Yang Shen

Jingyang Du, Yang Shen, Anling Xiang

Burrows-Wheeler-transform-based compressors rely on local context regularity, but structured text also contains dates, counters, identifiers, coordinates, and other digit runs whose values vary differently from their surrounding tokens. STC is a practical BWT-family compressor that separates this source of variation before the component BWT stage. It replaces digit runs in the main stream with an unambiguous placeholder and stores the removed digits in length- and context-conditioned side streams. The side streams use stable bucket ordering and compact digit packing, so the decoder can reconstruct the original run order from the normalized main stream without storing a separate permutation. The resulting components are encoded by a fixed internal BWT/M03-style component coder. On enwik9, STC produces a 157,388,188-byte archive with a 183,174-byte decoder source package, giving a local LTCB-style total of 157,571,362 bytes. A full-enwik9 same-coder ablation shows that the digit-context decomposition reduces the archive by 2,629,561 bytes relative to the no-split control. The result is locally verified by full decode and SHA-256 matching; official benchmark status requires independent maintainer-side verification.

Anling Xiang, Yuwen Yang, Yang Shen

Scholarly text classification supports literature organization, subject indexing, and research intelligence, but Chinese scholarly corpora often contain imbalanced and semantically adjacent disciplinary labels. We propose AutoTail-BSFGM, a class-balance-aware fine-tuning method that combines an automatically gated tail-prior adjustment, a weak Balanced Softmax auxiliary loss, and Fast Gradient Method adversarial regularization. The method changes only the training objective and procedure; inference uses the same single base-size encoder and linear classifier as the corresponding label-smoothed baseline. We evaluate the method on two CSL-based tasks: an abstract-to-discipline task with 67 labels and a title-to-category task with 13 categories. On the primary abstract task, AutoTail-BSFGM improves validation and lockbox accuracy under both Chinese RoBERTa-WWM and MacBERT-base. With MacBERT-base, validation accuracy increases by 0.83 percentage points and lockbox accuracy by 0.49 points, with a pooled paired McNemar signal on validation (p = 0.023). On the title task, the method improves validation accuracy by 0.70 points and validation balanced accuracy by 2.64 points; lockbox accuracy is approximately neutral while lockbox balanced accuracy improves by 1.22 points. The results support a bounded contribution: AutoTail-BSFGM improves class-balance-sensitive behavior and yields consistent gains for abstract-based scholarly classification, without uniformly improving every metric on every split.

Tianxin Wei, Yuning You, Tianlong Chen et al.

This paper targets at improving the generalizability of hypergraph neural networks in the low-label regime, through applying the contrastive learning approach from images/graphs (we refer to it as HyperGCL). We focus on the following question: How to construct contrastive views for hypergraphs via augmentations? We provide the solutions in two folds. First, guided by domain knowledge, we fabricate two schemes to augment hyperedges with higher-order relations encoded, and adopt three vertex augmentation strategies from graph-structured data. Second, in search of more effective views in a data-driven manner, we for the first time propose a hypergraph generative model to generate augmented views, and then an end-to-end differentiable pipeline to jointly learn hypergraph augmentations and model parameters. Our technical innovations are reflected in designing both fabricated and generative augmentations of hypergraphs. The experimental findings include: (i) Among fabricated augmentations in HyperGCL, augmenting hyperedges provides the most numerical gains, implying that higher-order information in structures is usually more downstream-relevant; (ii) Generative augmentations do better in preserving higher-order information to further benefit generalizability; (iii) HyperGCL also boosts robustness and fairness in hypergraph representation learning. Codes are released at https://github.com/weitianxin/HyperGCL.

Junjie Ye, Xuanting Chen, Nuo Xu et al.

GPT series models, such as GPT-3, CodeX, InstructGPT, ChatGPT, and so on, have gained considerable attention due to their exceptional natural language processing capabilities. However, despite the abundance of research on the difference in capabilities between GPT series models and fine-tuned models, there has been limited attention given to the evolution of GPT series models' capabilities over time. To conduct a comprehensive analysis of the capabilities of GPT series models, we select six representative models, comprising two GPT-3 series models (i.e., davinci and text-davinci-001) and four GPT-3.5 series models (i.e., code-davinci-002, text-davinci-002, text-davinci-003, and gpt-3.5-turbo). We evaluate their performance on nine natural language understanding (NLU) tasks using 21 datasets. In particular, we compare the performance and robustness of different models for each task under zero-shot and few-shot scenarios. Our extensive experiments reveal that the overall ability of GPT series models on NLU tasks does not increase gradually as the models evolve, especially with the introduction of the RLHF training strategy. While this strategy enhances the models' ability to generate human-like responses, it also compromises their ability to solve some tasks. Furthermore, our findings indicate that there is still room for improvement in areas such as model robustness.

Xiu-Shen Wei, Yang Shen, Xuhao Sun et al.

Our work focuses on tackling large-scale fine-grained image retrieval as ranking the images depicting the concept of interests (i.e., the same sub-category labels) highest based on the fine-grained details in the query. It is desirable to alleviate the challenges of both fine-grained nature of small inter-class variations with large intra-class variations and explosive growth of fine-grained data for such a practical task. In this paper, we propose attribute-aware hashing networks with self-consistency for generating attribute-aware hash codes to not only make the retrieval process efficient, but also establish explicit correspondences between hash codes and visual attributes. Specifically, based on the captured visual representations by attention, we develop an encoder-decoder structure network of a reconstruction task to unsupervisedly distill high-level attribute-specific vectors from the appearance-specific visual representations without attribute annotations. Our models are also equipped with a feature decorrelation constraint upon these attribute vectors to strengthen their representative abilities. Then, driven by preserving original entities' similarity, the required hash codes can be generated from these attribute-specific vectors and thus become attribute-aware. Furthermore, to combat simplicity bias in deep hashing, we consider the model design from the perspective of the self-consistency principle and propose to further enhance models' self-consistency by equipping an additional image reconstruction path. Comprehensive quantitative experiments under diverse empirical settings on six fine-grained retrieval datasets and two generic retrieval datasets show the superiority of our models over competing methods.

Yang Shen, Xuhao Sun, Xiu-Shen Wei et al.

In this paper, we propose Suppression-Enhancing Mask based attention and Interactive Channel transformatiON (SEMICON) to learn binary hash codes for dealing with large-scale fine-grained image retrieval tasks. In SEMICON, we first develop a suppression-enhancing mask (SEM) based attention to dynamically localize discriminative image regions. More importantly, different from existing attention mechanism simply erasing previous discriminative regions, our SEM is developed to restrain such regions and then discover other complementary regions by considering the relation between activated regions in a stage-by-stage fashion. In each stage, the interactive channel transformation (ICON) module is afterwards designed to exploit correlations across channels of attended activation tensors. Since channels could generally correspond to the parts of fine-grained objects, the part correlation can be also modeled accordingly, which further improves fine-grained retrieval accuracy. Moreover, to be computational economy, ICON is realized by an efficient two-step process. Finally, the hash learning of our SEMICON consists of both global- and local-level branches for better representing fine-grained objects and then generating binary hash codes explicitly corresponding to multiple levels. Experiments on five benchmark fine-grained datasets show our superiority over competing methods.

