Daily Papers

Parameter-efficient tuning (PET) methods can effectively drive extremely large pre-trained language models (PLMs) by only training minimal parameters. Different PET methods utilize different manually designed modules. In a small PLM, there are usually noticeable performance differences among PET methods. Nevertheless, when a PLM's scale grows up to tens of billions of parameters, all PET methods achieve almost the same performance and even perform on par with the full-parameter fine-tuning method. Hence, we hypothesize that model scaling can mitigate the design differences (the module structures and the number of trainable parameters) among PET methods. To study this hypothesis, we introduce a more flexible PET method - arbitrary PET (APET) method - to be compatible with arbitrary module structures and any number of trainable parameters. Then, we experiment on 11 NLP tasks of 5 types and 2 representative PLMs. From our investigations, we find that the model scaling (1) mitigates the effects of the arbitrary module structure on the performance of tuning methods, and (2) enables the tuning methods to optimize fewer parameters to achieve the full-parameter fine-tuning performance. Intriguingly, we also observe that all tuning methods require almost the same number of trainable parameters to drive PLMs. We discuss this phenomenon and the above two findings collectively from optimization perspectives to fathom the mechanisms behind them. These conclusions not only demonstrate the positive impact of model scaling on tuning methods but disclose its mechanisms, which help us design more effective and efficient tuning methods on larger-scale PLMs.

Speculative Decoding (SD) is a popular lossless technique for accelerating the inference of Large Language Models (LLMs). We show that the decoding speed of SD frameworks with static draft structures can be significantly improved by incorporating context-aware adaptive draft structures. However, current studies on adaptive draft structures are limited by their performance, modeling approaches, and applicability. In this paper, we introduce AdaEAGLE, the first SD framework that explicitly models adaptive draft structures. AdaEAGLE leverages the Lightweight Draft Length Predictor (LDLP) module to explicitly predict the optimal number of draft tokens during inference to guide the draft model. It achieves comparable speedup results without manual thresholds and allows for deeper, more specialized optimizations. Moreover, together with threshold-based strategies, AdaEAGLE achieves a 1.62times speedup over the vanilla AR decoding and outperforms fixed-length SotA baseline while maintaining output quality.

Attention based language models have become a critical component in state-of-the-art natural language processing systems. However, these models have significant computational requirements, due to long training times, dense operations and large parameter count. In this work we demonstrate a set of modifications to the structure of a Transformer layer, producing a more efficient architecture. First, we add a convolutional module to complement the self-attention module, decoupling the learning of local and global interactions. Secondly, we rely on grouped transformations to reduce the computational cost of dense feed-forward layers and convolutions, while preserving the expressivity of the model. We apply the resulting architecture to language representation learning and demonstrate its superior performance compared to BERT models of different scales. We further highlight its improved efficiency, both in terms of floating-point operations (FLOPs) and time-to-train.

Parse graphs of the human body can be obtained in the human brain to help humans complete the human pose estimation (HPE). It contains a hierarchical structure, like a tree structure, and context relations among nodes. Many researchers pre-design the parse graph of body structure, and then design framework for HPE. However, these frameworks are difficulty adapting when encountering situations that differ from the preset human structure. Different from them, we regard the feature map as a whole, similarly to human body, so the feature map can be optimized based on parse graphs and each node feature is learned implicitly instead of explicitly, which means it can flexibly respond to different human body structure. In this paper, we design the Refinement Module based on the Parse Graph of feature map (RMPG), which includes two stages: top-down decomposition and bottom-up combination. In the top-down decomposition stage, the feature map is decomposed into multiple sub-feature maps along the channel and their context relations are calculated to obtain their respective context information. In the bottom-up combination stage, the sub-feature maps and their context information are combined to obtain refined sub-feature maps, and then these refined sub-feature maps are concatenated to obtain the refined feature map. Additionally ,we design a top-down framework by using multiple RMPG modules for HPE, some of which are supervised to obtain context relations among body parts. Our framework achieves excellent results on the COCO keypoint detection, CrowdPose and MPII human pose datasets. More importantly, our experiments also demonstrate the effectiveness of RMPG on different methods, including SimpleBaselines, Hourglass, and ViTPose.

Pixel-level segmentation of structural cracks across various scenarios remains a considerable challenge. Current methods encounter challenges in effectively modeling crack morphology and texture, facing challenges in balancing segmentation quality with low computational resource usage. To overcome these limitations, we propose a lightweight Structure-Aware Vision Mamba Network (SCSegamba), capable of generating high-quality pixel-level segmentation maps by leveraging both the morphological information and texture cues of crack pixels with minimal computational cost. Specifically, we developed a Structure-Aware Visual State Space module (SAVSS), which incorporates a lightweight Gated Bottleneck Convolution (GBC) and a Structure-Aware Scanning Strategy (SASS). The key insight of GBC lies in its effectiveness in modeling the morphological information of cracks, while the SASS enhances the perception of crack topology and texture by strengthening the continuity of semantic information between crack pixels. Experiments on crack benchmark datasets demonstrate that our method outperforms other state-of-the-art (SOTA) methods, achieving the highest performance with only 2.8M parameters. On the multi-scenario dataset, our method reached 0.8390 in F1 score and 0.8479 in mIoU. The code is available at https://github.com/Karl1109/SCSegamba.

