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Stan Z Li

118 accepted papers

2026

CDBridge: A Cross-omics Post-training Bridge Strategy for Context-aware Biological Modeling

ICLR 2026poster

Linking genomic DNA to quantitative, context-specific expression remains a central challenge in computational biology. Current foundation models capture either tissue context or sequence features, but not both. Cross-omics systems, in turn, often overlook critical mechanisms such as alternative spli…

Cited by 0SourceScholar
2026

Departures: Distributional Transport for Single-Cell Perturbation Prediction with Neural Schrödinger Bridges

AAAI 2026technical

Predicting single-cell perturbation outcomes directly advances gene function analysis and facilitates drug candidate selection, making it a key driver of both basic and translational biomedical research. However, a major bottleneck in this task is the unpaired nature of single-cell data, as the same

Cited by 0SourcePDFScholar
2026

Doloris: Dual Conditional Diffusion Implicit Bridges with Sparsity Masking Strategy for Unpaired Single-Cell Perturbation Estimation

ICLR 2026poster

Estimating single-cell responses across various perturbations facilitates the identification of key genes and enhances drug screening, significantly boosting experimental efficiency. However, single-cell sequencing is a destructive process, making it impossible to capture the same cell's phenotype b…

Cited by 0SourcecodeScholar
2026

Geometric Flow Grounding: A Unified Manifold Decoupling Framework for Dynamics Discovery and Verification

ICML 2026oral

Modeling complex dynamics from observational data is fundamental to scientific discovery and artificial intelligence. However, existing approaches ranging from Neural ODEs to diffusion models are often plagued by the entanglement of static state representations and instantaneous motion, leading to a…

Cited by 0SourceScholar
2026

HDTree: Generative Modeling of Cellular Hierarchies for Robust Lineage Inference

ICML 2026poster

In single-cell research, tracing and analyzing high-throughput single-cell differentiation trajectories is crucial for understanding biological processes. Key to this is the robust modeling of hierarchical structures that govern cellular development. Traditional methods face limitations in computati…

Cited by 0SourceScholar
2026

Learning Cell-Aware Hierarchical Multi-Modal Representations for Robust Molecular Modeling

AAAI 2026technical

Understanding how chemical perturbations propagate through biological systems is essential for robust molecular property prediction. While most existing methods focus on chemical structures alone, recent advances highlight the crucial role of cellular responses such as morphology and gene expression

Cited by 0SourcePDFScholar
2026

MergeDNA: Context-Aware Genome Modeling with Dynamic Tokenization Through Token Merging

AAAI 2026technical

Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit. Relying on either four primitive bases or independently designed DNA tokenizers, existing approaches with naive masked

Cited by 0SourcePDFScholar
2026

On the Design of One-step Diffusion via Shortcutting Flow Paths

ICLR 2026poster

Recent advances in few-step diffusion models have demonstrated their efficiency and effectiveness by shortcutting the probabilistic paths of diffusion models, especially in training one-step diffusion models from scratch (a.k.a. shortcut models). However, their theoretical derivation and practical i…

Cited by 3SourcecodeScholar
2026

SYNC: Measuring and Advancing Synthesizability in Structure-Based Drug Design

ICLR 2026poster

Designing 3D ligands that bind to a given protein pocket with high affinity is a fundamental task in Structure-Based Drug Design (SBDD). However, the lack of synthesizability of 3D ligands has been hindering progress toward experimental validation; moreover, computationally evaluating synthesizabili…

Cited by 0SourcecodeScholar
2026

SteinsGate: Adding Causality to Diffusions for Long Video Generation via Path Integral

ICLR 2026poster

Video generation has advanced rapidly, but current models remain limited to short clips, far from the length and complexity of real-world narratives. Long video generation is thus both important and challenging. Existing approaches either attempt to extend the modeling length of video diffusion mode…

Cited by 0SourceScholar
2025

A Comprehensive and Systematic Review for Deep Learning-Based De Novo Peptide Sequencing

IJCAI 2025

Tandem mass spectrometry (MS/MS) has revolutionized the field of proteomics, enabling the high-throughput identification of proteins. However, one of the central challenges in mass spectrometry-based proteomics remains peptide identification, especially in the absence of a comprehensive peptide data