Yang Shen, Xuhao Sun, Xiu-Shen Wei

We propose Equiangular Basis Vectors (EBVs) for classification tasks. In deep neural networks, models usually end with a k-way fully connected layer with softmax to handle different classification tasks. The learning objective of these methods can be summarized as mapping the learned feature representations to the samples' label space. While in metric learning approaches, the main objective is to learn a transformation function that maps training data points from the original space to a new space where similar points are closer while dissimilar points become farther apart. Different from previous methods, our EBVs generate normalized vector embeddings as "predefined classifiers" which are required to not only be with the equal status between each other, but also be as orthogonal as possible. By minimizing the spherical distance of the embedding of an input between its categorical EBV in training, the predictions can be obtained by identifying the categorical EBV with the smallest distance during inference. Various experiments on the ImageNet-1K dataset and other downstream tasks demonstrate that our method outperforms the general fully connected classifier while it does not introduce huge additional computation compared with classical metric learning methods. Our EBVs won the first place in the 2022 DIGIX Global AI Challenge, and our code is open-source and available at https://github.com/NJUST-VIPGroup/Equiangular-Basis-Vectors.

Zhenxiao Yin, Xiaobing Dai, Zewen Yang et al.

The growing demand for accurate control in varying and unknown environments has sparked a corresponding increase in the requirements for power supply components, including permanent magnet synchronous motors (PMSMs). To infer the unknown part of the system, machine learning techniques are widely employed, especially Gaussian process regression (GPR) due to its flexibility of continuous system modeling and its guaranteed performance. For practical implementation, distributed GPR is adopted to alleviate the high computational complexity. However, the study of distributed GPR from a control perspective remains an open problem. In this paper, a control-aware optimal aggregation strategy of distributed GPR for PMSMs is proposed based on the Lyapunov stability theory. This strategy exclusively leverages the posterior mean, thereby obviating the need for computationally intensive calculations associated with posterior variance in alternative approaches. Moreover, the straightforward calculation process of our proposed strategy lends itself to seamless implementation in high-frequency PMSM control. The effectiveness of the proposed strategy is demonstrated in the simulations.

Xiu-Shen Wei, Xuhao Sun, Yang Shen et al.

Simplicity Bias (SB) is a phenomenon that deep neural networks tend to rely favorably on simpler predictive patterns but ignore some complex features when applied to supervised discriminative tasks. In this work, we investigate SB in long-tailed image recognition and find the tail classes suffer more severely from SB, which harms the generalization performance of such underrepresented classes. We empirically report that self-supervised learning (SSL) can mitigate SB and perform in complementary to the supervised counterpart by enriching the features extracted from tail samples and consequently taking better advantage of such rare samples. However, standard SSL methods are designed without explicitly considering the inherent data distribution in terms of classes and may not be optimal for long-tailed distributed data. To address this limitation, we propose a novel SSL method tailored to imbalanced data. It leverages SSL by triple diverse levels, i.e., holistic-, partial-, and augmented-level, to enhance the learning of predictive complex patterns, which provides the potential to overcome the severe SB on tail data. Both quantitative and qualitative experimental results on five long-tailed benchmark datasets show our method can effectively mitigate SB and significantly outperform the competing state-of-the-arts.

Tengjin Weng, Yang Shen, Kai Jin et al.

Automatic segmentation of fluid in Optical Coherence Tomography (OCT) images is beneficial for ophthalmologists to make an accurate diagnosis. Although semi-supervised OCT fluid segmentation networks enhance their performance by introducing additional unlabeled data, the performance enhancement is limited. To address this, we propose Superpixel and Confident Learning Guide Point Annotations Network (SCLGPA-Net) based on the teacher-student architecture, which can learn OCT fluid segmentation from limited fully-annotated data and abundant point-annotated data. Specifically, we use points to annotate fluid regions in unlabeled OCT images and the Superpixel-Guided Pseudo-Label Generation (SGPLG) module generates pseudo-labels and pixel-level label trust maps from the point annotations. The label trust maps provide an indication of the reliability of the pseudo-labels. Furthermore, we propose the Confident Learning Guided Label Refinement (CLGLR) module identifies error information in the pseudo-labels and leads to further refinement. Experiments on the RETOUCH dataset show that we are able to reduce the need for fully-annotated data by 94.22\%, closing the gap with the best fully supervised baselines to a mean IoU of only 2\%. Furthermore, We constructed a private 2D OCT fluid segmentation dataset for evaluation. Compared with other methods, comprehensive experimental results demonstrate that the proposed method can achieve excellent performance in OCT fluid segmentation.

Hao Xu, Jia Liu, Yang Shen et al.

Graph Pooling technology plays an important role in graph node classification tasks. Sorting pooling technologies maintain large-value units for pooling graphs of varying sizes. However, by analyzing the statistical characteristic of activated units after pooling, we found that a large number of units dropped by sorting pooling are negative-value units that contain useful information and can contribute considerably to the final decision. To maintain more useful information, a novel pooling technology, called Geometric Pooling (GP), was proposed to contain the unique node features with negative values by measuring the similarity of all node features. We reveal the effectiveness of GP from the entropy reduction view. The experiments were conducted on TUdatasets to show the effectiveness of GP. The results showed that the proposed GP outperforms the SOTA graph pooling technologies by 1%\sim5% with fewer parameters.

Jiabei He, Yang Shen, Xiu-Shen Wei et al.

Fine-Grained Image Recognition (FGIR) is a fundamental and challenging task in computer vision and multimedia that plays a crucial role in Intellectual Economy and Industrial Internet applications. However, the absence of a unified open-source software library covering various paradigms in FGIR poses a significant challenge for researchers and practitioners in the field. To address this gap, we present Hawkeye, a PyTorch-based library for FGIR with deep learning. Hawkeye is designed with a modular architecture, emphasizing high-quality code and human-readable configuration, providing a comprehensive solution for FGIR tasks. In Hawkeye, we have implemented 16 state-of-the-art fine-grained methods, covering 6 different paradigms, enabling users to explore various approaches for FGIR. To the best of our knowledge, Hawkeye represents the first open-source PyTorch-based library dedicated to FGIR. It is publicly available at https://github.com/Hawkeye-FineGrained/Hawkeye/, providing researchers and practitioners with a powerful tool to advance their research and development in the field of FGIR.

