Guangyong Chen

Hanqun Cao, Cheng Tan, Zhangyang Gao et al.

Deep generative models have unlocked another profound realm of human creativity. By capturing and generalizing patterns within data, we have entered the epoch of all-encompassing Artificial Intelligence for General Creativity (AIGC). Notably, diffusion models, recognized as one of the paramount generative models, materialize human ideation into tangible instances across diverse domains, encompassing imagery, text, speech, biology, and healthcare. To provide advanced and comprehensive insights into diffusion, this survey comprehensively elucidates its developmental trajectory and future directions from three distinct angles: the fundamental formulation of diffusion, algorithmic enhancements, and the manifold applications of diffusion. Each layer is meticulously explored to offer a profound comprehension of its evolution. Structured and summarized approaches are presented in https://github.com/chq1155/A-Survey-on-Generative-Diffusion-Model.

Bowen Wang, Guibao Shen, Dong Li et al. · pku

Precise congestion prediction from a placement solution plays a crucial role in circuit placement. This work proposes the lattice hypergraph (LH-graph), a novel graph formulation for circuits, which preserves netlist data during the whole learning process, and enables the congestion information propagated geometrically and topologically. Based on the formulation, we further developed a heterogeneous graph neural network architecture LHNN, jointing the routing demand regression to support the congestion spot classification. LHNN constantly achieves more than 35% improvements compared with U-nets and Pix2Pix on the F1 score. We expect our work shall highlight essential procedures using machine learning for congestion prediction.

Donghao Zhou, Jialin Li, Jinpeng Li et al.

Large-scale well-annotated datasets are of great importance for training an effective object detector. However, obtaining accurate bounding box annotations is laborious and demanding. Unfortunately, the resultant noisy bounding boxes could cause corrupt supervision signals and thus diminish detection performance. Motivated by the observation that the real ground-truth is usually situated in the aggregation region of the proposals assigned to a noisy ground-truth, we propose DIStribution-aware CalibratiOn (DISCO) to model the spatial distribution of proposals for calibrating supervision signals. In DISCO, spatial distribution modeling is performed to statistically extract the potential locations of objects. Based on the modeled distribution, three distribution-aware techniques, i.e., distribution-aware proposal augmentation (DA-Aug), distribution-aware box refinement (DA-Ref), and distribution-aware confidence estimation (DA-Est), are developed to improve classification, localization, and interpretability, respectively. Extensive experiments on large-scale noisy image datasets (i.e., Pascal VOC and MS-COCO) demonstrate that DISCO can achieve state-of-the-art detection performance, especially at high noise levels. Code is available at https://github.com/Correr-Zhou/DISCO.

Danruo Deng, Guangyong Chen, Yang Yu et al.

Uncertainty estimation is a key factor that makes deep learning reliable in practical applications. Recently proposed evidential neural networks explicitly account for different uncertainties by treating the network's outputs as evidence to parameterize the Dirichlet distribution, and achieve impressive performance in uncertainty estimation. However, for high data uncertainty samples but annotated with the one-hot label, the evidence-learning process for those mislabeled classes is over-penalized and remains hindered. To address this problem, we propose a novel method, Fisher Information-based Evidential Deep Learning ($\mathcal{I}$-EDL). In particular, we introduce Fisher Information Matrix (FIM) to measure the informativeness of evidence carried by each sample, according to which we can dynamically reweight the objective loss terms to make the network more focused on the representation learning of uncertain classes. The generalization ability of our network is further improved by optimizing the PAC-Bayesian bound. As demonstrated empirically, our proposed method consistently outperforms traditional EDL-related algorithms in multiple uncertainty estimation tasks, especially in the more challenging few-shot classification settings.

Hao Chen, Jiaze Wang, Kun Shao et al.

Trajectory prediction has been a crucial task in building a reliable autonomous driving system by anticipating possible dangers. One key issue is to generate consistent trajectory predictions without colliding. To overcome the challenge, we propose an efficient masked autoencoder for trajectory prediction (Traj-MAE) that better represents the complicated behaviors of agents in the driving environment. Specifically, our Traj-MAE employs diverse masking strategies to pre-train the trajectory encoder and map encoder, allowing for the capture of social and temporal information among agents while leveraging the effect of environment from multiple granularities. To address the catastrophic forgetting problem that arises when pre-training the network with multiple masking strategies, we introduce a continual pre-training framework, which can help Traj-MAE learn valuable and diverse information from various strategies efficiently. Our experimental results in both multi-agent and single-agent settings demonstrate that Traj-MAE achieves competitive results with state-of-the-art methods and significantly outperforms our baseline model.

Zhongwei Wan, Yichun Yin, Wei Zhang et al. · tsinghua

Recently, domain-specific PLMs have been proposed to boost the task performance of specific domains (e.g., biomedical and computer science) by continuing to pre-train general PLMs with domain-specific corpora. However, this Domain-Adaptive Pre-Training (DAPT; Gururangan et al. (2020)) tends to forget the previous general knowledge acquired by general PLMs, which leads to a catastrophic forgetting phenomenon and sub-optimal performance. To alleviate this problem, we propose a new framework of General Memory Augmented Pre-trained Language Model (G-MAP), which augments the domain-specific PLM by a memory representation built from the frozen general PLM without losing any general knowledge. Specifically, we propose a new memory-augmented layer, and based on it, different augmented strategies are explored to build the memory representation and then adaptively fuse it into the domain-specific PLM. We demonstrate the effectiveness of G-MAP on various domains (biomedical and computer science publications, news, and reviews) and different kinds (text classification, QA, NER) of tasks, and the extensive results show that the proposed G-MAP can achieve SOTA results on all tasks.

Yong Cao, Wei Li, Xianzhi Li et al.

Sign language recognition and translation first uses a recognition module to generate glosses from sign language videos and then employs a translation module to translate glosses into spoken sentences. Most existing works focus on the recognition step, while paying less attention to sign language translation. In this work, we propose a task-aware instruction network, namely TIN-SLT, for sign language translation, by introducing the instruction module and the learning-based feature fuse strategy into a Transformer network. In this way, the pre-trained model's language ability can be well explored and utilized to further boost the translation performance. Moreover, by exploring the representation space of sign language glosses and target spoken language, we propose a multi-level data augmentation scheme to adjust the data distribution of the training set. We conduct extensive experiments on two challenging benchmark datasets, PHOENIX-2014-T and ASLG-PC12, on which our method outperforms former best solutions by 1.65 and 1.42 in terms of BLEU-4. Our code is published at https://github.com/yongcaoplus/TIN-SLT.

