performs mathematically equivalent transformations between the two through quantization scale reparameterization, thus ensuring both accurate quantization and efficient inference. More specifically, we focus on two components with extreme distributions: LayerNorm activations and Softmax activations. Initially, we apply channel-wise quantization and log2 quantization, respectively, which are tailored to their distributions. In particular, for the former, we introduce a learnable per-channel dual clipping scheme, which is designed to efficiently identify outliers in the unbalanced activations with fine granularity. Then, we reparameterize the scales to hardware-friendly layer-wise quantization and log2 quantization for inference. Moreover, quantized weight reconstruction is seamlessly integrated into the above procedure to further push the performance limits. Extensive experiments are performed on different large-scale transformer variants on multiple tasks, including vision, language, and multi-modal transformers, and RepQuant encouragingly demonstrates significant performance advantages.

Recent advances in deep learning have mainly relied on Transformers due to their data dependency and ability to learn at scale. The attention module in these architectures, however, exhibits quadratic time and space in input size, limiting their scalability for long-sequence modeling. Despite recent attempts to design efficient and effective architecture backbone for multi-dimensional data, such as images and multivariate time series, existing models are either data independent, or fail to allow inter- and intra-dimension communication. Recently, State Space Models (SSMs), and more specifically Selective State Space Models, with efficient hardware-aware implementation, have shown promising potential for long sequence modeling. Motivated by the success of SSMs, we present MambaMixer, a new architecture with data-dependent weights that uses a dual selection mechanism across tokens and channels, called Selective Token and Channel Mixer. MambaMixer connects selective mixers using a weighted averaging mechanism, allowing layers to have direct access to early features. As a proof of concept, we design Vision MambaMixer (ViM2) and Time Series MambaMixer (TSM2) architectures based on the MambaMixer block and explore their performance in various vision and time series forecasting tasks. Our results underline the importance of selective mixing across both tokens and channels. In ImageNet classification, object detection, and semantic segmentation tasks, ViM2 achieves competitive performance with well-established vision models and outperforms SSM-based vision models. In time series forecasting, TSM2 achieves outstanding performance compared to state-of-the-art methods while demonstrating significantly improved computational cost. These results show that while Transformers, cross-channel attention, and MLPs are sufficient for good performance in time series forecasting, neither is necessary.

Transformer has recently gained considerable popularity in low-level vision tasks, including image super-resolution (SR). These networks utilize self-attention along different dimensions, spatial or channel, and achieve impressive performance. This inspires us to combine the two dimensions in Transformer for a more powerful representation capability. Based on the above idea, we propose a novel Transformer model, Dual Aggregation Transformer (DAT), for image SR. Our DAT aggregates features across spatial and channel dimensions, in the inter-block and intra-block dual manner. Specifically, we alternately apply spatial and channel self-attention in consecutive Transformer blocks. The alternate strategy enables DAT to capture the global context and realize inter-block feature aggregation. Furthermore, we propose the adaptive interaction module (AIM) and the spatial-gate feed-forward network (SGFN) to achieve intra-block feature aggregation. AIM complements two self-attention mechanisms from corresponding dimensions. Meanwhile, SGFN introduces additional non-linear spatial information in the feed-forward network. Extensive experiments show that our DAT surpasses current methods. Code and models are obtainable at https://github.com/zhengchen1999/DAT.

In this work, we introduce Dual Attention Vision Transformers (DaViT), a simple yet effective vision transformer architecture that is able to capture global context while maintaining computational efficiency. We propose approaching the problem from an orthogonal angle: exploiting self-attention mechanisms with both "spatial tokens" and "channel tokens". With spatial tokens, the spatial dimension defines the token scope, and the channel dimension defines the token feature dimension. With channel tokens, we have the inverse: the channel dimension defines the token scope, and the spatial dimension defines the token feature dimension. We further group tokens along the sequence direction for both spatial and channel tokens to maintain the linear complexity of the entire model. We show that these two self-attentions complement each other: (i) since each channel token contains an abstract representation of the entire image, the channel attention naturally captures global interactions and representations by taking all spatial positions into account when computing attention scores between channels; (ii) the spatial attention refines the local representations by performing fine-grained interactions across spatial locations, which in turn helps the global information modeling in channel attention. Extensive experiments show our DaViT achieves state-of-the-art performance on four different tasks with efficient computations. Without extra data, DaViT-Tiny, DaViT-Small, and DaViT-Base achieve 82.8%, 84.2%, and 84.6% top-1 accuracy on ImageNet-1K with 28.3M, 49.7M, and 87.9M parameters, respectively. When we further scale up DaViT with 1.5B weakly supervised image and text pairs, DaViT-Gaint reaches 90.4% top-1 accuracy on ImageNet-1K. Code is available at https://github.com/dingmyu/davit.