Cited by 0SourcePDFScholar
2025

A Simple yet Effective $\Delta\Delta G$ Predictor is An Unsupervised Antibody Optimizer and Explainer

ICLR 2025poster

The proteins that exist today have been optimized over billions of years of natural evolution, during which nature creates random mutations and selects them. The discovery of functionally promising mutations is challenged by the limited evolutionary accessible regions, i.e., only a small region on t…

Cited by 1SourcePDFScholar
2025

AlphaFold Database Debiasing for Robust Inverse Folding

NeurIPS 2025poster

The AlphaFold Protein Structure Database (AFDB) offers unparalleled structural coverage at near-experimental accuracy, positioning it as a valuable resource for data-driven protein design. However, its direct use in training deep models that are sensitive to fine-grained atomic geometry—such as inve…

Cited by 0SourceScholar
2025

Bridging the Gap between Database Search and \emph{De Novo} Peptide Sequencing with SearchNovo

ICLR 2025poster

Accurate protein identification from mass spectrometry (MS) data is fundamental to unraveling the complex roles of proteins in biological systems, with peptide sequencing being a pivotal step in this process. The two main paradigms for peptide sequencing are database search, which matches experiment…

2025

CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph

ICLR 2025spotlight

Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. However, a lack of systematic understanding persists due to the diverse settings, complex implementation, difficult reprodu…

2025

DapPep: Domain Adaptive Peptide-agnostic Learning for Universal T-cell Receptor-antigen Binding Affinity Prediction

ICASSP 2025accepted

Identifying T-cell receptors (TCRs) that interact with antigenic peptides provides the technical basis for developing vaccines and immunotherapies. The emergent deep learning methods excel at learning antigen binding patterns from known TCRs but struggle with novel or sparsely represented antigens.…

Cited by 0SourceScholar
2025

EVA: Geometric Inverse Design for Fast Protein Motif-Scaffolding with Coupled Flow

ICLR 2025poster

Motif-scaffolding is a fundamental component of protein design, which aims to construct the scaffold structure that stabilizes motifs conferring desired functions. Recent advances in generative models are promising for designing scaffolds, with two main approaches: training-based and sampling-based…

Cited by 0SourcePDFScholar
2025

FoldToken: Learning Protein Language via Vector Quantization and Beyond

AAAI 2025technical

Is there a foreign language describing protein sequences and structures simultaneously? Protein structures, represented by continuous 3D points, have long posed a challenge due to the contrasting modeling paradigms of discrete sequences. We introduce FoldTokenizer to represent protein sequence-struc…

Cited by 10SourcePDFScholar
2025

G2PDiffusion: Cross-Species Genotype-to-Phenotype Prediction via Evolutionary Diffusion

ICCV 2025poster

Understanding how genes influence phenotype across species is a fundamental challenge in genetic engineering, which will facilitate advances in various fields such as crop breeding, conservation biology, and personalized medicine. However, current phenotype prediction models are limited to individua…

Cited by 0SourcePDFScholar
2025

GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype

IJCAI 2025

Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene regulatory networks (GRN) is essential to understand and pred

2025

Generalized Implicit Neural Representations for Dynamic Molecular Surface Modeling

AAAI 2025technical

Molecular dynamics (MD) has long been the de facto choice for simulating intricate physical systems from first principles. Recent efforts utilize the implicit neural representation (INR) to directly learn surface point clouds' signed distance function (SDF) with promising outcomes. However, INR's te…

2025

MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction

ICLR 2025poster

Post-translational modifications (PTMs) profoundly expand the complexity and functionality of the proteome, regulating protein attributes and interactions that are crucial for biological processes. Accurately predicting PTM sites and their specific types is therefore essential for elucidating protei…

2025

PRING: Rethinking Protein-Protein Interaction Prediction from Pairs to Graphs

NeurIPS 2025poster

Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability to reconstruct biologically meaningful PPI networks, which…

Cited by 0SourcecodeScholar
2025

Pan-protein Design Learning Enables Task-adaptive Generalization for Low-resource Enzyme Design