Tengjin Weng, Yang Shen, Zhidong Zhao et al.

Optic disc and cup segmentation plays a crucial role in automating the screening and diagnosis of optic glaucoma. While data-driven convolutional neural networks (CNNs) show promise in this area, the inherent ambiguity of segmenting objects and background boundaries in the task of optic disc and cup segmentation leads to noisy annotations that impact model performance. To address this, we propose an innovative label-denoising method of Multiple Pseudo-labels Noise-aware Network (MPNN) for accurate optic disc and cup segmentation. Specifically, the Multiple Pseudo-labels Generation and Guided Denoising (MPGGD) module generates pseudo-labels by multiple different initialization networks trained on true labels, and the pixel-level consensus information extracted from these pseudo-labels guides to differentiate clean pixels from noisy pixels. The training framework of the MPNN is constructed by a teacher-student architecture to learn segmentation from clean pixels and noisy pixels. Particularly, such a framework adeptly leverages (i) reliable and fundamental insight from clean pixels and (ii) the supplementary knowledge within noisy pixels via multiple perturbation-based unsupervised consistency. Compared to other label-denoising methods, comprehensive experimental results on the RIGA dataset demonstrate our method's excellent performance. The code is available at https://github.com/wwwtttjjj/MPNN

Ziyi Zhao, Jinzhao Zhou, Xiaowei Jiang et al.

Decoding linguistic information from electroencephalography (EEG) remains challenging due to the brain's distributed and nonlinear organization. We present BrainStack, a functionally guided neuro-mixture-of-experts (Neuro-MoE) framework that models the brain's modular functional architecture through anatomically partitioned expert networks. Each functional region is represented by a specialized expert that learns localized neural dynamics, while a transformer-based global expert captures cross-regional dependencies. A learnable routing gate adaptively aggregates these heterogeneous experts, enabling context-dependent expert coordination and selective fusion. To promote coherent representation across the hierarchy, we introduce cross-regional distillation, where the global expert provides top-down regularization to the regional experts. We further release SilentSpeech-EEG (SS-EEG), a large-scale benchmark comprising over 120 hours of EEG recordings from 12 subjects performing 24 silent words, the largest dataset of its kind. Experiments demonstrate that BrainStack consistently outperforms state-of-the-art models, achieving superior accuracy and generalization across subjects. Our results establish BrainStack as a functionally modular, neuro-inspired MoE paradigm that unifies neuroscientific priors with adaptive expert routing, paving the way for scalable and interpretable brain-language decoding.

Xinyu Zhang, Li Wang, Zhiqiang Jiang et al.

Local Feature Matching, an essential component of several computer vision tasks (e.g., structure from motion and visual localization), has been effectively settled by Transformer-based methods. However, these methods only integrate long-range context information among keypoints with a fixed receptive field, which constrains the network from reconciling the importance of features with different receptive fields to realize complete image perception, hence limiting the matching accuracy. In addition, these methods utilize a conventional handcrafted encoding approach to integrate the positional information of keypoints into the visual descriptors, which limits the capability of the network to extract reliable positional encoding message. In this study, we propose Feature Matching with Reconciliatory Transformer (FMRT), a novel Transformer-based detector-free method that reconciles different features with multiple receptive fields adaptively and utilizes parallel networks to realize reliable positional encoding. Specifically, FMRT proposes a dedicated Reconciliatory Transformer (RecFormer) that consists of a Global Perception Attention Layer (GPAL) to extract visual descriptors with different receptive fields and integrate global context information under various scales, Perception Weight Layer (PWL) to measure the importance of various receptive fields adaptively, and Local Perception Feed-forward Network (LPFFN) to extract deep aggregated multi-scale local feature representation. Extensive experiments demonstrate that FMRT yields extraordinary performance on multiple benchmarks, including pose estimation, visual localization, homography estimation, and image matching.

Lei Yang, Xinyu Zhang, Jun Li et al.

Modern autonomous vehicle perception systems often struggle with occlusions and limited perception range. Previous studies have demonstrated the effectiveness of cooperative perception in extending the perception range and overcoming occlusions, thereby enhancing the safety of autonomous driving. In recent years, a series of cooperative perception datasets have emerged; however, these datasets primarily focus on cameras and LiDAR, neglecting 4D Radar, a sensor used in single-vehicle autonomous driving to provide robust perception in adverse weather conditions. In this paper, to bridge the gap created by the absence of 4D Radar datasets in cooperative perception, we present V2X-Radar, the first large-scale, real-world multi-modal dataset featuring 4D Radar. V2X-Radar dataset is collected using a connected vehicle platform and an intelligent roadside unit equipped with 4D Radar, LiDAR, and multi-view cameras. The collected data encompasses sunny and rainy weather conditions, spanning daytime, dusk, and nighttime, as well as various typical challenging scenarios. The dataset consists of 20K LiDAR frames, 40K camera images, and 20K 4D Radar data, including 350K annotated boxes across five categories. To support various research domains, we have established V2X-Radar-C for cooperative perception, V2X-Radar-I for roadside perception, and V2X-Radar-V for single-vehicle perception. Furthermore, we provide comprehensive benchmarks across these three sub-datasets. We will release all datasets and benchmark codebase at https://huggingface.co/datasets/yanglei18/V2X-Radar and https://github.com/yanglei18/V2X-Radar.

Shuai Wang, Tengjin Weng, Jingyi Wang et al.

Medical image segmentation annotations exhibit variations among experts due to the ambiguous boundaries of segmented objects and backgrounds in medical images. Although using multiple annotations for each image in the fully-supervised has been extensively studied for training deep models, obtaining a large amount of multi-annotated data is challenging due to the substantial time and manpower costs required for segmentation annotations, resulting in most images lacking any annotations. To address this, we propose Multi-annotated Semi-supervised Ensemble Networks (MSE-Nets) for learning segmentation from limited multi-annotated and abundant unannotated data. Specifically, we introduce the Network Pairwise Consistency Enhancement (NPCE) module and Multi-Network Pseudo Supervised (MNPS) module to enhance MSE-Nets for the segmentation task by considering two major factors: (1) to optimize the utilization of all accessible multi-annotated data, the NPCE separates (dis)agreement annotations of multi-annotated data at the pixel level and handles agreement and disagreement annotations in different ways, (2) to mitigate the introduction of imprecise pseudo-labels, the MNPS extends the training data by leveraging consistent pseudo-labels from unannotated data. Finally, we improve confidence calibration by averaging the predictions of base networks. Experiments on the ISIC dataset show that we reduced the demand for multi-annotated data by 97.75\% and narrowed the gap with the best fully-supervised baseline to just a Jaccard index of 4\%. Furthermore, compared to other semi-supervised methods that rely only on a single annotation or a combined fusion approach, the comprehensive experimental results on ISIC and RIGA datasets demonstrate the superior performance of our proposed method in medical image segmentation with ambiguous boundaries.