Large Language Models (LLMs) have reshaped our world with significant advancements in science, engineering, and society through applications ranging from scientific discoveries and medical diagnostics to Chatbots. Despite their ubiquity and utility, the underlying mechanisms of LLM remain concealed within billions of parameters and complex structures, making their inner architecture and cognitive processes challenging to comprehend. We address this gap by adopting approaches to understanding emerging cognition in biology and developing a network-based framework that links cognitive skills, LLM architectures, and datasets, ushering in a paradigm shift in foundation model analysis. The skill distribution in the module communities demonstrates that while LLMs do not strictly parallel the focalized specialization observed in specific biological systems, they exhibit unique communities of modules whose emergent skill patterns partially mirror the distributed yet interconnected cognitive organization seen in avian and small mammalian brains. Our numerical results highlight a key divergence from biological systems to LLMs, where skill acquisition benefits substantially from dynamic, cross-regional interactions and neural plasticity. By integrating cognitive science principles with machine learning, our framework provides new insights into LLM interpretability and suggests that effective fine-tuning strategies should leverage distributed learning dynamics rather than rigid modular interventions.

Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep learning-based approaches leading to improvements in blind docking efficiency, these methods have encountered notable challenges, such as limited generalization performance on unseen proteins, the inability to concurrently address the settings of blind docking and site-specific docking, and the frequent occurrence of physical implausibilities such as inter-molecular steric clash. In this study, we introduce DeltaDock, a robust and versatile framework designed for efficient molecular docking to overcome these challenges. DeltaDock operates in a two-step process: rapid initial complex structures sampling followed by multi-scale iterative refinement of the initial structures. In the initial stage, to sample accurate structures with high efficiency, we develop a ligand-dependent binding site prediction model founded on large protein models and graph neural networks. This model is then paired with GPU-accelerated sampling algorithms. The sampled structures are updated using a multi-scale iterative refinement module that captures both protein-ligand atom-atom interactions and residue-atom interactions in the following stage. Distinct from previous geometric deep learning methods that are conditioned on the blind docking setting, DeltaDock demonstrates superior performance in both blind docking and site-specific docking settings. Comprehensive experimental results reveal that DeltaDock consistently surpasses baseline methods in terms of docking accuracy. Furthermore, it displays remarkable generalization capabilities and proficiency for predicting physically valid structures, thereby attesting to its robustness and reliability in various scenarios.

3D lane detection which plays a crucial role in vehicle routing, has recently been a rapidly developing topic in autonomous driving. Previous works struggle with practicality due to their complicated spatial transformations and inflexible representations of 3D lanes. Faced with the issues, our work proposes an efficient and robust monocular 3D lane detection called BEV-LaneDet with three main contributions. First, we introduce the Virtual Camera that unifies the in/extrinsic parameters of cameras mounted on different vehicles to guarantee the consistency of the spatial relationship among cameras. It can effectively promote the learning procedure due to the unified visual space. We secondly propose a simple but efficient 3D lane representation called Key-Points Representation. This module is more suitable to represent the complicated and diverse 3D lane structures. At last, we present a light-weight and chip-friendly spatial transformation module named Spatial Transformation Pyramid to transform multiscale front-view features into BEV features. Experimental results demonstrate that our work outperforms the state-of-the-art approaches in terms of F-Score, being 10.6% higher on the OpenLane dataset and 5.9% higher on the Apollo 3D synthetic dataset, with a speed of 185 FPS. The source code will released at https://github.com/gigo-team/bev_lane_det.

Automated brain structure segmentation is important to many clinical quantitative analysis and diagnoses. In this work, we introduce MixNet, a 2D semantic-wise deep convolutional neural network to segment brain structure in multi-modality MRI images. The network is composed of our modified deep residual learning units. In the unit, we replace the traditional convolution layer with the dilated convolutional layer, which avoids the use of pooling layers and deconvolutional layers, reducing the number of network parameters. Final predictions are made by aggregating information from multiple scales and modalities. A pyramid pooling module is used to capture spatial information of the anatomical structures at the output end. In addition, we test three architectures (MixNetv1, MixNetv2 and MixNetv3) which fuse the modalities differently to see the effect on the results. Our network achieves the state-of-the-art performance. MixNetv2 was submitted to the MRBrainS challenge at MICCAI 2018 and won the 3rd place in the 3-label task. On the MRBrainS2018 dataset, which includes subjects with a variety of pathologies, the overall DSC (Dice Coefficient) of 84.7% (gray matter), 87.3% (white matter) and 83.4% (cerebrospinal fluid) were obtained with only 7 subjects as training data.

Image denoising is a fundamental challenge in computer vision, with applications in photography and medical imaging. While deep learning-based methods have shown remarkable success, their reliance on specific noise distributions limits generalization to unseen noise types and levels. Existing approaches attempt to address this with extensive training data and high computational resources but they still suffer from overfitting. To address these issues, we conduct image denoising by utilizing dynamically generated kernels via efficient operations. This approach helps prevent overfitting and improves resilience to unseen noise. Specifically, our method leverages a Feature Extraction Module for robust noise-invariant features, Global Statistics and Local Correlation Modules to capture comprehensive noise characteristics and structural correlations. The Kernel Prediction Module then employs these cues to produce pixel-wise varying kernels adapted to local structures, which are then applied iteratively for denoising. This ensures both efficiency and superior restoration quality. Despite being trained on single-level Gaussian noise, our compact model (~ 0.04 M) excels across diverse noise types and levels, demonstrating the promise of iterative dynamic filtering for practical image denoising.