ICASSP 2025accepted

Computational protein design (CPD) offers transformative potential for bioengineering, but current deep CPD models, focused on universal domains, struggle with function-specific designs. This work introduces a novel CPD paradigm tailored for functional design tasks, particularly for enzymes a key pr…

Cited by 0SourceScholar
2025

ReNovo: Retrieval-Based \emph{De Novo} Mass Spectrometry Peptide Sequencing

ICLR 2025poster

Proteomics is the large-scale study of proteins. Tandem mass spectrometry, as the only high-throughput technique for protein sequence identification, plays a pivotal role in proteomics research. One of the long-standing challenges in this field is peptide identification, which entails determining th…

Cited by 0SourcePDFScholar
2025

Relation-Aware Equivariant Graph Networks for Epitope-Unknown Antibody Design and Specificity Optimization

AAAI 2025technical

Antibodies are Y-shaped proteins that protect the host by binding to specific antigens, and their binding is mainly determined by the Complementary Determining Regions (CDRs) in the antibody. Despite the great progress made in CDR design, existing computational methods still encounter several challe…

2025

SketchAgent: Generating Structured Diagrams from Hand-Drawn Sketches

IJCAI 2025

Hand-drawn sketches are a natural and efficient medium for capturing and conveying ideas. Despite significant advancements in controllable natural image generation, translating freehand sketches into structured, machine-readable diagrams remains a labor-intensive and predominantly manual task. The p

Cited by 0SourcePDFScholar
2025

dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigen

AAAI 2025technical

The development of therapeutic antibodies heavily relies on accurate predictions of how antigens will interact with antibodies. Existing computational methods in antibody design often overlook crucial conformational changes that antigens undergo during the binding process, significantly impacting th…

2024

A Graph is Worth $K$ Words: Euclideanizing Graph using Pure Transformer

ICML 2024poster

Can we model Non-Euclidean graphs as pure language or even Euclidean vectors while retaining their inherent information? The Non-Euclidean property have posed a long term challenge in graph modeling. Despite recent graph neural networks and graph transformers efforts encoding graphs as Euclidean vec…

2024

AdaNovo: Towards Robust \emph{De Novo} Peptide Sequencing in Proteomics against Data Biases

NeurIPS 2024poster

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Despite the development of several deep learning methods for predicting amino acid sequences (peptides) responsible for generating the obser…

Cited by 0SourcePDFScholar
2024

Cross-Gate MLP with Protein Complex Invariant Embedding Is a One-Shot Antibody Designer

AAAI 2024technical

Antibodies are crucial proteins produced by the immune system in response to foreign substances or antigens. The specificity of an antibody is determined by its complementarity-determining regions (CDRs), which are located in the variable domains of the antibody chains and form the antigen-binding s…

2024

Deciphering RNA Secondary Structure Prediction: A Probabilistic K-Rook Matching Perspective

ICML 2024poster

The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field, current methods suffer from poor generalization and high complexit…

2024

Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks

ICLR 2024poster

Recent years have witnessed the great success of graph pre-training for graph representation learning. With hundreds of graph pre-training tasks proposed, integrating knowledge acquired from multiple pre-training tasks has become a popular research topic. In this paper, we identify two important col…

2024

Deep Graph Neural Networks via Posteriori-Sampling-based Node-Adaptative Residual Module

NeurIPS 2024poster

Graph Neural Networks (GNNs), a type of neural network that can learn from graph-structured data through neighborhood information aggregation, have shown superior performance in various downstream tasks. However, as the number of layers increases, node representations becomes indistinguishable, whic…

2024

DiffAug: Enhance Unsupervised Contrastive Learning with Domain-Knowledge-Free Diffusion-based Data Augmentation

ICML 2024poster

Unsupervised Contrastive learning has gained prominence in fields such as vision, and biology, leveraging predefined positive/negative samples for representation learning. Data augmentation, categorized into hand-designed and model-based methods, has been identified as a crucial component for enhanc…

2024

FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning

NeurIPS 2024poster

Molecular relational learning (MRL) is crucial for understanding the interaction behaviors between molecular pairs, a critical aspect of drug discovery and development. However, the large feasible model space of MRL poses significant challenges to benchmarking, and existing MRL frameworks face limit…