Luozhou Wang, Guibao Shen, Wenhang Ge et al.

Text-to-image diffusion models have advanced towards more controllable generation via supporting various additional conditions (e.g.,depth map, bounding box) beyond text. However, these models are learned based on the premise of perfect alignment between the text and extra conditions. If this alignment is not satisfied, the final output could be either dominated by one condition, or ambiguity may arise, failing to meet user expectations. To address this issue, we present a training free approach called Text-Anchored Score Composition (TASC) to further improve the controllability of existing models when provided with partially aligned conditions. The TASC firstly separates conditions based on pair relationships, computing the result individually for each pair. This ensures that each pair no longer has conflicting conditions. Then we propose an attention realignment operation to realign these independently calculated results via a cross-attention mechanism to avoid new conflicts when combining them back. Both qualitative and quantitative results demonstrate the effectiveness of our approach in handling unaligned conditions, which performs favorably against recent methods and more importantly adds flexibility to the controllable image generation process. Our code will be available at: https://github.com/EnVision-Research/Decompose-and-Realign.

Yi Wang, Jiaze Wang, Jinpeng Li et al.

Data augmentation is an effective regularization strategy for mitigating overfitting in deep neural networks, and it plays a crucial role in 3D vision tasks, where the point cloud data is relatively limited. While mixing-based augmentation has shown promise for point clouds, previous methods mix point clouds either on block level or point level, which has constrained their ability to strike a balance between generating diverse training samples and preserving the local characteristics of point clouds. Additionally, the varying importance of each part of the point clouds has not been fully considered, cause not all parts contribute equally to the classification task, and some parts may contain unimportant or redundant information. To overcome these challenges, we propose PointPatchMix, a novel approach that mixes point clouds at the patch level and integrates a patch scoring module to generate content-based targets for mixed point clouds. Our approach preserves local features at the patch level, while the patch scoring module assigns targets based on the content-based significance score from a pre-trained teacher model. We evaluate PointPatchMix on two benchmark datasets, ModelNet40 and ScanObjectNN, and demonstrate significant improvements over various baselines in both synthetic and real-world datasets, as well as few-shot settings. With Point-MAE as our baseline, our model surpasses previous methods by a significant margin, achieving 86.3% accuracy on ScanObjectNN and 94.1% accuracy on ModelNet40. Furthermore, our approach shows strong generalization across multiple architectures and enhances the robustness of the baseline model.

Bowen Wang, Chen Liang, Jiaze Wang et al.

Attaining the equilibrium state of a catalyst-adsorbate system is key to fundamentally assessing its effective properties, such as adsorption energy. Machine learning methods with finer supervision strategies have been applied to boost and guide the relaxation process of an atomic system and better predict its properties at the equilibrium state. In this paper, we present a novel graph neural network (GNN) supervision and prediction strategy DR-Label. The method enhances the supervision signal, reduces the multiplicity of solutions in edge representation, and encourages the model to provide node predictions that are graph structural variation robust. DR-Label first Deconstructs finer-grained equilibrium state information to the model by projecting the node-level supervision signal to each edge. Reversely, the model Reconstructs a more robust equilibrium state prediction by transforming edge-level predictions to node-level with a sphere-fitting algorithm. The DR-Label strategy was applied to three radically distinct models, each of which displayed consistent performance enhancements. Based on the DR-Label strategy, we further proposed DRFormer, which achieved a new state-of-the-art performance on the Open Catalyst 2020 (OC20) dataset and the Cu-based single-atom-alloyed CO adsorption (SAA) dataset. We expect that our work will highlight crucial steps for the development of a more accurate model in equilibrium state property prediction of a catalysis system.

Donghao Zhou, Chunbin Gu, Junde Xu et al.

In biological research, fluorescence staining is a key technique to reveal the locations and morphology of subcellular structures. However, it is slow, expensive, and harmful to cells. In this paper, we model it as a deep learning task termed subcellular structure prediction (SSP), aiming to predict the 3D fluorescent images of multiple subcellular structures from a 3D transmitted-light image. Unfortunately, due to the limitations of current biotechnology, each image is partially labeled in SSP. Besides, naturally, subcellular structures vary considerably in size, which causes the multi-scale issue of SSP. To overcome these challenges, we propose Re-parameterizing Mixture-of-Diverse-Experts (RepMode), a network that dynamically organizes its parameters with task-aware priors to handle specified single-label prediction tasks. In RepMode, the Mixture-of-Diverse-Experts (MoDE) block is designed to learn the generalized parameters for all tasks, and gating re-parameterization (GatRep) is performed to generate the specialized parameters for each task, by which RepMode can maintain a compact practical topology exactly like a plain network, and meanwhile achieves a powerful theoretical topology. Comprehensive experiments show that RepMode can achieve state-of-the-art overall performance in SSP.

Yang Yu, Zixu Zhao, Yueming Jin et al.

Surgical scene segmentation is fundamentally crucial for prompting cognitive assistance in robotic surgery. However, pixel-wise annotating surgical video in a frame-by-frame manner is expensive and time consuming. To greatly reduce the labeling burden, in this work, we study semi-supervised scene segmentation from robotic surgical video, which is practically essential yet rarely explored before. We consider a clinically suitable annotation situation under the equidistant sampling. We then propose PGV-CL, a novel pseudo-label guided cross-video contrast learning method to boost scene segmentation. It effectively leverages unlabeled data for a trusty and global model regularization that produces more discriminative feature representation. Concretely, for trusty representation learning, we propose to incorporate pseudo labels to instruct the pair selection, obtaining more reliable representation pairs for pixel contrast. Moreover, we expand the representation learning space from previous image-level to cross-video, which can capture the global semantics to benefit the learning process. We extensively evaluate our method on a public robotic surgery dataset EndoVis18 and a public cataract dataset CaDIS. Experimental results demonstrate the effectiveness of our method, consistently outperforming the state-of-the-art semi-supervised methods under different labeling ratios, and even surpassing fully supervised training on EndoVis18 with 10.1% labeling.