In this paper, we propose a novel network, SVDFormer, to tackle two specific challenges in point cloud completion: understanding faithful global shapes from incomplete point clouds and generating high-accuracy local structures. Current methods either perceive shape patterns using only 3D coordinates or import extra images with well-calibrated intrinsic parameters to guide the geometry estimation of the missing parts. However, these approaches do not always fully leverage the cross-modal self-structures available for accurate and high-quality point cloud completion. To this end, we first design a Self-view Fusion Network that leverages multiple-view depth image information to observe incomplete self-shape and generate a compact global shape. To reveal highly detailed structures, we then introduce a refinement module, called Self-structure Dual-generator, in which we incorporate learned shape priors and geometric self-similarities for producing new points. By perceiving the incompleteness of each point, the dual-path design disentangles refinement strategies conditioned on the structural type of each point. SVDFormer absorbs the wisdom of self-structures, avoiding any additional paired information such as color images with precisely calibrated camera intrinsic parameters. Comprehensive experiments indicate that our method achieves state-of-the-art performance on widely-used benchmarks. Code will be available at https://github.com/czvvd/SVDFormer.

Medical vision-language pre-training shows great potential in learning representative features from massive paired radiographs and reports. However, in computed tomography (CT) scans, the distribution of lesions which contain intricate structures is characterized by spatial sparsity. Besides, the complex and implicit relationships between different pathological descriptions in each sentence of the report and their corresponding sub-regions in radiographs pose additional challenges. In this paper, we propose a Similarity-Driven Cross-Granularity Pre-training (SimCroP) framework on chest CTs, which combines similarity-driven alignment and cross-granularity fusion to improve radiograph interpretation. We first leverage multi-modal masked modeling to optimize the encoder for understanding precise low-level semantics from radiographs. Then, similarity-driven alignment is designed to pre-train the encoder to adaptively select and align the correct patches corresponding to each sentence in reports. The cross-granularity fusion module integrates multimodal information across instance level and word-patch level, which helps the model better capture key pathology structures in sparse radiographs, resulting in improved performance for multi-scale downstream tasks. SimCroP is pre-trained on a large-scale paired CT-reports dataset and validated on image classification and segmentation tasks across five public datasets. Experimental results demonstrate that SimCroP outperforms both cutting-edge medical self-supervised learning methods and medical vision-language pre-training methods. Codes and models are available at https://github.com/ToniChopp/SimCroP.

Graph Retrieval Augmented Generation (GraphRAG) effectively enhances external knowledge integration capabilities by explicitly modeling knowledge relationships, thereby improving the factual accuracy and generation quality of Large Language Models (LLMs) in specialized domains. However, existing methods suffer from two inherent limitations: 1) Inefficient Information Aggregation: They rely on a single agent and fixed iterative patterns, making it difficult to adaptively capture multi-level textual, structural, and degree information within graph data. 2) Rigid Reasoning Mechanism: They employ preset reasoning schemes, which cannot dynamically adjust reasoning depth nor achieve precise semantic correction. To overcome these limitations, we propose Graph Counselor, an GraphRAG method based on multi-agent collaboration. This method uses the Adaptive Graph Information Extraction Module (AGIEM), where Planning, Thought, and Execution Agents work together to precisely model complex graph structures and dynamically adjust information extraction strategies, addressing the challenges of multi-level dependency modeling and adaptive reasoning depth. Additionally, the Self-Reflection with Multiple Perspectives (SR) module improves the accuracy and semantic consistency of reasoning results through self-reflection and backward reasoning mechanisms. Experiments demonstrate that Graph Counselor outperforms existing methods in multiple graph reasoning tasks, exhibiting higher reasoning accuracy and generalization ability. Our code is available at https://github.com/gjq100/Graph-Counselor.git.

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

Human mobility prediction is a fundamental task essential for various applications in urban planning, location-based services and intelligent transportation systems. Existing methods often ignore activity information crucial for reasoning human preferences and routines, or adopt a simplified representation of the dependencies between time, activities and locations. To address these issues, we present Hierarchical Graph Attention Recurrent Network (HGARN) for human mobility prediction. Specifically, we construct a hierarchical graph based on past mobility records and employ a Hierarchical Graph Attention Module to capture complex time-activity-location dependencies. This way, HGARN can learn representations with rich human travel semantics to model user preferences at the global level. We also propose a model-agnostic history-enhanced confidence (MAHEC) label to incorporate each user's individual-level preferences. Finally, we introduce a Temporal Module, which employs recurrent structures to jointly predict users' next activities and their associated locations, with the former used as an auxiliary task to enhance the latter prediction. For model evaluation, we test the performance of HGARN against existing state-of-the-art methods in both the recurring (i.e., returning to a previously visited location) and explorative (i.e., visiting a new location) settings. Overall, HGARN outperforms other baselines significantly in all settings based on two real-world human mobility data benchmarks. These findings confirm the important role that human activities play in determining mobility decisions, illustrating the need to develop activity-aware intelligent transportation systems. Source codes of this study are available at https://github.com/YihongT/HGARN.

Partial domain adaptation which assumes that the unknown target label space is a subset of the source label space has attracted much attention in computer vision. Despite recent progress, existing methods often suffer from three key problems: negative transfer, lack of discriminability, and domain invariance in the latent space. To alleviate the above issues, we develop a novel 'Select, Label, and Mix' (SLM) framework that aims to learn discriminative invariant feature representations for partial domain adaptation. First, we present an efficient "select" module that automatically filters out the outlier source samples to avoid negative transfer while aligning distributions across both domains. Second, the "label" module iteratively trains the classifier using both the labeled source domain data and the generated pseudo-labels for the target domain to enhance the discriminability of the latent space. Finally, the "mix" module utilizes domain mixup regularization jointly with the other two modules to explore more intrinsic structures across domains leading to a domain-invariant latent space for partial domain adaptation. Extensive experiments on several benchmark datasets for partial domain adaptation demonstrate the superiority of our proposed framework over state-of-the-art methods.