Jian Jin, Zhenbo Yu, Yang Shen et al.

Customized text-to-image generation renders user-specified concepts into novel contexts based on textual prompts. Scaling the number of concepts in customized generation meets a broader demand for user creation, whereas existing methods face challenges with generation quality and computational efficiency. In this paper, we propose LaTexBlend, a novel framework for effectively and efficiently scaling multi-concept customized generation. The core idea of LaTexBlend is to represent single concepts and blend multiple concepts within a Latent Textual space, which is positioned after the text encoder and a linear projection. LaTexBlend customizes each concept individually, storing them in a concept bank with a compact representation of latent textual features that captures sufficient concept information to ensure high fidelity. At inference, concepts from the bank can be freely and seamlessly combined in the latent textual space, offering two key merits for multi-concept generation: 1) excellent scalability, and 2) significant reduction of denoising deviation, preserving coherent layouts. Extensive experiments demonstrate that LaTexBlend can flexibly integrate multiple customized concepts with harmonious structures and high subject fidelity, substantially outperforming baselines in both generation quality and computational efficiency. Our code will be publicly available.

Jiwoong Park, Yang Shen

How can diffusion models process 3D geometries in a coarse-to-fine manner, akin to our multiscale view of the world? In this paper, we address the question by focusing on a fundamental biochemical problem of generating 3D molecular conformers conditioned on molecular graphs in a multiscale manner. Our approach consists of two hierarchical stages: i) generation of coarse-grained fragment-level 3D structure from the molecular graph, and ii) generation of fine atomic details from the coarse-grained approximated structure while allowing the latter to be adjusted simultaneously. For the challenging second stage, which demands preserving coarse-grained information while ensuring SE(3) equivariance, we introduce a novel generative model termed Equivariant Blurring Diffusion (EBD), which defines a forward process that moves towards the fragment-level coarse-grained structure by blurring the fine atomic details of conformers, and a reverse process that performs the opposite operation using equivariant networks. We demonstrate the effectiveness of EBD by geometric and chemical comparison to state-of-the-art denoising diffusion models on a benchmark of drug-like molecules. Ablation studies draw insights on the design of EBD by thoroughly analyzing its architecture, which includes the design of the loss function and the data corruption process. Codes are released at https://github.com/Shen-Lab/EBD .

Lei Yang, Xinyu Zhang, Jun Li et al.

Roadside perception can greatly increase the safety of autonomous vehicles by extending their perception ability beyond the visual range and addressing blind spots. However, current state-of-the-art vision-based roadside detection methods possess high accuracy on labeled scenes but have inferior performance on new scenes. This is because roadside cameras remain stationary after installation and can only collect data from a single scene, resulting in the algorithm overfitting these roadside backgrounds and camera poses. To address this issue, in this paper, we propose an innovative Scenario Generalization Framework for Vision-based Roadside 3D Object Detection, dubbed SGV3D. Specifically, we employ a Background-suppressed Module (BSM) to mitigate background overfitting in vision-centric pipelines by attenuating background features during the 2D to bird's-eye-view projection. Furthermore, by introducing the Semi-supervised Data Generation Pipeline (SSDG) using unlabeled images from new scenes, diverse instance foregrounds with varying camera poses are generated, addressing the risk of overfitting specific camera poses. We evaluate our method on two large-scale roadside benchmarks. Our method surpasses all previous methods by a significant margin in new scenes, including +42.57% for vehicle, +5.87% for pedestrian, and +14.89% for cyclist compared to BEVHeight on the DAIR-V2X-I heterologous benchmark. On the larger-scale Rope3D heterologous benchmark, we achieve notable gains of 14.48% for car and 12.41% for large vehicle. We aspire to contribute insights on the exploration of roadside perception techniques, emphasizing their capability for scenario generalization. The code will be available at https://github.com/yanglei18/SGV3D

Junzhu Mao, Yang Shen, Jinyang Guo et al.

Token compression is essential for reducing the computational and memory requirements of transformer models, enabling their deployment in resource-constrained environments. In this work, we propose an efficient and hardware-compatible token compression method called Prune and Merge. Our approach integrates token pruning and merging operations within transformer models to achieve layer-wise token compression. By introducing trainable merge and reconstruct matrices and utilizing shortcut connections, we efficiently merge tokens while preserving important information and enabling the restoration of pruned tokens. Additionally, we introduce a novel gradient-weighted attention scoring mechanism that computes token importance scores during the training phase, eliminating the need for separate computations during inference and enhancing compression efficiency. We also leverage gradient information to capture the global impact of tokens and automatically identify optimal compression structures. Extensive experiments on the ImageNet-1k and ADE20K datasets validate the effectiveness of our approach, achieving significant speed-ups with minimal accuracy degradation compared to state-of-the-art methods. For instance, on DeiT-Small, we achieve a 1.64$\times$ speed-up with only a 0.2\% drop in accuracy on ImageNet-1k. Moreover, by compressing segmenter models and comparing with existing methods, we demonstrate the superior performance of our approach in terms of efficiency and effectiveness. Code and models have been made available at https://github.com/NUST-Machine-Intelligence-Laboratory/prune_and_merge.

Yang Shen, Yusen Cai, Weronika Hryniewska-Guzik et al.

Existing self-supervised learning (SSL) methods primarily learn object-invariant representations but often neglect the spatial structure and relationships among object parts. To address this limitation, we introduce Spatial Prediction (SP), a spatially aware pretext regression task that predicts the relative position and scale between a pair of disentangled local views from the same image. By modeling part-to-part relationships in a continuous geometric space, SP encourages representations to capture fine-grained spatial dependencies beyond invariant categorical semantics, thereby learning the compositional structure of visual scenes. SP is implemented as a decoupled plug-in and can be seamlessly integrated into diverse SSL frameworks. Extensive experiments show consistent improvements across image recognition, fine-grained classification, semantic segmentation, and depth estimation, as well as substantial gains in out-of-distribution robustness for object recognition. To evaluate spatial reasoning, we introduce (1) a position and scale prediction task on image patch pairs and (2) a jigsaw understanding task requiring patch reordering and recognition after reconstruction. Strong performance on these tasks indicates improved spatial structure and geometric awareness. Overall, explicitly modeling spatial information provides an effective inductive bias for SSL, leading to more structured representations and better generalization. Code and models will be released.

Yuning You, Tianlong Chen, Zhangyang Wang et al.