Yang Yu, Danruo Deng, Furui Liu et al.

Semi-supervised learning (SSL) methods assume that labeled data, unlabeled data and test data are from the same distribution. Open-set semi-supervised learning (Open-set SSL) considers a more practical scenario, where unlabeled data and test data contain new categories (outliers) not observed in labeled data (inliers). Most previous works focused on outlier detection via binary classifiers, which suffer from insufficient scalability and inability to distinguish different types of uncertainty. In this paper, we propose a novel framework, Adaptive Negative Evidential Deep Learning (ANEDL) to tackle these limitations. Concretely, we first introduce evidential deep learning (EDL) as an outlier detector to quantify different types of uncertainty, and design different uncertainty metrics for self-training and inference. Furthermore, we propose a novel adaptive negative optimization strategy, making EDL more tailored to the unlabeled dataset containing both inliers and outliers. As demonstrated empirically, our proposed method outperforms existing state-of-the-art methods across four datasets.

Junde Xu, Zikai Lin, Donghao Zhou et al.

Masked Image Modeling (MIM) has achieved impressive representative performance with the aim of reconstructing randomly masked images. Despite the empirical success, most previous works have neglected the important fact that it is unreasonable to force the model to reconstruct something beyond recovery, such as those masked objects. In this work, we show that uniformly random masking widely used in previous works unavoidably loses some key objects and changes original semantic information, resulting in a misalignment problem and hurting the representative learning eventually. To address this issue, we augment MIM with a new masking strategy namely the DPPMask by substituting the random process with Determinantal Point Process (DPPs) to reduce the semantic change of the image after masking. Our method is simple yet effective and requires no extra learnable parameters when implemented within various frameworks. In particular, we evaluate our method on two representative MIM frameworks, MAE and iBOT. We show that DPPMask surpassed random sampling under both lower and higher masking ratios, indicating that DPPMask makes the reconstruction task more reasonable. We further test our method on the background challenge and multi-class classification tasks, showing that our method is more robust at various tasks.

Chen Liang, Bowen Wang, Shaogang Hao et al.

Graph neural networks (GNNs) have drawn more and more attention from material scientists and demonstrated a high capacity to establish connections between the structure and properties. However, with only unrelaxed structures provided as input, few GNN models can predict the thermodynamic properties of relaxed configurations with an acceptable level of error. In this work, we develop a multi-task (MT) architecture based on DimeNet++ and mixture density networks to improve the performance of such task. Taking CO adsorption on Cu-based single-atom alloy catalysts as an illustration, we show that our method can reliably estimate CO adsorption energy with a mean absolute error of 0.087 eV from the initial CO adsorption structures without costly first-principles calculations. Further, compared to other state-of-the-art GNN methods, our model exhibits improved generalization ability when predicting catalytic performance of out-of-domain configurations, built with either unseen substrate surfaces or doping species. We show that the proposed MT GNN strategy can facilitate catalyst discovery.

Kexin Chen, Guangyong Chen, Junyou Li et al.

Artificial intelligence has deeply revolutionized the field of medicinal chemistry with many impressive applications, but the success of these applications requires a massive amount of training samples with high-quality annotations, which seriously limits the wide usage of data-driven methods. In this paper, we focus on the reaction yield prediction problem, which assists chemists in selecting high-yield reactions in a new chemical space only with a few experimental trials. To attack this challenge, we first put forth MetaRF, an attention-based differentiable random forest model specially designed for the few-shot yield prediction, where the attention weight of a random forest is automatically optimized by the meta-learning framework and can be quickly adapted to predict the performance of new reagents while given a few additional samples. To improve the few-shot learning performance, we further introduce a dimension-reduction based sampling method to determine valuable samples to be experimentally tested and then learned. Our methodology is evaluated on three different datasets and acquires satisfactory performance on few-shot prediction. In high-throughput experimentation (HTE) datasets, the average yield of our methodology's top 10 high-yield reactions is relatively close to the results of ideal yield selection.

Kexin Chen, Jiamin Lu, Junyou Li et al.

Recent AI research plots a promising future of automatic chemical reactions within the chemistry society. This study proposes Chemist-X, a comprehensive AI agent that automates the reaction condition optimization (RCO) task in chemical synthesis with retrieval-augmented generation (RAG) technology and AI-controlled wet-lab experiment executions. To begin with, as an emulation on how chemical experts solve the RCO task, Chemist-X utilizes a novel RAG scheme to interrogate available molecular and literature databases to narrow the searching space for later processing. The agent then leverages a computer-aided design (CAD) tool we have developed through a large language model (LLM) supervised programming interface. With updated chemical knowledge obtained via RAG, as well as the ability in using CAD tools, our agent significantly outperforms conventional RCO AIs confined to the fixed knowledge within its training data. Finally, Chemist-X interacts with the physical world through an automated robotic system, which can validate the suggested chemical reaction condition without human interventions. The control of the robotic system was achieved with a novel algorithm we have developed for the equipment, which relies on LLMs for reliable script generation. Results of our automatic wet-lab experiments, achieved by fully LLM-supervised end-to-end operation with no human in the lope, prove Chemist-X's ability in self-driving laboratories.

Chunbin Gu, Mutian He, Hanqun Cao et al.

In the realm of drug discovery, DNA-encoded library (DEL) screening technology has emerged as an efficient method for identifying high-affinity compounds. However, DEL screening faces a significant challenge: noise arising from nonspecific interactions within complex biological systems. Neural networks trained on DEL libraries have been employed to extract compound features, aiming to denoise the data and uncover potential binders to the desired therapeutic target. Nevertheless, the inherent structure of DEL, constrained by the limited diversity of building blocks, impacts the performance of compound encoders. Moreover, existing methods only capture compound features at a single level, further limiting the effectiveness of the denoising strategy. To mitigate these issues, we propose a Multimodal Pretraining DEL-Fusion model (MPDF) that enhances encoder capabilities through pretraining and integrates compound features across various scales. We develop pretraining tasks applying contrastive objectives between different compound representations and their text descriptions, enhancing the compound encoders' ability to acquire generic features. Furthermore, we propose a novel DEL-fusion framework that amalgamates compound information at the atomic, submolecular, and molecular levels, as captured by various compound encoders. The synergy of these innovations equips MPDF with enriched, multi-scale features, enabling comprehensive downstream denoising. Evaluated on three DEL datasets, MPDF demonstrates superior performance in data processing and analysis for validation tasks. Notably, MPDF offers novel insights into identifying high-affinity molecules, paving the way for improved DEL utility in drug discovery.