Generating fluent and informative responses is of critical importance for task-oriented dialogue systems. Existing pipeline approaches generally predict multiple dialogue acts first and use them to assist response generation. There are at least two shortcomings with such approaches. First, the inherent structures of multi-domain dialogue acts are neglected. Second, the semantic associations between acts and responses are not taken into account for response generation. To address these issues, we propose a neural co-generation model that generates dialogue acts and responses concurrently. Unlike those pipeline approaches, our act generation module preserves the semantic structures of multi-domain dialogue acts and our response generation module dynamically attends to different acts as needed. We train the two modules jointly using an uncertainty loss to adjust their task weights adaptively. Extensive experiments are conducted on the large-scale MultiWOZ dataset and the results show that our model achieves very favorable improvement over several state-of-the-art models in both automatic and human evaluations.

Realistic image super-resolution (Real-ISR) aims to reproduce perceptually realistic image details from a low-quality input. The commonly used adversarial training based Real-ISR methods often introduce unnatural visual artifacts and fail to generate realistic textures for natural scene images. The recently developed generative stable diffusion models provide a potential solution to Real-ISR with pre-learned strong image priors. However, the existing methods along this line either fail to keep faithful pixel-wise image structures or resort to extra skipped connections to reproduce details, which requires additional training in image space and limits their extension to other related tasks in latent space such as image stylization. In this work, we propose a pixel-aware stable diffusion (PASD) network to achieve robust Real-ISR as well as personalized stylization. In specific, a pixel-aware cross attention module is introduced to enable diffusion models perceiving image local structures in pixel-wise level, while a degradation removal module is used to extract degradation insensitive features to guide the diffusion process together with image high level information. By simply replacing the base diffusion model with a personalized one, our method can generate diverse stylized images without the need to collect pairwise training data. PASD can be easily integrated into existing diffusion models such as Stable Diffusion. Experiments on Real-ISR and personalized stylization demonstrate the effectiveness of our proposed approach. The source code and models can be found at https://github.com/yangxy/PASD.

High-resolution (HR) medical videos are vital for accurate diagnosis, yet are hard to acquire due to hardware limitations and physiological constraints. Clinically, the collected low-resolution (LR) medical videos present unique challenges for video super-resolution (VSR) models, including camera shake, noise, and abrupt frame transitions, which result in significant optical flow errors and alignment difficulties. Additionally, tissues and organs exhibit continuous and nuanced structures, but current VSR models are prone to introducing artifacts and distorted features that can mislead doctors. To this end, we propose MedVSR, a tailored framework for medical VSR. It first employs Cross State-Space Propagation (CSSP) to address the imprecise alignment by projecting distant frames as control matrices within state-space models, enabling the selective propagation of consistent and informative features to neighboring frames for effective alignment. Moreover, we design an Inner State-Space Reconstruction (ISSR) module that enhances tissue structures and reduces artifacts with joint long-range spatial feature learning and large-kernel short-range information aggregation. Experiments across four datasets in diverse medical scenarios, including endoscopy and cataract surgeries, show that MedVSR significantly outperforms existing VSR models in reconstruction performance and efficiency. Code released at https://github.com/CUHK-AIM-Group/MedVSR.

We propose Lizard, a linearization framework that transforms pretrained Transformer-based Large Language Models (LLMs) into flexible, subquadratic architectures for infinite-context generation. Transformer-based LLMs face significant memory and computational bottlenecks as context lengths increase, due to the quadratic complexity of softmax attention and the growing key-value (KV) cache. Lizard addresses these limitations by introducing a subquadratic attention mechanism that closely approximates softmax attention while preserving the output quality. Unlike previous linearization methods, which are often limited by fixed model structures and therefore exclude gating mechanisms, Lizard incorporates a gating module inspired by recent state-of-the-art linear models. This enables adaptive memory control, supports constant-memory inference, offers strong length generalization, and allows more flexible model design. Lizard combines gated linear attention for global context compression with sliding window attention enhanced by meta memory, forming a hybrid mechanism that captures both long-range dependencies and fine-grained local interactions. Moreover, we introduce a hardware-aware algorithm that accelerates the training speed of our models. Extensive experiments show that Lizard achieves near-lossless recovery of the teacher model's performance across standard language modeling tasks, while significantly outperforming previous linearization methods. On the 5-shot MMLU benchmark, Lizard improves over prior models by 18 points and shows significant improvements on associative recall tasks.

Despite the significant advancements in pre-training methods for point cloud understanding, directly capturing intricate shape information from irregular point clouds without reliance on external data remains a formidable challenge. To address this problem, we propose GPSFormer, an innovative Global Perception and Local Structure Fitting-based Transformer, which learns detailed shape information from point clouds with remarkable precision. The core of GPSFormer is the Global Perception Module (GPM) and the Local Structure Fitting Convolution (LSFConv). Specifically, GPM utilizes Adaptive Deformable Graph Convolution (ADGConv) to identify short-range dependencies among similar features in the feature space and employs Multi-Head Attention (MHA) to learn long-range dependencies across all positions within the feature space, ultimately enabling flexible learning of contextual representations. Inspired by Taylor series, we design LSFConv, which learns both low-order fundamental and high-order refinement information from explicitly encoded local geometric structures. Integrating the GPM and LSFConv as fundamental components, we construct GPSFormer, a cutting-edge Transformer that effectively captures global and local structures of point clouds. Extensive experiments validate GPSFormer's effectiveness in three point cloud tasks: shape classification, part segmentation, and few-shot learning. The code of GPSFormer is available at https://github.com/changshuowang/GPSFormer.