Self-supervision is recently surging at its new frontier of graph learning. It facilitates graph representations beneficial to downstream tasks; but its success could hinge on domain knowledge for handcraft or the often expensive trials and errors. Even its state-of-the-art representative, graph contrastive learning (GraphCL), is not completely free of those needs as GraphCL uses a prefabricated prior reflected by the ad-hoc manual selection of graph data augmentations. Our work aims at advancing GraphCL by answering the following questions: How to represent the space of graph augmented views? What principle can be relied upon to learn a prior in that space? And what framework can be constructed to learn the prior in tandem with contrastive learning? Accordingly, we have extended the prefabricated discrete prior in the augmentation set, to a learnable continuous prior in the parameter space of graph generators, assuming that graph priors per se, similar to the concept of image manifolds, can be learned by data generation. Furthermore, to form contrastive views without collapsing to trivial solutions due to the prior learnability, we have leveraged both principles of information minimization (InfoMin) and information bottleneck (InfoBN) to regularize the learned priors. Eventually, contrastive learning, InfoMin, and InfoBN are incorporated organically into one framework of bi-level optimization. Our principled and automated approach has proven to be competitive against the state-of-the-art graph self-supervision methods, including GraphCL, on benchmarks of small graphs; and shown even better generalizability on large-scale graphs, without resorting to human expertise or downstream validation. Our code is publicly released at https://github.com/Shen-Lab/GraphCL_Automated.

Yue Cao, Payel Das, Vijil Chenthamarakshan et al.

Designing novel protein sequences for a desired 3D topological fold is a fundamental yet non-trivial task in protein engineering. Challenges exist due to the complex sequence--fold relationship, as well as the difficulties to capture the diversity of the sequences (therefore structures and functions) within a fold. To overcome these challenges, we propose Fold2Seq, a novel transformer-based generative framework for designing protein sequences conditioned on a specific target fold. To model the complex sequence--structure relationship, Fold2Seq jointly learns a sequence embedding using a transformer and a fold embedding from the density of secondary structural elements in 3D voxels. On test sets with single, high-resolution and complete structure inputs for individual folds, our experiments demonstrate improved or comparable performance of Fold2Seq in terms of speed, coverage, and reliability for sequence design, when compared to existing state-of-the-art methods that include data-driven deep generative models and physics-based RosettaDesign. The unique advantages of fold-based Fold2Seq, in comparison to a structure-based deep model and RosettaDesign, become more evident on three additional real-world challenges originating from low-quality, incomplete, or ambiguous input structures. Source code and data are available at https://github.com/IBM/fold2seq.

Yuning You, Tianlong Chen, Yang Shen et al.

Self-supervised learning on graph-structured data has drawn recent interest for learning generalizable, transferable and robust representations from unlabeled graphs. Among many, graph contrastive learning (GraphCL) has emerged with promising representation learning performance. Unfortunately, unlike its counterpart on image data, the effectiveness of GraphCL hinges on ad-hoc data augmentations, which have to be manually picked per dataset, by either rules of thumb or trial-and-errors, owing to the diverse nature of graph data. That significantly limits the more general applicability of GraphCL. Aiming to fill in this crucial gap, this paper proposes a unified bi-level optimization framework to automatically, adaptively and dynamically select data augmentations when performing GraphCL on specific graph data. The general framework, dubbed JOint Augmentation Optimization (JOAO), is instantiated as min-max optimization. The selections of augmentations made by JOAO are shown to be in general aligned with previous "best practices" observed from handcrafted tuning: yet now being automated, more flexible and versatile. Moreover, we propose a new augmentation-aware projection head mechanism, which will route output features through different projection heads corresponding to different augmentations chosen at each training step. Extensive experiments demonstrate that JOAO performs on par with or sometimes better than the state-of-the-art competitors including GraphCL, on multiple graph datasets of various scales and types, yet without resorting to any laborious dataset-specific tuning on augmentation selection. We release the code at https://github.com/Shen-Lab/GraphCL_Automated.

Yuning You, Tianlong Chen, Yongduo Sui et al.

Generalizable, transferrable, and robust representation learning on graph-structured data remains a challenge for current graph neural networks (GNNs). Unlike what has been developed for convolutional neural networks (CNNs) for image data, self-supervised learning and pre-training are less explored for GNNs. In this paper, we propose a graph contrastive learning (GraphCL) framework for learning unsupervised representations of graph data. We first design four types of graph augmentations to incorporate various priors. We then systematically study the impact of various combinations of graph augmentations on multiple datasets, in four different settings: semi-supervised, unsupervised, and transfer learning as well as adversarial attacks. The results show that, even without tuning augmentation extents nor using sophisticated GNN architectures, our GraphCL framework can produce graph representations of similar or better generalizability, transferrability, and robustness compared to state-of-the-art methods. We also investigate the impact of parameterized graph augmentation extents and patterns, and observe further performance gains in preliminary experiments. Our codes are available at https://github.com/Shen-Lab/GraphCL.

Yuning You, Tianlong Chen, Zhangyang Wang et al.

Self-supervision as an emerging technique has been employed to train convolutional neural networks (CNNs) for more transferrable, generalizable, and robust representation learning of images. Its introduction to graph convolutional networks (GCNs) operating on graph data is however rarely explored. In this study, we report the first systematic exploration and assessment of incorporating self-supervision into GCNs. We first elaborate three mechanisms to incorporate self-supervision into GCNs, analyze the limitations of pretraining & finetuning and self-training, and proceed to focus on multi-task learning. Moreover, we propose to investigate three novel self-supervised learning tasks for GCNs with theoretical rationales and numerical comparisons. Lastly, we further integrate multi-task self-supervision into graph adversarial training. Our results show that, with properly designed task forms and incorporation mechanisms, self-supervision benefits GCNs in gaining more generalizability and robustness. Our codes are available at https://github.com/Shen-Lab/SS-GCNs.

Yuning You, Tianlong Chen, Zhangyang Wang et al.

Graph convolution networks (GCN) are increasingly popular in many applications, yet remain notoriously hard to train over large graph datasets. They need to compute node representations recursively from their neighbors. Current GCN training algorithms suffer from either high computational costs that grow exponentially with the number of layers, or high memory usage for loading the entire graph and node embeddings. In this paper, we propose a novel efficient layer-wise training framework for GCN (L-GCN), that disentangles feature aggregation and feature transformation during training, hence greatly reducing time and memory complexities. We present theoretical analysis for L-GCN under the graph isomorphism framework, that L-GCN leads to as powerful GCNs as the more costly conventional training algorithm does, under mild conditions. We further propose L$^2$-GCN, which learns a controller for each layer that can automatically adjust the training epochs per layer in L-GCN. Experiments show that L-GCN is faster than state-of-the-arts by at least an order of magnitude, with a consistent of memory usage not dependent on dataset size, while maintaining comparable prediction performance. With the learned controller, L$^2$-GCN can further cut the training time in half. Our codes are available at https://github.com/Shen-Lab/L2-GCN.