Kexin Chen, Yuyang Du, Junyou Li et al.

The development of AI-assisted chemical synthesis tools requires comprehensive datasets covering diverse reaction types, yet current high-throughput experimental (HTE) approaches are expensive and limited in scope. Chemical literature represents a vast, underexplored data source containing thousands of reactions published annually. However, extracting reaction information from literature faces significant challenges including varied writing styles, complex coreference relationships, and multimodal information presentation. This paper proposes ChemMiner, a novel end-to-end framework leveraging multiple agents powered by large language models (LLMs) to extract high-fidelity chemical data from literature. ChemMiner incorporates three specialized agents: a text analysis agent for coreference mapping, a multimodal agent for non-textual information extraction, and a synthesis analysis agent for data generation. Furthermore, we developed a comprehensive benchmark with expert-annotated chemical literature to evaluate both extraction efficiency and precision. Experimental results demonstrate reaction identification rates comparable to human chemists while significantly reducing processing time, with high accuracy, recall, and F1 scores. Our open-sourced benchmark facilitates future research in chemical literature data mining.

Yaodong Yang, Yang Wang, Jinpeng Li et al.

Protein evolution through amino acid sequence mutations is a cornerstone of life sciences. While current in-silicon directed evolution algorithms largely focus on designing heuristic search strategies, they overlook how to integrate the transformative protein language models, which encode rich evolutionary patterns, with reinforcement learning to learn to directly evolve proteins. To bridge this gap, we propose AlphaDE, a novel framework to optimize protein sequences by harnessing the innovative paradigms of large language models such as fine-tuning and test-time inference. First, AlphaDE fine-tunes pretrained protein language models using masked language modeling on homologous protein sequences to activate the evolutionary plausibility for the interested protein class. Second, AlphaDE introduces test-time inference based on Monte Carlo tree search, which effectively evolves proteins with evolutionary guidance from the fine-tuned protein language model. Extensive benchmark experiments show that AlphaDE remarkably outperforms previous state-of-the-art methods even with few-shot fine-tuning. A further case study demonstrates that AlphaDE supports condensing the protein sequence space of avGFP through computational evolution.

Donghao Zhou, Pengfei Chen, Qiong Wang et al.

Due to the difficulty of collecting exhaustive multi-label annotations, multi-label datasets often contain partial labels. We consider an extreme of this weakly supervised learning problem, called single positive multi-label learning (SPML), where each multi-label training image has only one positive label. Traditionally, all unannotated labels are assumed as negative labels in SPML, which introduces false negative labels and causes model training to be dominated by assumed negative labels. In this work, we choose to treat all unannotated labels from an alternative perspective, i.e. acknowledging they are unknown. Hence, we propose entropy-maximization (EM) loss to attain a special gradient regime for providing proper supervision signals. Moreover, we propose asymmetric pseudo-labeling (APL), which adopts asymmetric-tolerance strategies and a self-paced procedure, to cooperate with EM loss and then provide more precise supervision. Experiments show that our method significantly improves performance and achieves state-of-the-art results on all four benchmarks. Code is available at https://github.com/Correr-Zhou/SPML-AckTheUnknown.

Guibao Shen, Luozhou Wang, Jiantao Lin et al.

Recent advancements in text-to-image generation have been propelled by the development of diffusion models and multi-modality learning. However, since text is typically represented sequentially in these models, it often falls short in providing accurate contextualization and structural control. So the generated images do not consistently align with human expectations, especially in complex scenarios involving multiple objects and relationships. In this paper, we introduce the Scene Graph Adapter(SG-Adapter), leveraging the structured representation of scene graphs to rectify inaccuracies in the original text embeddings. The SG-Adapter's explicit and non-fully connected graph representation greatly improves the fully connected, transformer-based text representations. This enhancement is particularly notable in maintaining precise correspondence in scenarios involving multiple relationships. To address the challenges posed by low-quality annotated datasets like Visual Genome, we have manually curated a highly clean, multi-relational scene graph-image paired dataset MultiRels. Furthermore, we design three metrics derived from GPT-4V to effectively and thoroughly measure the correspondence between images and scene graphs. Both qualitative and quantitative results validate the efficacy of our approach in controlling the correspondence in multiple relationships.

Donghao Zhou, Jiancheng Huang, Jinbin Bai et al.

Text-to-image diffusion models can generate high-quality images but lack fine-grained control of visual concepts, limiting their creativity. Thus, we introduce component-controllable personalization, a new task that enables users to customize and reconfigure individual components within concepts. This task faces two challenges: semantic pollution, where undesired elements disrupt the target concept, and semantic imbalance, which causes disproportionate learning of the target concept and component. To address these, we design MagicTailor, a framework that uses Dynamic Masked Degradation to adaptively perturb unwanted visual semantics and Dual-Stream Balancing for more balanced learning of desired visual semantics. The experimental results show that MagicTailor achieves superior performance in this task and enables more personalized and creative image generation.

Hao Chen, Jiaze Wang, Ziyu Guo et al.

Sign language recognition (SLR) plays a vital role in facilitating communication for the hearing-impaired community. SLR is a weakly supervised task where entire videos are annotated with glosses, making it challenging to identify the corresponding gloss within a video segment. Recent studies indicate that the main bottleneck in SLR is the insufficient training caused by the limited availability of large-scale datasets. To address this challenge, we present SignVTCL, a multi-modal continuous sign language recognition framework enhanced by visual-textual contrastive learning, which leverages the full potential of multi-modal data and the generalization ability of language model. SignVTCL integrates multi-modal data (video, keypoints, and optical flow) simultaneously to train a unified visual backbone, thereby yielding more robust visual representations. Furthermore, SignVTCL contains a visual-textual alignment approach incorporating gloss-level and sentence-level alignment to ensure precise correspondence between visual features and glosses at the level of individual glosses and sentence. Experimental results conducted on three datasets, Phoenix-2014, Phoenix-2014T, and CSL-Daily, demonstrate that SignVTCL achieves state-of-the-art results compared with previous methods.