Recently, State Space Models (SSMs), with Mamba as a prime example, have shown great promise for long-range dependency modeling with linear complexity. Then, Vision Mamba and the subsequent architectures are presented successively, and they perform well on visual tasks. The crucial step of applying Mamba to visual tasks is to construct 2D visual features in sequential manners. To effectively organize and construct visual features within the 2D image space through 1D selective scan, we propose a novel Multi-Head Scan (MHS) module. The embeddings extracted from the preceding layer are projected into multiple lower-dimensional subspaces. Subsequently, within each subspace, the selective scan is performed along distinct scan routes. The resulting sub-embeddings, obtained from the multi-head scan process, are then integrated and ultimately projected back into the high-dimensional space. Moreover, we incorporate a Scan Route Attention (SRA) mechanism to enhance the module's capability to discern complex structures. To validate the efficacy of our module, we exclusively substitute the 2D-Selective-Scan (SS2D) block in VM-UNet with our proposed module, and we train our models from scratch without using any pre-trained weights. The results indicate a significant improvement in performance while reducing the parameters of the original VM-UNet. The code for this study is publicly available at https://github.com/PixDeep/MHS-VM.

We introduce a new generative model that combines latent diffusion with persistent homology to create 3D shapes with high diversity, with a special emphasis on their topological characteristics. Our method involves representing 3D shapes as implicit fields, then employing persistent homology to extract topological features, including Betti numbers and persistence diagrams. The shape generation process consists of two steps. Initially, we employ a transformer-based autoencoding module to embed the implicit representation of each 3D shape into a set of latent vectors. Subsequently, we navigate through the learned latent space via a diffusion model. By strategically incorporating topological features into the diffusion process, our generative module is able to produce a richer variety of 3D shapes with different topological structures. Furthermore, our framework is flexible, supporting generation tasks constrained by a variety of inputs, including sparse and partial point clouds, as well as sketches. By modifying the persistence diagrams, we can alter the topology of the shapes generated from these input modalities.

The rapid development of AR/VR brings tremendous demands for 3D content. While the widely-used Computer-Aided Design (CAD) method requires a time-consuming and labor-intensive modeling process, sketch-based 3D modeling offers a potential solution as a natural form of computer-human interaction. However, the sparsity and ambiguity of sketches make it challenging to generate high-fidelity content reflecting creators' ideas. Precise drawing from multiple views or strategic step-by-step drawings is often required to tackle the challenge but is not friendly to novice users. In this work, we introduce a novel end-to-end approach, Deep3DSketch+, which performs 3D modeling using only a single free-hand sketch without inputting multiple sketches or view information. Specifically, we introduce a lightweight generation network for efficient inference in real-time and a structural-aware adversarial training approach with a Stroke Enhancement Module (SEM) to capture the structural information to facilitate learning of the realistic and fine-detailed shape structures for high-fidelity performance. Extensive experiments demonstrated the effectiveness of our approach with the state-of-the-art (SOTA) performance on both synthetic and real datasets.

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.

Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and the expanded availability of experimental 3D protein structures have accelerated structure prediction, the dynamic nature of protein structures has received limited attention. This study introduces an innovative 4D diffusion model incorporating molecular dynamics (MD) simulation data to learn dynamic protein structures. Our approach is distinguished by the following components: (1) a unified diffusion model capable of generating dynamic protein structures, including both the backbone and side chains, utilizing atomic grouping and side-chain dihedral angle predictions; (2) a reference network that enhances structural consistency by integrating the latent embeddings of the initial 3D protein structures; and (3) a motion alignment module aimed at improving temporal structural coherence across multiple time steps. To our knowledge, this is the first diffusion-based model aimed at predicting protein trajectories across multiple time steps simultaneously. Validation on benchmark datasets demonstrates that our model exhibits high accuracy in predicting dynamic 3D structures of proteins containing up to 256 amino acids over 32 time steps, effectively capturing both local flexibility in stable states and significant conformational changes.

With the advent of convolutional neural networks, stereo matching algorithms have recently gained tremendous progress. However, it remains a great challenge to accurately extract disparities from real-world image pairs taken by consumer-level devices like smartphones, due to practical complicating factors such as thin structures, non-ideal rectification, camera module inconsistencies and various hard-case scenes. In this paper, we propose a set of innovative designs to tackle the problem of practical stereo matching: 1) to better recover fine depth details, we design a hierarchical network with recurrent refinement to update disparities in a coarse-to-fine manner, as well as a stacked cascaded architecture for inference; 2) we propose an adaptive group correlation layer to mitigate the impact of erroneous rectification; 3) we introduce a new synthetic dataset with special attention to difficult cases for better generalizing to real-world scenes. Our results not only rank 1st on both Middlebury and ETH3D benchmarks, outperforming existing state-of-the-art methods by a notable margin, but also exhibit high-quality details for real-life photos, which clearly demonstrates the efficacy of our contributions.

Neural Module Networks, originally proposed for the task of visual question answering, are a class of neural network architectures that involve human-specified neural modules, each designed for a specific form of reasoning. In current formulations of such networks only the parameters of the neural modules and/or the order of their execution is learned. In this work, we further expand this approach and also learn the underlying internal structure of modules in terms of the ordering and combination of simple and elementary arithmetic operators. Our results show that one is indeed able to simultaneously learn both internal module structure and module sequencing without extra supervisory signals for module execution sequencing. With this approach, we report performance comparable to models using hand-designed modules.