2024

General Point Model Pretraining with Autoencoding and Autoregressive

CVPR 2024poster

The pre-training architectures of large language models encompass various types including autoencoding models autoregressive models and encoder-decoder models. We posit that any modality can potentially benefit from a large language model as long as it undergoes vector quantization to become discret…

2024

GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation

ICML 2024poster

Increasing works for antibody design are emerging to generate sequences and structures in Complementarity Determining Regions (CDRs), but problems still exist. We focus on two of them: (i) authenticity of the generated structure and (ii) rationality of the affinity maturation, and propose GeoAB as a…

Cited by 13SourcePDFScholar
2024

Instructor-inspired Machine Learning for Robust Molecular Property Prediction

NeurIPS 2024poster

Machine learning catalyzes a revolution in chemical and biological science. However, its efficacy is heavily dependent on the availability of labeled data, and annotating biochemical data is extremely laborious. To surmount this data sparsity challenge, we present an instructive learning algorithm n…

Cited by 1SourcePDFScholar
2024

KW-Design: Pushing the Limit of Protein Design via Knowledge Refinement

ICLR 2024poster

Recent studies have shown competitive performance in protein inverse folding, while most of them disregard the importance of predictive confidence, fail to cover the vast protein space, and do not incorporate common protein knowledge. Given the great success of pretrained models on diverse protein-r…

2024

Learning Complete Protein Representation by Dynamically Coupling of Sequence and Structure

NeurIPS 2024poster

Learning effective representations is imperative for comprehending proteins and deciphering their biological functions. Recent strides in language models and graph neural networks have empowered protein models to harness primary or tertiary structure information for representation learning. Neverthe…

Cited by 0SourcePDFScholar
2024

Learning to Predict Mutational Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning

ICML 2024poster

Protein-protein bindings play a key role in a variety of fundamental biological processes, and thus predicting the effects of amino acid mutations on protein-protein binding is crucial. To tackle the scarcity of annotated mutation data, pre-training with massive unlabeled data has emerged as a promi…

Cited by 16SourcePDFScholar
2024

LongVQ: Long Sequence Modeling with Vector Quantization on Structured Memory

IJCAI 2024poster

Transformer models have been successful in various sequence processing tasks, but the self-attention mechanism's computational cost limits its practicality for long sequences. Although there are existing attention variants that improve computational efficiency, they have a limited ability to abstrac…

Cited by 2SourcePDFScholar
2024

MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding

ICLR 2024spotlight

Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays require computational methods for efficient PPI prediction. While existing methods rely heavily on protein sequence for P…

2024

MLIP: Enhancing Medical Visual Representation with Divergence Encoder and Knowledge-guided Contrastive Learning

CVPR 2024poster

The scarcity of annotated data has sparked significant interest in unsupervised pre-training methods that leverage medical reports as auxiliary signals for medical visual representation learning. However existing research overlooks the multi-granularity nature of medical visual representation and la…

Cited by 15SourcePDFScholar
2024

MogaNet: Multi-order Gated Aggregation Network

ICLR 2024poster

By contextualizing the kernel as global as possible, Modern ConvNets have shown great potential in computer vision tasks. However, recent progress on \textit{multi-order game-theoretic interaction} within deep neural networks (DNNs) reveals the representation bottleneck of modern ConvNets, where the…

2024

NovoBench: Benchmarking Deep Learning-based \emph{De Novo} Sequencing Methods in Proteomics

NeurIPS 2024poster

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological tissues. Many deep learning methods have been developed for \emph{de novo} peptide sequencing task, i.e., predicting the peptide sequence for the observed mass spect…

2024

PPFLOW: Target-Aware Peptide Design with Torsional Flow Matching

ICML 2024poster

Therapeutic peptides have proven to have great pharmaceutical value and potential in recent decades. However, methods of AI-assisted peptide drug discovery are not fully explored. To fill the gap, we propose a target-aware peptide design method called PPFlow, based on conditional flow matching on to…

2024

PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction

AAAI 2024technical

Compound-Protein Interaction (CPI) prediction aims to predict the pattern and strength of compound-protein interactions for rational drug discovery. Existing deep learning-based methods utilize only the single modality of protein sequences or structures and lack the co-modeling of the joint distribu…