Hanqun Cao, Marcelo D. T. Torres, Jingjie Zhang et al.

Antimicrobial resistance (AMR) is projected to cause up to 10 million deaths annually by 2050, underscoring the urgent need for new antibiotics. Here we present ApexAmphion, a deep-learning framework for de novo design of antibiotics that couples a 6.4-billion-parameter protein language model with reinforcement learning. The model is first fine-tuned on curated peptide data to capture antimicrobial sequence regularities, then optimised with proximal policy optimization against a composite reward that combines predictions from a learned minimum inhibitory concentration (MIC) classifier with differentiable physicochemical objectives. In vitro evaluation of 100 designed peptides showed low MIC values (nanomolar range in some cases) for all candidates (100% hit rate). Moreover, 99 our of 100 compounds exhibited broad-spectrum antimicrobial activity against at least two clinically relevant bacteria. The lead molecules killed bacteria primarily by potently targeting the cytoplasmic membrane. By unifying generation, scoring and multi-objective optimization with deep reinforcement learning in a single pipeline, our approach rapidly produces diverse, potent candidates, offering a scalable route to peptide antibiotics and a platform for iterative steering toward potency and developability within hours.

Junde Xu, Zijun Gao, Xinyi Zhou et al.

The inverse folding problem, aiming to design amino acid sequences that fold into desired three-dimensional structures, is pivotal for various biotechnological applications. Here, we introduce a novel approach leveraging Direct Preference Optimization (DPO) to fine-tune an inverse folding model using feedback from a protein folding model. Given a target protein structure, we begin by sampling candidate sequences from the inverse-folding model, then predict the three-dimensional structure of each sequence with the folding model to generate pairwise structural-preference labels. These labels are used to fine-tune the inverse-folding model under the DPO objective. Our results on the CATH 4.2 test set demonstrate that DPO fine-tuning not only improves sequence recovery of baseline models but also leads to a significant improvement in average TM-Score from 0.77 to 0.81, indicating enhanced structure similarity. Furthermore, iterative application of our DPO-based method on challenging protein structures yields substantial gains, with an average TM-Score increase of 79.5\% with regard to the baseline model. This work establishes a promising direction for enhancing protein sequence design ability from structure feedback by effectively utilizing preference optimization.

Yaodong Yang, Guangyong Chen, Hongyao Tang et al.

Overestimation in single-agent reinforcement learning has been extensively studied. In contrast, overestimation in the multiagent setting has received comparatively little attention although it increases with the number of agents and leads to severe learning instability. Previous works concentrate on reducing overestimation in the estimation process of target Q-value. They ignore the follow-up optimization process of online Q-network, thus making it hard to fully address the complex multiagent overestimation problem. To solve this challenge, in this study, we first establish an iterative estimation-optimization analysis framework for multiagent value-mixing Q-learning. Our analysis reveals that multiagent overestimation not only comes from the computation of target Q-value but also accumulates in the online Q-network's optimization. Motivated by it, we propose the Dual Ensembled Multiagent Q-Learning with Hypernet Regularizer algorithm to tackle multiagent overestimation from two aspects. First, we extend the random ensemble technique into the estimation of target individual and global Q-values to derive a lower update target. Second, we propose a novel hypernet regularizer on hypernetwork weights and biases to constrain the optimization of online global Q-network to prevent overestimation accumulation. Extensive experiments in MPE and SMAC show that the proposed method successfully addresses overestimation across various tasks.

Yi Wang, Jiaze Wang, Ziyu Guo et al.

Recently Transformer-based models have advanced point cloud understanding by leveraging self-attention mechanisms, however, these methods often overlook latent information in less prominent regions, leading to increased sensitivity to perturbations and limited global comprehension. To solve this issue, we introduce PointACL, an attention-driven contrastive learning framework designed to address these limitations. Our method employs an attention-driven dynamic masking strategy that guides the model to focus on under-attended regions, enhancing the understanding of global structures within the point cloud. Then we combine the original pre-training loss with a contrastive learning loss, improving feature discrimination and generalization. Extensive experiments validate the effectiveness of PointACL, as it achieves state-of-the-art performance across a variety of 3D understanding tasks, including object classification, part segmentation, and few-shot learning. Specifically, when integrated with different Transformer backbones like Point-MAE and PointGPT, PointACL demonstrates improved performance on datasets such as ScanObjectNN, ModelNet40, and ShapeNetPart. This highlights its superior capability in capturing both global and local features, as well as its enhanced robustness against perturbations and incomplete data.

Xinyi Zhou, Xing Li, Yingzhao Lian et al.

We introduce SeaDAG, a semi-autoregressive diffusion model for conditional generation of Directed Acyclic Graphs (DAGs). Considering their inherent layer-wise structure, we simulate layer-wise autoregressive generation by designing different denoising speed for different layers. Unlike conventional autoregressive generation that lacks a global graph structure view, our method maintains a complete graph structure at each diffusion step, enabling operations such as property control that require the full graph structure. Leveraging this capability, we evaluate the DAG properties during training by employing a graph property decoder. We explicitly train the model to learn graph conditioning with a condition loss, which enhances the diffusion model's capacity to generate graphs that are both realistic and aligned with specified properties. We evaluate our method on two representative conditional DAG generation tasks: (1) circuit generation from truth tables, where precise DAG structures are crucial for realizing circuit functionality, and (2) molecule generation based on quantum properties. Our approach demonstrates promising results, generating high-quality and realistic DAGs that closely align with given conditions.

Junde Xu, Yapin Shi, Lijun Lang et al.