Due to the over-parameterization of neural networks, many model compression methods based on pruning and quantization have emerged. They are remarkable in reducing the size, parameter number, and computational complexity of the model. However, most of the models compressed by such methods need the support of special hardware and software, which increases the deployment cost. Moreover, these methods are mainly used in classification tasks, and rarely directly used in detection tasks. To address these issues, for the object detection network we introduce a three-stage model compression method: dynamic sparse training, group channel pruning, and spatial attention distilling. Firstly, to select out the unimportant channels in the network and maintain a good balance between sparsity and accuracy, we put forward a dynamic sparse training method, which introduces a variable sparse rate, and the sparse rate will change with the training process of the network. Secondly, to reduce the effect of pruning on network accuracy, we propose a novel pruning method called group channel pruning. In particular, we divide the network into multiple groups according to the scales of the feature layer and the similarity of module structure in the network, and then we use different pruning thresholds to prune the channels in each group. Finally, to recover the accuracy of the pruned network, we use an improved knowledge distillation method for the pruned network. Especially, we extract spatial attention information from the feature maps of specific scales in each group as knowledge for distillation. In the experiments, we use YOLOv4 as the object detection network and PASCAL VOC as the training dataset. Our method reduces the parameters of the model by 64.7 % and the calculation by 34.9%.

NeMo (Neural Modules) is a Python framework-agnostic toolkit for creating AI applications through re-usability, abstraction, and composition. NeMo is built around neural modules, conceptual blocks of neural networks that take typed inputs and produce typed outputs. Such modules typically represent data layers, encoders, decoders, language models, loss functions, or methods of combining activations. NeMo makes it easy to combine and re-use these building blocks while providing a level of semantic correctness checking via its neural type system. The toolkit comes with extendable collections of pre-built modules for automatic speech recognition and natural language processing. Furthermore, NeMo provides built-in support for distributed training and mixed precision on latest NVIDIA GPUs. NeMo is open-source https://github.com/NVIDIA/NeMo

Large language models (LLMs) have demonstrated remarkable prediction performance for a growing array of tasks. However, their rapid proliferation and increasing opaqueness have created a growing need for interpretability. Here, we ask whether we can automatically obtain natural language explanations for black box text modules. A "text module" is any function that maps text to a scalar continuous value, such as a submodule within an LLM or a fitted model of a brain region. "Black box" indicates that we only have access to the module's inputs/outputs. We introduce Summarize and Score (SASC), a method that takes in a text module and returns a natural language explanation of the module's selectivity along with a score for how reliable the explanation is. We study SASC in 3 contexts. First, we evaluate SASC on synthetic modules and find that it often recovers ground truth explanations. Second, we use SASC to explain modules found within a pre-trained BERT model, enabling inspection of the model's internals. Finally, we show that SASC can generate explanations for the response of individual fMRI voxels to language stimuli, with potential applications to fine-grained brain mapping. All code for using SASC and reproducing results is made available on Github.

Incorporating modular designs into neural networks demonstrates superior out-of-generalization, learning efficiency, etc. Existing modular neural networks are generally explicit because their modular architectures are pre-defined, and individual modules are expected to implement distinct functions. Conversely, recent works reveal that there exist implicit modular structures in standard pre-trained transformers, namely Emergent Modularity. They indicate that such modular structures exhibit during the early pre-training phase and are totally spontaneous. However, most transformers are still treated as monolithic models with their modular natures underutilized. Therefore, given the excellent properties of explicit modular architecture, we explore whether and how dense pre-trained transformers can benefit from emergent modular structures. To study this question, we construct Emergent Mixture-of-Experts (EMoE). Without introducing additional parameters, EMoE can be seen as the modular counterpart of the original model and can be effortlessly incorporated into downstream tuning. Extensive experiments (we tune 1785 models) on various downstream tasks (vision and language) and models (22M to1.5B) demonstrate that EMoE effectively boosts in-domain and out-of-domain generalization abilities. Further analysis and ablation study suggest that EMoE mitigates negative knowledge transfer and is robust to various configurations. Code is available at https://github.com/qiuzh20/EMoE

Transfer learning has recently become the dominant paradigm of machine learning. Pre-trained models fine-tuned for downstream tasks achieve better performance with fewer labelled examples. Nonetheless, it remains unclear how to develop models that specialise towards multiple tasks without incurring negative interference and that generalise systematically to non-identically distributed tasks. Modular deep learning has emerged as a promising solution to these challenges. In this framework, units of computation are often implemented as autonomous parameter-efficient modules. Information is conditionally routed to a subset of modules and subsequently aggregated. These properties enable positive transfer and systematic generalisation by separating computation from routing and updating modules locally. We offer a survey of modular architectures, providing a unified view over several threads of research that evolved independently in the scientific literature. Moreover, we explore various additional purposes of modularity, including scaling language models, causal inference, programme induction, and planning in reinforcement learning. Finally, we report various concrete applications where modularity has been successfully deployed such as cross-lingual and cross-modal knowledge transfer. Related talks and projects to this survey, are available at https://www.modulardeeplearning.com/.

We introduce the category of information structures, whose objects are suitable diagrams of measurable sets that encode the possible outputs of a given family of observables and their mutual relationships of refinement; they serve as mathematical models of contextuality in classical and quantum settings. Each information structure can be regarded as a ringed site with trivial topology; the structure ring is generated by the observables themselves and its multiplication corresponds to joint measurement. We extend Baudot and Bennequin's definition of information cohomology to this setting, as a derived functor in the category of modules over the structure ring, and show explicitly that the bar construction gives a projective resolution in that category, recovering in this way the cochain complexes previously considered in the literature. Finally, we study the particular case of a one-parameter family of coefficients made of functions of probability distributions. The only 1-cocycles are Shannon entropy or Tsallis alpha-entropy, depending on the value of the parameter.