2024

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation

NeurIPS 2024poster

Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov Chain Monte Carlo methods face slow convergence and co…

Cited by 2SourcePDFScholar
2024

ProtGO: Function-Guided Protein Modeling for Unified Representation Learning

NeurIPS 2024poster

Protein representation learning is indispensable for various downstream applications of artificial intelligence for bio-medicine research, such as drug design and function prediction. However, achieving effective representation learning for proteins poses challenges due to the diversity of data moda…

Cited by 0SourcePDFScholar
2024

Protein 3D Graph Structure Learning for Robust Structure-Based Protein Property Prediction

AAAI 2024technical

Protein structure-based property prediction has emerged as a promising approach for various biological tasks, such as protein function prediction and sub-cellular location estimation. The existing methods highly rely on experimental protein structure data and fail in scenarios where these data are u…

Cited by 12SourcePDFScholar
2024

RDesign: Hierarchical Data-efficient Representation Learning for Tertiary Structure-based RNA Design

ICLR 2024poster

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have th…

2024

Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge

ICML 2024spotlight

Accurate prediction of protein-ligand binding structures, a task known as molecular docking is crucial for drug design but remains challenging. While deep learning has shown promise, existing methods often depend on holo-protein structures (docked, and not accessible in realistic tasks) or neglect p…

Cited by 10SourcePDFScholar
2024

SemiReward: A General Reward Model for Semi-supervised Learning

ICLR 2024poster

Semi-supervised learning (SSL) has witnessed great progress with various improvements in the self-training framework with pseudo labeling. The main challenge is how to distinguish high-quality pseudo labels against the confirmation bias. However, existing pseudo-label selection strategies are limite…

2024

Short-Long Convolutions Help Hardware-Efficient Linear Attention to Focus on Long Sequences

ICML 2024poster

To mitigate the computational complexity in the self-attention mechanism on long sequences, linear attention utilizes computation tricks to achieve linear complexity, while state space models (SSMs) popularize a favourable practice of using non-data-dependent memory pattern, *i.e.,* emphasize the ne…

Cited by 6SourcePDFScholar
2024

UniIF: Unified Molecule Inverse Folding

NeurIPS 2024poster

Molecule inverse folding has been a long-standing challenge in chemistry and biology, with the potential to revolutionize drug discovery and material science. Despite specified models have been proposed for different small- or macro-molecules, few have attempted to unify the learning process, result…

Cited by 16SourcePDFScholar
2024

VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling

ICML 2024poster

Similar to natural language models, pre-trained genome language models are proposed to capture the underlying intricacies within genomes with unsupervised sequence modeling. They have become essential tools for researchers and practitioners in biology. However, the hand-crafted tokenization policies…

Cited by 9SourcePDFScholar
2024

Wavelet-Driven Spatiotemporal Predictive Learning: Bridging Frequency and Time Variations

AAAI 2024technical

Spatiotemporal predictive learning is a paradigm that empowers models to learn spatial and temporal patterns by predicting future frames from past frames in an unsupervised manner. This method typically uses recurrent units to capture long-term dependencies, but these units often come with high comp…

2023

Architecture-Agnostic Masked Image Modeling -- From ViT back to CNN

ICML 2023poster

Masked image modeling, an emerging self-supervised pre-training method, has shown impressive success across numerous downstream vision tasks with Vision transformers. Its underlying idea is simple: a portion of the input image is masked out and then reconstructed via a pre-text task. However, the wo…

Cited by 47SourcePDFScholar
2023

Boosting Novel Category Discovery Over Domains with Soft Contrastive Learning and All in One Classifier

ICCV 2023oral

Unsupervised domain adaptation (UDA) has proven to be highly effective in transferring knowledge from a label-rich source domain to a label-scarce target domain. However, the presence of additional novel categories in the target domain has led to the development of open-set domain adaptation (ODA) a…

Cited by 19PDFcodeScholar
2023

CVT-SLR: Contrastive Visual-Textual Transformation for Sign Language Recognition With Variational Alignment

CVPR 2023highlight

Sign language recognition (SLR) is a weakly supervised task that annotates sign videos as textual glosses. Recent studies show that insufficient training caused by the lack of large-scale available sign datasets becomes the main bottleneck for SLR. Most SLR works thereby adopt pretrained visual modu…