Multimodal protein language models deliver strong performance on mutation-effect prediction, but training such models from scratch demands substantial computational resources. In this paper, we propose a fine-tuning framework called InstructPLM-mu and try to answer a question: \textit{Can multimodal fine-tuning of a pretrained, sequence-only protein language model match the performance of models trained end-to-end? } Surprisingly, our experiments show that fine-tuning ESM2 with structural inputs can reach performance comparable to ESM3. To understand how this is achieved, we systematically compare three different feature-fusion designs and fine-tuning recipes. Our results reveal that both the fusion method and the tuning strategy strongly affect final accuracy, indicating that the fine-tuning process is not trivial. We hope this work offers practical guidance for injecting structure into pretrained protein language models and motivates further research on better fusion mechanisms and fine-tuning protocols.

Zheng Cheng, Wenri Wang, Guangyong Chen et al.

Underwater image enhancement (UIE) techniques aim to improve visual quality of images captured in aquatic environments by addressing degradation issues caused by light absorption and scattering effects, including color distortion, blurring, and low contrast. Current mainstream solutions predominantly employ multi-scale feature extraction (MSFE) mechanisms to enhance reconstruction quality through multi-resolution feature fusion. However, our extensive experiments demonstrate that high-quality image reconstruction does not necessarily rely on multi-scale feature fusion. Contrary to popular belief, our experiments show that single-scale feature extraction alone can match or surpass the performance of multi-scale methods, significantly reducing complexity. To comprehensively explore single-scale feature potential in underwater enhancement, we propose an innovative Single-Scale Decomposition Network (SSD-Net). This architecture introduces an asymmetrical decomposition mechanism that disentangles input image into clean layer along with degradation layer. The former contains scene-intrinsic information and the latter encodes medium-induced interference. It uniquely combines CNN's local feature extraction capabilities with Transformer's global modeling strengths through two core modules: 1) Parallel Feature Decomposition Block (PFDB), implementing dual-branch feature space decoupling via efficient attention operations and adaptive sparse transformer; 2) Bidirectional Feature Communication Block (BFCB), enabling cross-layer residual interactions for complementary feature mining and fusion. This synergistic design preserves feature decomposition independence while establishing dynamic cross-layer information pathways, effectively enhancing degradation decoupling capacity.

Danruo Deng, Guangyong Chen, Jianye Hao et al.

The backpropagation networks are notably susceptible to catastrophic forgetting, where networks tend to forget previously learned skills upon learning new ones. To address such the 'sensitivity-stability' dilemma, most previous efforts have been contributed to minimizing the empirical risk with different parameter regularization terms and episodic memory, but rarely exploring the usages of the weight loss landscape. In this paper, we investigate the relationship between the weight loss landscape and sensitivity-stability in the continual learning scenario, based on which, we propose a novel method, Flattening Sharpness for Dynamic Gradient Projection Memory (FS-DGPM). In particular, we introduce a soft weight to represent the importance of each basis representing past tasks in GPM, which can be adaptively learned during the learning process, so that less important bases can be dynamically released to improve the sensitivity of new skill learning. We further introduce Flattening Sharpness (FS) to reduce the generalization gap by explicitly regulating the flatness of the weight loss landscape of all seen tasks. As demonstrated empirically, our proposed method consistently outperforms baselines with the superior ability to learn new skills while alleviating forgetting effectively.

Weiwen Liu, Feng Liu, Ruiming Tang et al.

Fairness in recommendation has attracted increasing attention due to bias and discrimination possibly caused by traditional recommenders. In Interactive Recommender Systems (IRS), user preferences and the system's fairness status are constantly changing over time. Existing fairness-aware recommenders mainly consider fairness in static settings. Directly applying existing methods to IRS will result in poor recommendation. To resolve this problem, we propose a reinforcement learning based framework, FairRec, to dynamically maintain a long-term balance between accuracy and fairness in IRS. User preferences and the system's fairness status are jointly compressed into the state representation to generate recommendations. FairRec aims at maximizing our designed cumulative reward that combines accuracy and fairness. Extensive experiments validate that FairRec can improve fairness, while preserving good recommendation quality.

Hongyao Tang, Jianye Hao, Guangyong Chen et al.

Value function is the central notion of Reinforcement Learning (RL). Value estimation, especially with function approximation, can be challenging since it involves the stochasticity of environmental dynamics and reward signals that can be sparse and delayed in some cases. A typical model-free RL algorithm usually estimates the values of a policy by Temporal Difference (TD) or Monte Carlo (MC) algorithms directly from rewards, without explicitly taking dynamics into consideration. In this paper, we propose Value Decomposition with Future Prediction (VDFP), providing an explicit two-step understanding of the value estimation process: 1) first foresee the latent future, 2) and then evaluate it. We analytically decompose the value function into a latent future dynamics part and a policy-independent trajectory return part, inducing a way to model latent dynamics and returns separately in value estimation. Further, we derive a practical deep RL algorithm, consisting of a convolutional model to learn compact trajectory representation from past experiences, a conditional variational auto-encoder to predict the latent future dynamics and a convex return model that evaluates trajectory representation. In experiments, we empirically demonstrate the effectiveness of our approach for both off-policy and on-policy RL in several OpenAI Gym continuous control tasks as well as a few challenging variants with delayed reward.

Pengfei Chen, Junjie Ye, Guangyong Chen et al.

Supervised learning under label noise has seen numerous advances recently, while existing theoretical findings and empirical results broadly build up on the class-conditional noise (CCN) assumption that the noise is independent of input features given the true label. In this work, we present a theoretical hypothesis testing and prove that noise in real-world dataset is unlikely to be CCN, which confirms that label noise should depend on the instance and justifies the urgent need to go beyond the CCN assumption.The theoretical results motivate us to study the more general and practical-relevant instance-dependent noise (IDN). To stimulate the development of theory and methodology on IDN, we formalize an algorithm to generate controllable IDN and present both theoretical and empirical evidence to show that IDN is semantically meaningful and challenging. As a primary attempt to combat IDN, we present a tiny algorithm termed self-evolution average label (SEAL), which not only stands out under IDN with various noise fractions, but also improves the generalization on real-world noise benchmark Clothing1M. Our code is released. Notably, our theoretical analysis in Section 2 provides rigorous motivations for studying IDN, which is an important topic that deserves more research attention in future.

Pengfei Chen, Junjie Ye, Guangyong Chen et al.