Many complex tasks can be decomposed into simpler, independent parts. Discovering such underlying compositional structure has the potential to enable compositional generalization. Despite progress, our most powerful systems struggle to compose flexibly. It therefore seems natural to make models more modular to help capture the compositional nature of many tasks. However, it is unclear under which circumstances modular systems can discover hidden compositional structure. To shed light on this question, we study a teacher-student setting with a modular teacher where we have full control over the composition of ground truth modules. This allows us to relate the problem of compositional generalization to that of identification of the underlying modules. In particular we study modularity in hypernetworks representing a general class of multiplicative interactions. We show theoretically that identification up to linear transformation purely from demonstrations is possible without having to learn an exponential number of module combinations. We further demonstrate empirically that under the theoretically identified conditions, meta-learning from finite data can discover modular policies that generalize compositionally in a number of complex environments.

Two well-studied Diophantine equations are those of Pythagorean triples and elliptic curves, for the first we have a parametrization through rational points on the unit circle, and for the second we have a structure theorem for the group of rational solutions. Recently, Yekutieli discussed a connection between these two problems, and described the group structure of Pythagorean triples and the number of triples for a given hypotenuse. In arXiv:2112.03663 we generalized these methods and results to Pell's equation. We find a similar group structure and count on the number of solutions for a given z to x^2 + Dy^2 = z^2 when D is 1 or 2 modulo 4 and the class group of Q[-D] is a free Z_2 module, which always happens if the class number is at most 2. In this paper, we discuss the main results of arXiv:2112.03663 using some concrete examples in the case of D=105.

Despite the power of Large Language Models (LLMs) like GPT-4, they still struggle with tasks that require generating complex, structured outputs. In this study, we assess the capability of Current LLMs in generating complex structured data and propose a structure-aware fine-tuning approach as a solution to improve this ability. To perform a comprehensive evaluation, we propose Struc-Bench, include five representative LLMs (i.e., GPT-NeoX 20B, GPT-3.5, GPT-4, and Vicuna) and evaluate them on our carefully constructed datasets spanning raw text, HTML, and LaTeX tables. Based on our analysis of current model performance, we identify specific common formatting errors and areas of potential improvement. To address complex formatting requirements, we utilize FormatCoT (Chain-of-Thought) to generate format instructions from target outputs. Our experiments show that our structure-aware fine-tuning method, when applied to LLaMA-7B, significantly improves adherence to natural language constraints, outperforming other evaluated LLMs. Based on these results, we present an ability map of model capabilities from six dimensions (i.e., coverage, formatting, reasoning, comprehension, pragmatics, and hallucination). This map highlights the weaknesses of LLMs in handling complex structured outputs and suggests promising directions for future work. Our code and models can be found at https://github.com/gersteinlab/Struc-Bench.

Instance level detection and segmentation of thoracic diseases or abnormalities are crucial for automatic diagnosis in chest X-ray images. Leveraging on constant structure and disease relations extracted from domain knowledge, we propose a structure-aware relation network (SAR-Net) extending Mask R-CNN. The SAR-Net consists of three relation modules: 1. the anatomical structure relation module encoding spatial relations between diseases and anatomical parts. 2. the contextual relation module aggregating clues based on query-key pair of disease RoI and lung fields. 3. the disease relation module propagating co-occurrence and causal relations into disease proposals. Towards making a practical system, we also provide ChestX-Det, a chest X-Ray dataset with instance-level annotations (boxes and masks). ChestX-Det is a subset of the public dataset NIH ChestX-ray14. It contains ~3500 images of 13 common disease categories labeled by three board-certified radiologists. We evaluate our SAR-Net on it and another dataset DR-Private. Experimental results show that it can enhance the strong baseline of Mask R-CNN with significant improvements. The ChestX-Det is released at https://github.com/Deepwise-AILab/ChestX-Det-Dataset.

Proteins, as essential biomolecules, play a central role in biological processes, including metabolic reactions and DNA replication. Accurate prediction of their properties and functions is crucial in biological applications. Recent development of protein language models (pLMs) with supervised fine tuning provides a promising solution to this problem. However, the fine-tuned model is tailored for particular downstream prediction task, and achieving general-purpose protein understanding remains a challenge. In this paper, we introduce Structure-Enhanced Protein Instruction Tuning (SEPIT) framework to bridge this gap. Our approach integrates a noval structure-aware module into pLMs to inform them with structural knowledge, and then connects these enhanced pLMs to large language models (LLMs) to generate understanding of proteins. In this framework, we propose a novel two-stage instruction tuning pipeline that first establishes a basic understanding of proteins through caption-based instructions and then refines this understanding using a mixture of experts (MoEs) to learn more complex properties and functional information with the same amount of activated parameters. Moreover, we construct the largest and most comprehensive protein instruction dataset to date, which allows us to train and evaluate the general-purpose protein understanding model. Extensive experimental results on open-ended generation and closed-set answer tasks demonstrate the superior performance of SEPIT over both closed-source general LLMs and open-source LLMs trained with protein knowledge.