Yue Cao, Yang Shen

Motivation: Ab initio protein docking represents a major challenge for optimizing a noisy and costly "black box"-like function in a high-dimensional space. Despite progress in this field, there is no docking method available for rigorous uncertainty quantification (UQ) of its solution quality (e.g. interface RMSD or iRMSD). Results: We introduce a novel algorithm, Bayesian Active Learning (BAL), for optimization and UQ of such black-box functions and flexible protein docking. BAL directly models the posterior distribution of the global optimum (or native structures for protein docking) with active sampling and posterior estimation iteratively feeding each other. Furthermore, we use complex normal modes to represent a homogeneous Euclidean conformation space suitable for high-dimension optimization and construct funnel-like energy models for encounter complexes. Over a protein docking benchmark set and a CAPRI set including homology docking, we establish that BAL significantly improve against both starting points by rigid docking and refinements by particle swarm optimization, providing for one third targets a top-3 near-native prediction. BAL also generates tight confidence intervals with half range around 25% of iRMSD and confidence level at 85%. Its estimated probability of a prediction being native or not achieves binary classification AUROC at 0.93 and AUPRC over 0.60 (compared to 0.14 by chance); and also found to help ranking predictions. To the best of our knowledge, this study represents the first uncertainty quantification solution for protein docking, with theoretical rigor and comprehensive assessment. Source codes are available at https://github.com/Shen-Lab/BAL.

Mostafa Karimi, Di Wu, Zhangyang Wang et al.

Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and interpretability. Results: We present a seamless integration of domain knowledges and learning-based approaches. Under novel representations of structurally-annotated protein sequences, a semi-supervised deep learning model that unifies recurrent and convolutional neural networks has been proposed to exploit both unlabeled and labeled data, for jointly encoding molecular representations and predicting affinities. Our representations and models outperform conventional options in achieving relative error in IC$_{50}$ within 5-fold for test cases and 20-fold for protein classes not included for training. Performances for new protein classes with few labeled data are further improved by transfer learning. Furthermore, separate and joint attention mechanisms are developed and embedded to our model to add to its interpretability, as illustrated in case studies for predicting and explaining selective drug-target interactions. Lastly, alternative representations using protein sequences or compound graphs and a unified RNN/GCNN-CNN model using graph CNN (GCNN) are also explored to reveal algorithmic challenges ahead. Availability: Data and source codes are available at https://github.com/Shen-Lab/DeepAffinity Supplementary Information: Supplementary data are available at http://shen-lab.github.io/deep-affinity-bioinf18-supp-rev.pdf

Shihao Yang, Zhicong Lu, Yong Yang et al.

Multi-character role-playing aims to equip models with the capability to simulate diverse roles. Existing methods either use one shared parameterized module across all roles or assign a separate parameterized module to each role. However, the role-shared module may ignore distinct traits of each role, weakening personality learning, while the role-specific module may overlook shared traits across multiple roles, hindering commonality modeling. In this paper, we propose a novel HyCoRA: Hyper-Contrastive Role-Adaptive learning framework, which efficiently improves multi-character role-playing ability by balancing the learning of distinct and shared traits. Specifically, we propose a Hyper-Half Low-Rank Adaptation structure, where one half is a role-specific module generated by a lightweight hyper-network, and the other half is a trainable role-shared module. The role-specific module is devised to represent distinct persona signatures, while the role-shared module serves to capture common traits. Moreover, to better reflect distinct personalities across different roles, we design a hyper-contrastive learning mechanism to help the hyper-network distinguish their unique characteristics. Extensive experimental results on both English and Chinese available benchmarks demonstrate the superiority of our framework. Further GPT-4 evaluations and visual analyses also verify the capability of HyCoRA to capture role characteristics.

Lijun Sun, Yijun Yang, Qiqi Duan et al.

Multi-agent coordination studies the underlying mechanism enabling the trending spread of diverse multi-agent systems (MAS) and has received increasing attention, driven by the expansion of emerging applications and rapid AI advances. This survey outlines the current state of coordination research across applications through a unified understanding that answers four fundamental coordination questions: (1) what is coordination; (2) why coordination; (3) who to coordinate with; and (4) how to coordinate. Our purpose is to explore existing ideas and expertise in coordination and their connections across diverse applications, while identifying and highlighting emerging and promising research directions. First, general coordination problems that are essential to varied applications are identified and analyzed. Second, a number of MAS applications are surveyed, ranging from widely studied domains, e.g., search and rescue, warehouse automation and logistics, and transportation systems, to emerging fields including humanoid and anthropomorphic robots, satellite systems, and large language models (LLMs). Finally, open challenges about the scalability, heterogeneity, and learning mechanisms of MAS are analyzed and discussed. In particular, we identify the hybridization of hierarchical and decentralized coordination, human-MAS coordination, and LLM-based MAS as promising future directions.

Yang Shen, Zhenyi Yi, Ziyi Zhao et al.

As AI agents evolve, the community is rapidly shifting from single Large Language Models (LLMs) to Multi-Agent Systems (MAS) to overcome cognitive bottlenecks in automated research. However, the optimal multi-agent coordination framework for these autonomous agents remains largely unexplored. In this paper, we present a systematic empirical study investigating the comparative efficacy of distinct multi-agent structures for automated machine learning optimization. Utilizing a rigorously controlled, execution-based testbed equipped with Git worktree isolation and explicit global memory, we benchmark a single-agent baseline against two multi-agent paradigms: a subagent architecture (parallel exploration with post-hoc consolidation) and an agent team architecture (experts with pre-execution handoffs). By evaluating these systems under strictly fixed computational time budgets, our findings reveal a fundamental trade-off between operational stability and theoretical deliberation. The subagent mode functions as a highly resilient, high-throughput search engine optimal for broad, shallow optimizations under strict time constraints. Conversely, the agent team topology exhibits higher operational fragility due to multi-author code generation but achieves the deep theoretical alignment necessary for complex architectural refactoring given extended compute budgets. These empirical insights provide actionable guidelines for designing future autoresearch systems, advocating for dynamically routed architectures that adapt their collaborative structures to real-time task complexity.

Jian Jin, Yang Shen, Zhenyong Fu et al.