2023

Deep Manifold Graph Auto-Encoder For Attributed Graph Embedding

ICASSP 2023accepted

Representing graph data in a low-dimensional space for subsequent tasks is the purpose of attributed graph embedding. Most existing neural network approaches learn latent representations by minimizing reconstruction errors. Rare work considers the data distribution and the topological structure of l…

Cited by 0SourceScholar
2023

Dink-Net: Neural Clustering on Large Graphs

ICML 2023poster

Deep graph clustering, which aims to group the nodes of a graph into disjoint clusters with deep neural networks, has achieved promising progress in recent years. However, the existing methods fail to scale to the large graph with million nodes. To solve this problem, a scalable deep graph clusterin…

2023

Extracting Low-/High- Frequency Knowledge from Graph Neural Networks and Injecting It into MLPs: An Effective GNN-to-MLP Distillation Framework

AAAI 2023technical

Recent years have witnessed the great success of Graph Neural Networks (GNNs) in handling graph-related tasks. However, MLPs remain the primary workhorse for practical industrial applications due to their desirable inference efficiency and scalability. To reduce their gaps, one can directly distill…

2023

Functional-Group-Based Diffusion for Pocket-Specific Molecule Generation and Elaboration

NeurIPS 2023poster

In recent years, AI-assisted drug design methods have been proposed to generate molecules given the pockets' structures of target proteins. Most of them are {\em atom-level-based} methods, which consider atoms as basic components and generate atom positions and types. In this way, however, it is ha…

Cited by 25SourcePDFScholar
2023

Harnessing Hard Mixed Samples with Decoupled Regularizer

NeurIPS 2023poster

Mixup is an efficient data augmentation approach that improves the generalization of neural networks by smoothing the decision boundary with mixed data. Recently, dynamic mixup methods have improved previous \textit{static} policies effectively (e.g., linear interpolation) by maximizing target-relat…

2023

Mole-BERT: Rethinking Pre-training Graph Neural Networks for Molecules

ICLR 2023poster

Recent years have witnessed the prosperity of pre-training graph neural networks (GNNs) for molecules. Typically, atom types as node attributes are randomly masked, and GNNs are then trained to predict masked types as in AttrMask \citep{hu2020strategies}, following the Masked Language Modeling (MLM)…

2023

Molformer: Motif-Based Transformer on 3D Heterogeneous Molecular Graphs

AAAI 2023technical

Procuring expressive molecular representations underpins AI-driven molecule design and scientific discovery. The research mainly focuses on atom-level homogeneous molecular graphs, ignoring the rich information in subgraphs or motifs. However, it has been widely accepted that substructures play a do…

2023

OpenSTL: A Comprehensive Benchmark of Spatio-Temporal Predictive Learning

NeurIPS 2023poster

Spatio-temporal predictive learning is a learning paradigm that enables models to learn spatial and temporal patterns by predicting future frames from given past frames in an unsupervised manner. Despite remarkable progress in recent years, a lack of systematic understanding persists due to the dive…

2023

ProteinInvBench: Benchmarking Protein Inverse Folding on Diverse Tasks, Models, and Metrics

NeurIPS 2023poster

Protein inverse folding has attracted increasing attention in recent years. However, we observe that current methods are usually limited to the CATH dataset and the recovery metric. The lack of a unified framework for ensembling and comparing different methods hinders the comprehensive investigation…

2023

Quantifying the Knowledge in GNNs for Reliable Distillation into MLPs

ICML 2023poster

To bridge the gaps between topology-aware Graph Neural Networks (GNNs) and inference-efficient Multi-Layer Perceptron (MLPs), GLNN proposes to distill knowledge from a well-trained teacher GNN into a student MLP. Despite their great progress, comparatively little work has been done to explore the re…

2023

Rethinking Explaining Graph Neural Networks via Non-parametric Subgraph Matching

ICML 2023poster

The success of graph neural networks (GNNs) provokes the question about explainability: ``Which fraction of the input graph is the most determinant of the prediction?'' Particularly, parametric explainers prevail in existing approaches because of their more robust capability to decipher the black-bo…