For multi-class classification under class-conditional label noise, we prove that the accuracy metric itself can be robust. We concretize this finding's inspiration in two essential aspects: training and validation, with which we address critical issues in learning with noisy labels. For training, we show that maximizing training accuracy on sufficiently many noisy samples yields an approximately optimal classifier. For validation, we prove that a noisy validation set is reliable, addressing the critical demand of model selection in scenarios like hyperparameter-tuning and early stopping. Previously, model selection using noisy validation samples has not been theoretically justified. We verify our theoretical results and additional claims with extensive experiments. We show characterizations of models trained with noisy labels, motivated by our theoretical results, and verify the utility of a noisy validation set by showing the impressive performance of a framework termed noisy best teacher and student (NTS). Our code is released.

Xianzhi Li, Ruihui Li, Guangyong Chen et al.

Recently, many deep neural networks were designed to process 3D point clouds, but a common drawback is that rotation invariance is not ensured, leading to poor generalization to arbitrary orientations. In this paper, we introduce a new low-level purely rotation-invariant representation to replace common 3D Cartesian coordinates as the network inputs. Also, we present a network architecture to embed these representations into features, encoding local relations between points and their neighbors, and the global shape structure. To alleviate inevitable global information loss caused by the rotation-invariant representations, we further introduce a region relation convolution to encode local and non-local information. We evaluate our method on multiple point cloud analysis tasks, including shape classification, part segmentation, and shape retrieval. Experimental results show that our method achieves consistent, and also the best performance, on inputs at arbitrary orientations, compared with the state-of-the-arts.

Yitong Meng, Guangyong Chen, Benben Liao et al.

The item cold-start problem seriously limits the recommendation performance of Collaborative Filtering (CF) methods when new items have either none or very little interactions. To solve this issue, many modern Internet applications propose to predict a new item's interaction from the possessing contents. However, it is difficult to design and learn a map between the item's interaction history and the corresponding contents. In this paper, we apply the Wasserstein distance to address the item cold-start problem. Given item content information, we can calculate the similarity between the interacted items and cold-start ones, so that a user's preference on cold-start items can be inferred by minimizing the Wasserstein distance between the distributions over these two types of items. We further adopt the idea of CF and propose Wasserstein CF (WCF) to improve the recommendation performance on cold-start items. Experimental results demonstrate the superiority of WCF over state-of-the-art approaches.

Yitong Meng, Xinyan Dai, Xiao Yan et al.

Collaborative filtering, a widely-used recommendation technique, predicts a user's preference by aggregating the ratings from similar users. As a result, these measures cannot fully utilize the rating information and are not suitable for real world sparse data. To solve these issues, we propose a novel user distance measure named Preference Mover's Distance (PMD) which makes full use of all ratings made by each user. Our proposed PMD can properly measure the distance between a pair of users even if they have no co-rated items. We show that this measure can be cast as an instance of the Earth Mover's Distance, a well-studied transportation problem for which several highly efficient solvers have been developed. Experimental results show that PMD can help achieve superior recommendation accuracy than state-of-the-art methods, especially when training data is very sparse.

Yi Ma, Jianye Hao, Yaodong Yang et al.

Graph convolutional networks(GCNs) have become the most popular approaches for graph data in these days because of their powerful ability to extract features from graph. GCNs approaches are divided into two categories, spectral-based and spatial-based. As the earliest convolutional networks for graph data, spectral-based GCNs have achieved impressive results in many graph related analytics tasks. However, spectral-based models cannot directly work on directed graphs. In this paper, we propose an improved spectral-based GCN for the directed graph by leveraging redefined Laplacians to improve its propagation model. Our approach can work directly on directed graph data in semi-supervised nodes classification tasks. Experiments on a number of directed graph datasets demonstrate that our approach outperforms the state-of-the-art methods.

Guangyong Chen, Pengfei Chen, Chang-Yu Hsieh et al.

We introduce a new molecular dataset, named Alchemy, for developing machine learning models useful in chemistry and material science. As of June 20th 2019, the dataset comprises of 12 quantum mechanical properties of 119,487 organic molecules with up to 14 heavy atoms, sampled from the GDB MedChem database. The Alchemy dataset expands the volume and diversity of existing molecular datasets. Our extensive benchmarks of the state-of-the-art graph neural network models on Alchemy clearly manifest the usefulness of new data in validating and developing machine learning models for chemistry and material science. We further launch a contest to attract attentions from researchers in the related fields. More details can be found on the contest website \footnote{https://alchemy.tencent.com}. At the time of benchamrking experiment, we have generated 119,487 molecules in our Alchemy dataset. More molecular samples are generated since then. Hence, we provide a list of molecules used in the reported benchmarks.

Pengfei Chen, Benben Liao, Guangyong Chen et al.

Noisy labels are ubiquitous in real-world datasets, which poses a challenge for robustly training deep neural networks (DNNs) since DNNs can easily overfit to the noisy labels. Most recent efforts have been devoted to defending noisy labels by discarding noisy samples from the training set or assigning weights to training samples, where the weight associated with a noisy sample is expected to be small. Thereby, these previous efforts result in a waste of samples, especially those assigned with small weights. The input $x$ is always useful regardless of whether its observed label $y$ is clean. To make full use of all samples, we introduce a manifold regularizer, named as Paired Softmax Divergence Regularization (PSDR), to penalize the Kullback-Leibler (KL) divergence between softmax outputs of similar inputs. In particular, similar inputs can be effectively generated by data augmentation. PSDR can be easily implemented on any type of DNNs to improve the robustness against noisy labels. As empirically demonstrated on benchmark datasets, our PSDR impressively improve state-of-the-art results by a significant margin.

Pengfei Chen, Weiwen Liu, Chang-Yu Hsieh et al.

Graph Neural Networks (GNNs) achieve an impressive performance on structured graphs by recursively updating the representation vector of each node based on its neighbors, during which parameterized transformation matrices should be learned for the node feature updating. However, existing propagation schemes are far from being optimal since they do not fully utilize the relational information between nodes. We propose the information maximizing graph neural networks (IGNN), which maximizes the mutual information between edge states and transform parameters. We reformulate the mutual information as a differentiable objective via a variational approach. We compare our model against several recent variants of GNNs and show that our model achieves the state-of-the-art performance on multiple tasks including quantum chemistry regression on QM9 dataset, generalization capability from QM9 to larger molecular graphs, and prediction of molecular bioactivities relevant for drug discovery. The IGNN model is based on an elegant and fundamental idea in information theory as explained in the main text, and it could be easily generalized beyond the contexts of molecular graphs considered in this work. To encourage more future work in this area, all datasets and codes used in this paper will be released for public access.