Customized generation aims to incorporate a novel concept into a pre-trained text-to-image model, enabling new generations of the concept in novel contexts guided by textual prompts. However, customized generation suffers from an inherent trade-off between concept fidelity and editability, i.e., between precisely modeling the concept and faithfully adhering to the prompts. Previous methods reluctantly seek a compromise and struggle to achieve both high concept fidelity and ideal prompt alignment simultaneously. In this paper, we propose a Divide, Conquer, then Integrate (DCI) framework, which performs a surgical adjustment in the early stage of denoising to liberate the fine-tuned model from the fidelity-editability trade-off at inference. The two conflicting components in the trade-off are decoupled and individually conquered by two collaborative branches, which are then selectively integrated to preserve high concept fidelity while achieving faithful prompt adherence. To obtain a better fine-tuned model, we introduce an Image-specific Context Optimization} (ICO) strategy for model customization. ICO replaces manual prompt templates with learnable image-specific contexts, providing an adaptive and precise fine-tuning direction to promote the overall performance. Extensive experiments demonstrate the effectiveness of our method in reconciling the fidelity-editability trade-off.

Yuning You, Ruida Zhou, Yang Shen

Accurate modeling of system dynamics holds intriguing potential in broad scientific fields including cytodynamics and fluid mechanics. This task often presents significant challenges when (i) observations are limited to cross-sectional samples (where individual trajectories are inaccessible for learning), and moreover, (ii) the behaviors of individual particles are heterogeneous (especially in biological systems due to biodiversity). To address them, we introduce a novel framework dubbed correlational Lagrangian Schrödinger bridge (CLSB), aiming to seek for the evolution "bridging" among cross-sectional observations, while regularized for the minimal population "cost". In contrast to prior methods relying on \textit{individual}-level regularizers for all particles \textit{homogeneously} (e.g. restraining individual motions), CLSB operates at the population level admitting the heterogeneity nature, resulting in a more generalizable modeling in practice. To this end, our contributions include (1) a new class of population regularizers capturing the temporal variations in multivariate relations, with the tractable formulation derived, (2) three domain-informed instantiations based on genetic co-expression stability, and (3) an integration of population regularizers into data-driven generative models as constrained optimization, and a numerical solution, with further extension to conditional generative models. Empirically, we demonstrate the superiority of CLSB in single-cell sequencing data analyses such as simulating cell development over time and predicting cellular responses to drugs of varied doses.

Zhanjiang Yang, Yang Shen, Yueming Li et al.

Multi-agent path finding (MAPF) is the problem of planning conflict-free paths from the designated start locations to goal positions for multiple agents. It underlies a variety of real-world tasks, including multi-robot coordination, robot-assisted logistics, and social navigation. Recent decentralized learnable solvers have shown great promise for large-scale MAPF, especially when leveraging foundation models and large datasets. However, these agents are reactive policy models and exhibit limited modeling of environmental temporal dynamics and inter-agent dependencies, resulting in performance degradation in complex, long-term planning scenarios. To address these limitations, we propose MAPF-World, an autoregressive action world model for MAPF that unifies situation understanding and action generation, guiding decisions beyond immediate local observations. It improves situational awareness by explicitly modeling environmental dynamics, including spatial features and temporal dependencies, through future state and actions prediction. By incorporating these predicted futures, MAPF-World enables more informed, coordinated, and far-sighted decision-making, especially in complex multi-agent settings. Furthermore, we augment MAPF benchmarks by introducing an automatic map generator grounded in real-world scenarios, capturing practical map layouts for training and evaluating MAPF solvers. Extensive experiments demonstrate that MAPF-World outperforms state-of-the-art learnable solvers, showcasing superior zero-shot generalization to out-of-distribution cases. Notably, MAPF-World is trained with a 96.5% smaller model size and 92% reduced data.

Qiang Zhang, Ruida Zhou, Yang Shen et al.

This paper considers the problem of offline optimization, where the objective function is unknown except for a collection of ``offline" data examples. While recent years have seen a flurry of work on applying various machine learning techniques to the offline optimization problem, the majority of these work focused on learning a surrogate of the unknown objective function and then applying existing optimization algorithms. While the idea of modeling the unknown objective function is intuitive and appealing, from the learning point of view it also makes it very difficult to tune the objective of the learner according to the objective of optimization. Instead of learning and then optimizing the unknown objective function, in this paper we take on a less intuitive but more direct view that optimization can be thought of as a process of sampling from a generative model. To learn an effective generative model from the offline data examples, we consider the standard technique of ``re-weighting", and our main technical contribution is a probably approximately correct (PAC) lower bound on the natural optimization objective, which allows us to jointly learn a weight function and a score-based generative model. The robustly competitive performance of the proposed approach is demonstrated via empirical studies using the standard offline optimization benchmarks.

Yang Shen, Xiu-Shen Wei, Yifan Sun et al.

Computer Vision (CV) has yet to fully achieve the zero-shot task generalization observed in Natural Language Processing (NLP), despite following many of the milestones established in NLP, such as large transformer models, extensive pre-training, and the auto-regression paradigm, among others. In this paper, we explore the idea that CV adopts discrete and terminological task definitions (\eg, ``image segmentation''), which may be a key barrier to zero-shot task generalization. Our hypothesis is that without truly understanding previously-seen tasks--due to these terminological definitions--deep models struggle to generalize to novel tasks. To verify this, we introduce Explanatory Instructions, which provide an intuitive way to define CV task objectives through detailed linguistic transformations from input images to outputs. We create a large-scale dataset comprising 12 million ``image input $\to$ explanatory instruction $\to$ output'' triplets, and train an auto-regressive-based vision-language model (AR-based VLM) that takes both images and explanatory instructions as input. By learning to follow these instructions, the AR-based VLM achieves instruction-level zero-shot capabilities for previously-seen tasks and demonstrates strong zero-shot generalization for unseen CV tasks. Code and dataset will be openly available on our GitHub repository.

Yang Shen, Sanjoy Dasgupta, Saket Navlakha

Continual learning in computational systems is challenging due to catastrophic forgetting. We discovered a two layer neural circuit in the fruit fly olfactory system that addresses this challenge by uniquely combining sparse coding and associative learning. In the first layer, odors are encoded using sparse, high dimensional representations, which reduces memory interference by activating non overlapping populations of neurons for different odors. In the second layer, only the synapses between odor activated neurons and the output neuron associated with the odor are modified during learning; the rest of the weights are frozen to prevent unrelated memories from being overwritten. We show empirically and analytically that this simple and lightweight algorithm significantly boosts continual learning performance. The fly associative learning algorithm is strikingly similar to the classic perceptron learning algorithm, albeit two modifications, which we show are critical for reducing catastrophic forgetting. Overall, fruit flies evolved an efficient lifelong learning algorithm, and circuit mechanisms from neuroscience can be translated to improve machine computation.