2023

Temporal Attention Unit: Towards Efficient Spatiotemporal Predictive Learning

CVPR 2023poster

Spatiotemporal predictive learning aims to generate future frames by learning from historical frames. In this paper, we investigate existing methods and present a general framework of spatiotemporal predictive learning, in which the spatial encoder and decoder capture intra-frame features and the mi…

2023

Understanding the Limitations of Deep Models for Molecular property prediction: Insights and Solutions

NeurIPS 2023poster

Molecular Property Prediction (MPP) is a crucial task in the AI-driven Drug Discovery (AIDD) pipeline, which has recently gained considerable attention thanks to advancements in deep learning. However, recent research has revealed that deep models struggle to beat traditional non-deep ones on MPP. I…

Cited by 37SourcePDFScholar
2023

Wordreg: Mitigating the Gap between Training and Inference with Worst-Case Drop Regularization

ICASSP 2023accepted

Dropout has emerged as one of the most frequently used techniques for training deep neural networks (DNNs). Although effective, the sampled sub-model by random dropout during training is inconsistent with the full model (without dropout) during inference. To mitigate this undesirable gap, we propose…

Cited by 0SourceScholar
2022

AutoMix: Unveiling the Power of Mixup for Stronger Classifiers

ECCV 2022poster

"Data mixing augmentation have proved to be effective for improving the generalization ability of deep neural networks. While early methods mix samples by hand-crafted policies (\textit{e.g.}, linear interpolation), recent methods utilize saliency information to match the mixed samples and labels vi…

2022

CAViT: Contextual Alignment Vision Transformer for Video Object Re-identification

ECCV 2022poster

"Video object re-identification (reID) aims at re-identifying the same object under non-overlapping cameras by matching the video tracklets with cropped video frames. The key point is how to make full use of spatio-temporal interactions to extract more accurate representation. However, there are dil…

2022

Conditional Local Convolution for Spatio-Temporal Meteorological Forecasting

AAAI 2022technical

Spatio-temporal forecasting is challenging attributing to the high nonlinearity in temporal dynamics as well as complex location-characterized patterns in spatial domains, especially in fields like weather forecasting. Graph convolutions are usually used for modeling the spatial dependency in meteor…

2022

DLME: Deep Local-Flatness Manifold Embedding

ECCV 2022poster

"Manifold learning (ML) aims to seek low-dimensional embedding from high-dimensional data. The problem is challenging on real-world datasets, especially with under-sampling data, and we find that previous methods perform poorly in this case. Generally, ML methods first transform input data into a lo…

2022

Exploiting Sentiment and Common Sense for Zero-shot Stance Detection

COLING 2022main

The stance detection task aims to classify the stance toward given documents and topics. Since the topics can be implicit in documents and unseen in training data for zero-shot settings, we propose to boost the transferability of the stance detection model by using sentiment and commonsense knowledg…

2022

Knowledge Distillation Improves Graph Structure Augmentation for Graph Neural Networks

NeurIPS 2022accept

Graph (structure) augmentation aims to perturb the graph structure through heuristic or probabilistic rules, enabling the nodes to capture richer contextual information and thus improving generalization performance. While there have been a few graph structure augmentation methods proposed recently,…

Cited by 59SourcePDFScholar
2022

ProGCL: Rethinking Hard Negative Mining in Graph Contrastive Learning

ICML 2022spotlight

Contrastive Learning (CL) has emerged as a dominant technique for unsupervised representation learning which embeds augmented versions of the anchor close to each other (positive samples) and pushes the embeddings of other samples (negatives) apart. As revealed in recent studies, CL can benefit from…

2022

Towards Reasonable Budget Allocation in Untargeted Graph Structure Attacks via Gradient Debias

NeurIPS 2022accept

It has become cognitive inertia to employ cross-entropy loss function in classification related tasks. In the untargeted attacks on graph structure, the gradients derived from the attack objective are the attacker's basis for evaluating a perturbation scheme. Previous methods use negative cross-entr…

2020

Beyond 3DMM Space: Towards Fine-grained 3D Face Reconstruction

ECCV 2020poster

Recently, deep learning based 3D face reconstruction methods have shown promising results in both quality and efficiency. However, most of their training data is constructed by 3D Morphable Model, whose space spanned is only a small part of the shape space. As a result, the reconstruction results lo…