Electroencephalography (EEG)-based brain-computer interfaces (BCIs) transform spontaneous/evoked neural activity into control commands for external communication. While convolutional neural networks (CNNs) remain the mainstream backbone for EEG decoding, their inherently short receptive field makes it difficult to capture long-range temporal dependencies and global inter-channel relationships. Recent CNN-Transformer (Conformers) hybrids partially address this issue, but most adopt a serial design, resulting in suboptimal integration of local and global features, and often overlook explicit channel-wise modeling. To address these limitations, we propose DBConformer, a dual-branch convolutional Transformer network tailored for EEG decoding. It integrates a temporal Conformer to model long-range temporal dependencies and a spatial Conformer to extract inter-channel interactions, capturing both temporal dynamics and spatial patterns in EEG signals. A lightweight channel attention module further refines spatial representations by assigning data-driven importance to EEG channels. Extensive experiments on five motor imagery (MI) datasets and two seizure detection datasets under three evaluation settings demonstrate that DBConformer consistently outperforms 10 competitive baseline models, with over eight times fewer parameters than the high-capacity EEG Conformer baseline. Further, the visualization results confirm that the features extracted by DBConformer are physiologically interpretable and aligned with sensorimotor priors in MI. The superior performance and interpretability of DBConformer make it reliable for robust and explainable EEG decoding. Code is publicized at https://github.com/wzwvv/DBConformer.

Facial landmark detection is a fundamental problem in computer vision for many downstream applications. This paper introduces a new facial landmark detector based on vision transformers, which consists of two unique designs: Dual Vision Transformer (D-ViT) and Long Skip Connections (LSC). Based on the observation that the channel dimension of feature maps essentially represents the linear bases of the heatmap space, we propose learning the interconnections between these linear bases to model the inherent geometric relations among landmarks via Channel-split ViT. We integrate such channel-split ViT into the standard vision transformer (i.e., spatial-split ViT), forming our Dual Vision Transformer to constitute the prediction blocks. We also suggest using long skip connections to deliver low-level image features to all prediction blocks, thereby preventing useful information from being discarded by intermediate supervision. Extensive experiments are conducted to evaluate the performance of our proposal on the widely used benchmarks, i.e., WFLW, COFW, and 300W, demonstrating that our model outperforms the previous SOTAs across all three benchmarks.

In healthcare, medical image segmentation is crucial for accurate disease diagnosis and the development of effective treatment strategies. Early detection can significantly aid in managing diseases and potentially prevent their progression. Machine learning, particularly deep convolutional neural networks, has emerged as a promising approach to addressing segmentation challenges. Traditional methods like U-Net use encoding blocks for local representation modeling and decoding blocks to uncover semantic relationships. However, these models often struggle with multi-scale objects exhibiting significant variations in texture and shape, and they frequently fail to capture long-range dependencies in the input data. Transformers designed for sequence-to-sequence predictions have been proposed as alternatives, utilizing global self-attention mechanisms. Yet, they can sometimes lack precise localization due to insufficient granular details. To overcome these limitations, we introduce TransDAE: a novel approach that reimagines the self-attention mechanism to include both spatial and channel-wise associations across the entire feature space, while maintaining computational efficiency. Additionally, TransDAE enhances the skip connection pathway with an inter-scale interaction module, promoting feature reuse and improving localization accuracy. Remarkably, TransDAE outperforms existing state-of-the-art methods on the Synaps multi-organ dataset, even without relying on pre-trained weights.

In recent years, the application of transformer-based models in time-series forecasting has received significant attention. While often demonstrating promising results, the transformer architecture encounters challenges in fully exploiting the temporal relations within time series data due to its attention mechanism. In this work, we design eXponential Patch (xPatch for short), a novel dual-stream architecture that utilizes exponential decomposition. Inspired by the classical exponential smoothing approaches, xPatch introduces the innovative seasonal-trend exponential decomposition module. Additionally, we propose a dual-flow architecture that consists of an MLP-based linear stream and a CNN-based non-linear stream. This model investigates the benefits of employing patching and channel-independence techniques within a non-transformer model. Finally, we develop a robust arctangent loss function and a sigmoid learning rate adjustment scheme, which prevent overfitting and boost forecasting performance. The code is available at the following repository: https://github.com/stitsyuk/xPatch.

