45 accepted papers
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
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…
Diffusion models generate synthetic images through an iterative refinement process. However, the misalignment between the simulation-free objective and the iterative process often causes accumulated gradient error along the sampling trajectory, which leads to unsatisfactory results and a failure to
While passive agents merely follow instructions, proactive agents align with higher-level objectives, such as assistance and safety by continuously monitoring the environment to determine when and how to act. However, developing proactive agents is hindered by the lack of specialized resources. To a…
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…
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…
Teaching large language models (LLMs) to be faithful in the provided context is crucial for building reliable information-seeking systems. Therefore, we propose a systematic framework, CANOE, to reduce faithfulness hallucinations of LLMs across different downstream tasks without human annotations. S
Traditional network inference methods, such as Gaussian Graphical Models, which are built on continuity and homogeneity, face challenges when modeling discrete data and heterogeneous frameworks. Furthermore, under high-dimensionality, the parameter estimation of such models can be hindered by the no…
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…
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…
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…
Score Distillation Sampling (SDS) has been successfully extended to text-driven 3D scene editing with 2D pretrained diffusion models. However, SDS-based editing methods suffer from lengthy optimization processes with slow inference and low quality. We attribute the issue of lengthy optimization to t…
Retrieval-augmented generation (RAG) enhances large language models (LLMs) by integrating external knowledge. A critical yet underexplored challenge in RAG is document segmentation, also known as document chunking. Existing widely-used rule-based chunking methods usually lead to suboptimal splits, w…
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…
Automatic understanding of figures in scientific papers is challenging since they often contain subfigures and subcaptions in complex layouts. In this paper, we propose FigEx, a vision-language model to extract aligned pairs of subfigures and subcaptions from scientific papers. We also release BioSc
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…
Knowledge Graph Completion (KGC), which aims to infer missing or incomplete facts, is a crucial task for KGs. However, integrating the vital structural information of KGs into Large Language Models (LLMs) and outputting predictions deterministically remains challenging. To address this, we propose a…
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…
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…
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…
Holistically measuring societal biases of large language models is crucial for detecting and reducing ethical risks in highly capable AI models. In this work, we present a Chinese Bias Benchmark dataset that consists of over 100K questions jointly constructed by human experts and generative language…
What a large language model (LLM) would respond in ethically relevant context? In this paper, we curate a large benchmark CMoralEval for morality evaluation of Chinese LLMs. The data sources of CMoralEval are two-fold: 1) a Chinese TV program discussing Chinese moral norms with stories from the soci…
Assessing the capabilities of large language models (LLMs) as agents in decision making and operational tasks is crucial for the development of LLM-as-agent service. We propose CToolEval, a benchmark designed to evaluate LLMs in the context of Chinese societal applications, featuring 398 APIs across…
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…
Open Domain Question Answering (ODQA) has been advancing rapidly in recent times, driven by significant developments in dense passage retrieval and pretrained language models. State-of-the-art models typically incorporate the FiD framework, which is composed by a neural retriever alongside an encode…
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…
Instruction tuning has demonstrated its superiority in unlocking the abilities of pre-trained large language models (LLMs), including their capability to respond to diverse human instructions and conduct complex reasoning. In order to further enhance the continuous learning capabilities of pre-train…
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…
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…
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…
The rapid development of Chinese large language models (LLMs) poses big challenges for efficient LLM evaluation. While current initiatives have introduced new benchmarks or evaluation platforms for assessing Chinese LLMs, many of these focus primarily on capabilities, usually overlooking potential a…
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…
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…
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…
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…
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…
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…
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…
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…
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…
Recently, prompt tuning (PT) has gained increasing attention as a parameter-efficient way of tuning pre-trained language models (PLMs). Despite extensively reducing the number of tunable parameters and achieving satisfying performance, PT is training-inefficient due to its slow convergence. To impro…
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,…
Although contextualized embeddings generated from large-scale pre-trained models perform well in many tasks, traditional static embeddings (e.g., Skip-gram, Word2Vec) still play an important role in low-resource and lightweight settings due to their low computational cost, ease of deployment, and st…
Human behavior is the confluence of output from voluntary and involuntary motor systems. The neural activities that mediate behavior, from individual cells to distributed networks, are in a state of constant flux. Artificial intelligence (AI) research over the past decade shows that behavior, in the…
Existing pre-trained language models (PLMs) are often computationally expensive in inference, making them impractical in various resource-limited real-world applications. To address this issue, we propose a dynamic token reduction approach to accelerate PLMs’ inference, named TR-BERT, which could fl…