Large Language Models (LLMs) are increasingly used as autonomous agents for multi-step tasks. However, most existing frameworks fail to maintain a structured understanding of the task state, often relying on linear prompt concatenation or shallow memory buffers. This leads to brittle performance, frequent hallucinations, and poor long-range coherence. In this work, we propose the Task Memory Engine (TME), a lightweight and structured memory module that tracks task execution using a hierarchical Task Memory Tree (TMT). Each node in the tree corresponds to a task step, storing relevant input, output, status, and sub-task relationships. We introduce a prompt synthesis method that dynamically generates LLM prompts based on the active node path, significantly improving execution consistency and contextual grounding. Through case studies and comparative experiments on multi-step agent tasks, we demonstrate that TME leads to better task completion accuracy and more interpretable behavior with minimal implementation overhead. A reference implementation of the core TME components is available at https://github.com/biubiutomato/TME-Agent, including basic examples and structured memory integration. While the current implementation uses a tree-based structure, TME is designed to be graph-aware, supporting reusable substeps, converging task paths, and shared dependencies. This lays the groundwork for future DAG-based memory architectures.

In "Backprop as functor", the authors show that the fundamental elements of deep learning -- gradient descent and backpropagation -- can be conceptualized as a strong monoidal functor Para(Euc)toLearn from the category of parameterized Euclidean spaces to that of learners, a category developed explicitly to capture parameter update and backpropagation. It was soon realized that there is an isomorphism LearncongPara(Slens), where Slens is the symmetric monoidal category of simple lenses as used in functional programming. In this note, we observe that Slens is a full subcategory of Poly, the category of polynomial functors in one variable, via the functor Amapsto Ay^A. Using the fact that (Poly,otimes) is monoidal closed, we show that a map Ato B in Para(Slens) has a natural interpretation in terms of dynamical systems (more precisely, generalized Moore machines) whose interface is the internal-hom type [Ay^A,By^B]. Finally, we review the fact that the category p-Coalg of dynamical systems on any p in Poly forms a topos, and consider the logical propositions that can be stated in its internal language. We give gradient descent as an example, and we conclude by discussing some directions for future work.

Chain-of-Thought (CoT) prompting enhances the reasoning of large language models (LLMs) by decomposing problems into sequential steps, mimicking human logic and reducing errors. However, complex tasks with vast solution spaces and vague constraints often exceed the capacity of a single reasoning chain. Inspired by Minimal Free Resolution (MFR) in commutative algebra and algebraic geometry, we propose Syzygy of Thoughts (SoT)-a novel framework that extends CoT by introducing auxiliary, interrelated reasoning paths. SoT captures deeper logical dependencies, enabling more robust and structured problem-solving. MFR decomposes a module into a sequence of free modules with minimal rank, providing a structured analytical approach to complex systems. This method introduces the concepts of "Module", "Betti numbers","Freeness", "Mapping", "Exactness" and "Minimality", enabling the systematic decomposition of the original complex problem into logically complete minimal subproblems while preserving key problem features and reducing reasoning length. We tested SoT across diverse datasets (e.g., GSM8K, MATH) and models (e.g., GPT-4o-mini, Qwen2.5), achieving inference accuracy that matches or surpasses mainstream CoTs standards. Additionally, by aligning the sampling process with algebraic constraints, our approach enhances the scalability of inference time in LLMs, ensuring both transparent reasoning and high performance. Our code will be publicly available at https://github.com/dlMARiA/Syzygy-of-thoughts.

Structure reasoning is a fundamental capability of large language models (LLMs), enabling them to reason about structured commonsense and answer multi-hop questions. However, existing benchmarks for structure reasoning mainly focus on horizontal and coordinate structures (e.g. graphs), overlooking the hierarchical relationships within them. Hierarchical structure reasoning is crucial for human cognition, particularly in memory organization and problem-solving. It also plays a key role in various real-world tasks, such as information extraction and decision-making. To address this gap, we propose HiBench, the first framework spanning from initial structure generation to final proficiency assessment, designed to benchmark the hierarchical reasoning capabilities of LLMs systematically. HiBench encompasses six representative scenarios, covering both fundamental and practical aspects, and consists of 30 tasks with varying hierarchical complexity, totaling 39,519 queries. To evaluate LLMs comprehensively, we develop five capability dimensions that depict different facets of hierarchical structure understanding. Through extensive evaluation of 20 LLMs from 10 model families, we reveal key insights into their capabilities and limitations: 1) existing LLMs show proficiency in basic hierarchical reasoning tasks; 2) they still struggle with more complex structures and implicit hierarchical representations, especially in structural modification and textual reasoning. Based on these findings, we create a small yet well-designed instruction dataset, which enhances LLMs' performance on HiBench by an average of 88.84\% (Llama-3.1-8B) and 31.38\% (Qwen2.5-7B) across all tasks. The HiBench dataset and toolkit are available here, https://github.com/jzzzzh/HiBench, to encourage evaluation.

Optics and lenses are abstract categorical gadgets that model systems with bidirectional data flow. In this paper we observe that the denotational definition of optics - identifying two optics as equivalent by observing their behaviour from the outside - is not suitable for operational, software oriented approaches where optics are not merely observed, but built with their internal setups in mind. We identify operational differences between denotationally isomorphic categories of cartesian optics and lenses: their different composition rule and corresponding space-time tradeoffs, positioning them at two opposite ends of a spectrum. With these motivations we lift the existing categorical constructions and their relationships to the 2-categorical level, showing that the relevant operational concerns become visible. We define the 2-category 2-Optic(C) whose 2-cells explicitly track optics' internal configuration. We show that the 1-category Optic(C) arises by locally quotienting out the connected components of this 2-category. We show that the embedding of lenses into cartesian optics gets weakened from a functor to an oplax functor whose oplaxator now detects the different composition rule. We determine the difficulties in showing this functor forms a part of an adjunction in any of the standard 2-categories. We establish a conjecture that the well-known isomorphism between cartesian lenses and optics arises out of the lax 2-adjunction between their double-categorical counterparts. In addition to presenting new research, this paper is also meant to be an accessible introduction to the topic.