Yuning You, Yang Shen

Compound-protein pairs dominate FDA-approved drug-target pairs and the prediction of compound-protein affinity and contact (CPAC) could help accelerate drug discovery. In this study we consider proteins as multi-modal data including 1D amino-acid sequences and (sequence-predicted) 2D residue-pair contact maps. We empirically evaluate the embeddings of the two single modalities in their accuracy and generalizability of CPAC prediction (i.e. structure-free interpretable compound-protein affinity prediction). And we rationalize their performances in both challenges of embedding individual modalities and learning generalizable embedding-label relationship. We further propose two models involving cross-modality protein embedding and establish that the one with cross interaction (thus capturing correlations among modalities) outperforms SOTAs and our single modality models in affinity, contact, and binding-site predictions for proteins never seen in the training set.

Mostafa Karimi, Arman Hasanzadeh, Yang shen

Combination therapy has shown to improve therapeutic efficacy while reducing side effects. Importantly, it has become an indispensable strategy to overcome resistance in antibiotics, anti-microbials, and anti-cancer drugs. Facing enormous chemical space and unclear design principles for small-molecule combinations, the computational drug-combination design has not seen generative models to meet its potential to accelerate resistance-overcoming drug combination discovery. We have developed the first deep generative model for drug combination design, by jointly embedding graph-structured domain knowledge and iteratively training a reinforcement learning-based chemical graph-set designer. First, we have developed Hierarchical Variational Graph Auto-Encoders (HVGAE) trained end-to-end to jointly embed gene-gene, gene-disease, and disease-disease networks. Novel attentional pooling is introduced here for learning disease-representations from associated genes' representations. Second, targeting diseases in learned representations, we have recast the drug-combination design problem as graph-set generation and developed a deep learning-based model with novel rewards. Specifically, besides chemical validity rewards, we have introduced a novel generative adversarial award, being generalized sliced Wasserstein, for chemically diverse molecules with distributions similar to known drugs. We have also designed a network principle-based reward for drug combinations. Numerical results indicate that, compared to graph embedding methods, HVGAE learns more informative and generalizable disease representations. Case studies on four diseases show that network-principled drug combinations tend to have low toxicity. The generated drug combinations collectively cover the disease module similar to FDA-approved drug combinations and could potentially suggest novel systems-pharmacology strategies.

Mostafa Karimi, Di Wu, Zhangyang Wang et al.

Predicting compound-protein affinity is critical for accelerating drug discovery. Recent progress made by machine learning focuses on accuracy but leaves much to be desired for interpretability. Through molecular contacts underlying affinities, our large-scale interpretability assessment finds commonly-used attention mechanisms inadequate. We thus formulate a hierarchical multi-objective learning problem whose predicted contacts form the basis for predicted affinities. We further design a physics-inspired deep relational network, DeepRelations, with intrinsically explainable architecture. Specifically, various atomic-level contacts or "relations" lead to molecular-level affinity prediction. And the embedded attentions are regularized with predicted structural contexts and supervised with partially available training contacts. DeepRelations shows superior interpretability to the state-of-the-art: without compromising affinity prediction, it boosts the AUPRC of contact prediction 9.5, 16.9, 19.3 and 5.7-fold for the test, compound-unique, protein-unique, and both-unique sets, respectively. Our study represents the first dedicated model development and systematic model assessment for interpretable machine learning of compound-protein affinity.

Yue Cao, Yang Shen

Structural information about protein-protein interactions, often missing at the interactome scale, is important for mechanistic understanding of cells and rational discovery of therapeutics. Protein docking provides a computational alternative to predict such information. However, ranking near-native docked models high among a large number of candidates, often known as the scoring problem, remains a critical challenge. Moreover, estimating model quality, also known as the quality assessment problem, is rarely addressed in protein docking. In this study the two challenging problems in protein docking are regarded as relative and absolute scoring, respectively, and addressed in one physics-inspired deep learning framework. We represent proteins' and encounter complexes' 3D structures as intra- and inter-molecular residue contact graphs with atom-resolution node and edge features. And we propose a novel graph convolutional kernel that pool interacting nodes' features through edge features so that generalized interaction energies can be learned directly from graph data. The resulting energy-based graph convolutional networks (EGCN) with multi-head attention are trained to predict intra- and inter-molecular energies, binding affinities, and quality measures (interface RMSD) for encounter complexes. Compared to a state-of-the-art scoring function for model ranking, EGCN has significantly improved ranking for a CAPRI test set involving homology docking; and is comparable for Score_set, a CAPRI benchmark set generated by diverse community-wide docking protocols not known to training data. For Score_set quality assessment, EGCN shows about 27% improvement to our previous efforts. Directly learning from 3D structure data in graph representation, EGCN represents the first successful development of graph convolutional networks for protein docking.

Yue Cao, Tianlong Chen, Zhangyang Wang et al.

Learning to optimize has emerged as a powerful framework for various optimization and machine learning tasks. Current such "meta-optimizers" often learn in the space of continuous optimization algorithms that are point-based and uncertainty-unaware. To overcome the limitations, we propose a meta-optimizer that learns in the algorithmic space of both point-based and population-based optimization algorithms. The meta-optimizer targets at a meta-loss function consisting of both cumulative regret and entropy. Specifically, we learn and interpret the update formula through a population of LSTMs embedded with sample- and feature-level attentions. Meanwhile, we estimate the posterior directly over the global optimum and use an uncertainty measure to help guide the learning process. Empirical results over non-convex test functions and the protein-docking application demonstrate that this new meta-optimizer outperforms existing competitors.

Weiyao Lin, Yang Shen, Junchi Yan et al.

This paper addresses the problem of handling spatial misalignments due to camera-view changes or human-pose variations in person re-identification. We first introduce a boosting-based approach to learn a correspondence structure which indicates the patch-wise matching probabilities between images from a target camera pair. The learned correspondence structure can not only capture the spatial correspondence pattern between cameras but also handle the viewpoint or human-pose variation in individual images. We further introduce a global constraint-based matching process. It integrates a global matching constraint over the learned correspondence structure to exclude cross-view misalignments during the image patch matching process, hence achieving a more reliable matching score between images. Finally, we also extend our approach by introducing a multi-structure scheme, which learns a set of local correspondence structures to capture the spatial correspondence sub-patterns between a camera pair, so as to handle the spatial misalignments between individual images in a more precise way. Experimental results on various datasets demonstrate the effectiveness of our approach.

Yang Shen, Weiyao Lin, Junchi Yan et al.

This paper addresses the problem of handling spatial misalignments due to camera-view changes or human-pose variations in person re-identification. We first introduce a boosting-based approach to learn a correspondence structure which indicates the patch-wise matching probabilities between images from a target camera pair. The learned correspondence structure can not only capture the spatial correspondence pattern between cameras but also handle the viewpoint or human-pose variation in individual images. We further introduce a global-based matching process. It integrates a global matching constraint over the learned correspondence structure to exclude cross-view misalignments during the image patch matching process, hence achieving a more reliable matching score between images. Experimental results on various datasets demonstrate the effectiveness of our approach.