Foundation models are reshaping EEG analysis, yet an important problem of EEG tokenization remains a challenge. This paper presents TFM-Tokenizer, a novel tokenization framework that learns a vocabulary of time-frequency motifs from single-channel EEG signals and encodes them into discrete tokens. We propose a dual-path architecture with time-frequency masking to capture robust motif representations, and it is model-agnostic, supporting both lightweight transformers and existing foundation models for downstream tasks. Our study demonstrates three key benefits: Accuracy: Experiments on four diverse EEG benchmarks demonstrate consistent performance gains across both single- and multi-dataset pretraining settings, achieving up to 17% improvement in Cohen's Kappa over strong baselines. Generalization: Moreover, as a plug-and-play component, it consistently boosts the performance of diverse foundation models, including BIOT and LaBraM. Scalability: By operating at the single-channel level rather than relying on the strict 10-20 EEG system, our method has the potential to be device-agnostic. Experiments on ear-EEG sleep staging, which differs from the pretraining data in signal format, channel configuration, recording device, and task, show that our tokenizer outperforms baselines by 14%. A comprehensive token analysis reveals strong class-discriminative, frequency-aware, and consistent structure, enabling improved representation quality and interpretability. Code is available at https://github.com/Jathurshan0330/TFM-Tokenizer.

This letter introduces LYT-Net, a novel lightweight transformer-based model for low-light image enhancement (LLIE). LYT-Net consists of several layers and detachable blocks, including our novel blocks--Channel-Wise Denoiser (CWD) and Multi-Stage Squeeze & Excite Fusion (MSEF)--along with the traditional Transformer block, Multi-Headed Self-Attention (MHSA). In our method we adopt a dual-path approach, treating chrominance channels U and V and luminance channel Y as separate entities to help the model better handle illumination adjustment and corruption restoration. Our comprehensive evaluation on established LLIE datasets demonstrates that, despite its low complexity, our model outperforms recent LLIE methods. The source code and pre-trained models are available at https://github.com/albrateanu/LYT-Net

Learning-based 3D reconstruction models, represented by Visual Geometry Grounded Transformers (VGGTs), have made remarkable progress with the use of large-scale transformers. Their prohibitive computational and memory costs severely hinder real-world deployment. Post-Training Quantization (PTQ) has become a common practice for compressing and accelerating models. However, we empirically observe that PTQ faces unique obstacles when compressing billion-scale VGGTs: the data-independent special tokens induce heavy-tailed activation distributions, while the multi-view nature of 3D data makes calibration sample selection highly unstable. This paper proposes the first Quantization framework for VGGTs, namely QuantVGGT. This mainly relies on two technical contributions: First, we introduce Dual-Smoothed Fine-Grained Quantization, which integrates pre-global Hadamard rotation and post-local channel smoothing to mitigate heavy-tailed distributions and inter-channel variance robustly. Second, we design Noise-Filtered Diverse Sampling, which filters outliers via deep-layer statistics and constructs frame-aware diverse calibration clusters to ensure stable quantization ranges. Comprehensive experiments demonstrate that QuantVGGT achieves the state-of-the-art results across different benchmarks and bit-width, surpassing the previous state-of-the-art generic quantization method with a great margin. We highlight that our 4-bit QuantVGGT can deliver a 3.7times memory reduction and 2.5times acceleration in real-hardware inference, while maintaining reconstruction accuracy above 98\% of its full-precision counterpart. This demonstrates the vast advantages and practicality of QuantVGGT in resource-constrained scenarios. Our code is released in https://github.com/wlfeng0509/QuantVGGT.

Transformers have revolutionized performance in Natural Language Processing and Vision, paving the way for their integration with Graph Neural Networks (GNNs). One key challenge in enhancing graph transformers is strengthening the discriminative power of distinguishing isomorphisms of graphs, which plays a crucial role in boosting their predictive performances. To address this challenge, we introduce 'Topology-Informed Graph Transformer (TIGT)', a novel transformer enhancing both discriminative power in detecting graph isomorphisms and the overall performance of Graph Transformers. TIGT consists of four components: A topological positional embedding layer using non-isomorphic universal covers based on cyclic subgraphs of graphs to ensure unique graph representation: A dual-path message-passing layer to explicitly encode topological characteristics throughout the encoder layers: A global attention mechanism: And a graph information layer to recalibrate channel-wise graph features for better feature representation. TIGT outperforms previous Graph Transformers in classifying synthetic dataset aimed at distinguishing isomorphism classes of graphs. Additionally, mathematical analysis and empirical evaluations highlight our model's competitive edge over state-of-the-art Graph Transformers across various benchmark datasets.