Yujun Shi, Benben Liao, Guangyong Chen et al.

The vulnerability to slight input perturbations is a worrying yet intriguing property of deep neural networks (DNNs). Despite many previous works studying the reason behind such adversarial behavior, the relationship between the generalization performance and adversarial behavior of DNNs is still little understood. In this work, we reveal such relation by introducing a metric characterizing the generalization performance of a DNN. The metric can be disentangled into an information-theoretic non-robust component, responsible for adversarial behavior, and a robust component. Then, we show by experiments that current DNNs rely heavily on optimizing the non-robust component in achieving decent performance. We also demonstrate that current state-of-the-art adversarial training algorithms indeed try to robustify the DNNs by preventing them from using the non-robust component to distinguish samples from different categories. Also, based on our findings, we take a step forward and point out the possible direction for achieving decent standard performance and adversarial robustness simultaneously. We believe that our theory could further inspire the community to make more interesting discoveries about the relationship between standard generalization and adversarial generalization of deep learning models.

Hongyao Tang, Jianye Hao, Guangyong Chen et al.

Value functions are crucial for model-free Reinforcement Learning (RL) to obtain a policy implicitly or guide the policy updates. Value estimation heavily depends on the stochasticity of environmental dynamics and the quality of reward signals. In this paper, we propose a two-step understanding of value estimation from the perspective of future prediction, through decomposing the value function into a reward-independent future dynamics part and a policy-independent trajectory return part. We then derive a practical deep RL algorithm from the above decomposition, consisting of a convolutional trajectory representation model, a conditional variational dynamics model to predict the expected representation of future trajectory and a convex trajectory return model that maps a trajectory representation to its return. Our algorithm is evaluated in MuJoCo continuous control tasks and shows superior results under both common settings and delayed reward settings.

Guangyong Chen, Pengfei Chen, Yujun Shi et al.

In this work, we propose a novel technique to boost training efficiency of a neural network. Our work is based on an excellent idea that whitening the inputs of neural networks can achieve a fast convergence speed. Given the well-known fact that independent components must be whitened, we introduce a novel Independent-Component (IC) layer before each weight layer, whose inputs would be made more independent. However, determining independent components is a computationally intensive task. To overcome this challenge, we propose to implement an IC layer by combining two popular techniques, Batch Normalization and Dropout, in a new manner that we can rigorously prove that Dropout can quadratically reduce the mutual information and linearly reduce the correlation between any pair of neurons with respect to the dropout layer parameter $p$. As demonstrated experimentally, the IC layer consistently outperforms the baseline approaches with more stable training process, faster convergence speed and better convergence limit on CIFAR10/100 and ILSVRC2012 datasets. The implementation of our IC layer makes us rethink the common practices in the design of neural networks. For example, we should not place Batch Normalization before ReLU since the non-negative responses of ReLU will make the weight layer updated in a suboptimal way, and we can achieve better performance by combining Batch Normalization and Dropout together as an IC layer.

Pengfei Chen, Benben Liao, Guangyong Chen et al.

Noisy labels are ubiquitous in real-world datasets, which poses a challenge for robustly training deep neural networks (DNNs) as DNNs usually have the high capacity to memorize the noisy labels. In this paper, we find that the test accuracy can be quantitatively characterized in terms of the noise ratio in datasets. In particular, the test accuracy is a quadratic function of the noise ratio in the case of symmetric noise, which explains the experimental findings previously published. Based on our analysis, we apply cross-validation to randomly split noisy datasets, which identifies most samples that have correct labels. Then we adopt the Co-teaching strategy which takes full advantage of the identified samples to train DNNs robustly against noisy labels. Compared with extensive state-of-the-art methods, our strategy consistently improves the generalization performance of DNNs under both synthetic and real-world training noise.

Guangyong Chen, Fengyuan Zhu, Pheng Ann Heng

Dyadic Data Prediction (DDP) is an important problem in many research areas. This paper develops a novel fully Bayesian nonparametric framework which integrates two popular and complementary approaches, discrete mixed membership modeling and continuous latent factor modeling into a unified Heterogeneous Matrix Factorization~(HeMF) model, which can predict the unobserved dyadics accurately. The HeMF can determine the number of communities automatically and exploit the latent linear structure for each bicluster efficiently. We propose a Variational Bayesian method to estimate the parameters and missing data. We further develop a novel online learning approach for Variational inference and use it for the online learning of HeMF, which can efficiently cope with the important large-scale DDP problem. We evaluate the performance of our method on the EachMoive, MovieLens and Netflix Prize collaborative filtering datasets. The experiment shows that, our model outperforms state-of-the-art methods on all benchmarks. Compared with Stochastic Gradient Method (SGD), our online learning approach achieves significant improvement on the estimation accuracy and robustness.

Fengyuan Zhu, Guangyong Chen, Jianye Hao et al.

Most existing image denoising approaches assumed the noise to be homogeneous white Gaussian distributed with known intensity. However, in real noisy images, the noise models are usually unknown beforehand and can be much more complex. This paper addresses this problem and proposes a novel blind image denoising algorithm to recover the clean image from noisy one with the unknown noise model. To model the empirical noise of an image, our method introduces the mixture of Gaussian distribution, which is flexible enough to approximate different continuous distributions. The problem of blind image denoising is reformulated as a learning problem. The procedure is to first build a two-layer structural model for noisy patches and consider the clean ones as latent variable. To control the complexity of the noisy patch model, this work proposes a novel Bayesian nonparametric prior called "Dependent Dirichlet Process Tree" to build the model. Then, this study derives a variational inference algorithm to estimate model parameters and recover clean patches. We apply our method on synthesis and real noisy images with different noise models. Comparing with previous approaches, ours achieves better performance. The experimental results indicate the efficiency of the proposed algorithm to cope with practical image denoising tasks.