2020

Bridging the Gap Between Anchor-Based and Anchor-Free Detection via Adaptive Training Sample Selection

CVPR 2020oral

Object detection has been dominated by anchor-based detectors for several years. Recently, anchor-free detectors have become popular due to the proposal of FPN and Focal Loss. In this paper, we first point out that the essential difference between anchor-based and anchor-free detection is actually h…

Cited by 2298PDFcodeScholar
2020

Learning Meta Face Recognition in Unseen Domains

CVPR 2020oral

Face recognition systems are usually faced with unseen domains in real-world applications and show unsatisfactory performance due to their poor generalization. For example, a well-trained model on webface data cannot deal with the ID vs. Spot task in surveillance scenario. In this paper, we aim to l…

Cited by 189PDFcodeScholar
2020

Towards Fast, Accurate and Stable 3D Dense Face Alignment

ECCV 2020poster

Accurate and Stable 3D Dense Face Alignment","Existing methods of 3D dense face alignment mainly concentrate on accuracy, thus limiting the scope of their practical applications. In this paper, we propose a novel regression framework which makes a balance among speed, accuracy and stability. Firstly…

2019

A Dataset and Benchmark for Large-Scale Multi-Modal Face Anti-Spoofing

CVPR 2019poster

Face anti-spoofing is essential to prevent face recognition systems from a security breach. Much of the progresses have been made by the availability of face anti-spoofing benchmark datasets in recent years. However, existing face anti-spoofing benchmarks have limited number of subjects (<=170) and…

Cited by 215PDFScholar
2019

Unsupervised Graph Association for Person Re-Identification

ICCV 2019poster

In this paper, we propose an unsupervised graph association (UGA) framework to learn the underlying viewinvariant representations from the video pedestrian tracklets. The core points of UGA are mining the underlying cross-view associations and reducing the damage of noise associations. To this end,…

Cited by 131PDFcodeScholar
2018

Occlusion-aware R-CNN: Detecting Pedestrians in a Crowd

ECCV 2018poster

Pedestrian detection in crowded scenes is a challenging problem since the pedestrians often gather together and occlude each other. In this paper, we propose a new occlusion-aware R-CNN (OR-CNN) to improve the detection accuracy in the crowd. Specifically, we design a new aggregation loss to enforce…

Cited by 544SourcePDFScholar
2018

Single-Shot Refinement Neural Network for Object Detection

CVPR 2018poster

For object detection, the two-stage approach (e.g., Faster R-CNN) has been achieving the highest accuracy, whereas the one-stage approach (e.g., SSD) has the advantage of high efficiency. To inherit the merits of both while overcoming their disadvantages, in this paper, we propose a novel single-sho…

2017

Exclusivity-Consistency Regularized Multi-View Subspace Clustering

CVPR 2017spotlight

Multi-view subspace clustering aims to partition a set of multi-source data into their underlying groups. To boost the performance of multi-view clustering, numerous subspace learning algorithms have been developed in recent years, but with rare exploitation of the representation complementarity bet…

Cited by 324PDFScholar
2017

S3FD: Single Shot Scale-Invariant Face Detector

ICCV 2017poster

This paper presents a real-time face detector, named Single Shot Scale-invariant Face Detector (S3FD), which performs superiorly on various scales of faces with a single deep neural network, especially for small faces. Specifically, we try to solve the common problem that anchor-based detectors dete…

Cited by 887PDFcodeScholar
2015

High-Fidelity Pose and Expression Normalization for Face Recognition in the Wild

CVPR 2015poster

Pose and expression normalization is a crucial step to recover the canonical view of faces under arbitrary conditions, so as to improve the face recognition performance. An ideal normalization method is desired to be automatic, database independent and high-fidelity, where the face appearance should…

Cited by 726SourcePDFScholar
2015

Person Re-Identification by Local Maximal Occurrence Representation and Metric Learning

CVPR 2015poster

Person re-identification is an important technique towards automatic search of a person's presence in a surveillance video. Two fundamental problems are critical for person re-identification, feature representation and metric learning. An effective feature representation should be robust to illumina…

Cited by 2616SourcePDFScholar