49 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…
While large and diverse datasets have driven recent advances in large models, identifying the optimal data mixture for pre-training and post-training remains a significant open problem. We address this challenge with FastMix, a novel framework that automates data mixture discovery while training onl…
Molecular interactions are a common phenomenon in physical chemistry field, which could produce unexpected biochemical properties harmful to humans, such as drug-drug interactions. Machine learning has the potential to deliver rapid and accurate predictions. However, the complexity of molecular stru…
Inferring molecular structures from multimodal spectroscopic measurements requires integrating complementary yet highly heterogeneous signals. However, the common paradigm of directly concatenating multispectral sequences can exhibit anomalous performance degradation, primarily due to pronounced het…
The discovery of novel proteins relies on sensitive protein identification, for which de novo peptide sequencing (DNPS) from mass spectra is a crucial approach. While deep learning has advanced DNPS, existing models inadequately enforce the fundamental mass consistency constraint—that a predicted pe
Although current watermarking techniques for 3D Gaussian Splatting (3DGS) are promising in protecting the copyrights of both 3DGS models and their rendered images, they greatly suffer from low watermark robustness and poor rendering quality when applying quantization to large 3DGS models to accommod
2D Gaussian Splatting has emerged as a novel image representation technique that can support efficient rendering on low-end devices. However, scaling to high-resolution images requires optimizing and storing millions of unstructured Gaussian primitives independently, leading to slow convergence and
Automatic Prompt Optimization (APO) enables Large Language Models (LLMs) to adapt to specific tasks while minimizing manual engineering costs. However, since existing APO approaches either rely solely on multi-round iterative procedures or use model-specific generators tailored to optimizing prompts…
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
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…
Existing molecular machine learning force fields (MLFFs) generally focus on the learning of atoms, molecules, and simple quantum chemical properties (such as energy and force), but ignore the importance of electron density (ED) $\rho(r)$ in accurately understanding molecular force fields (MFFs). ED…
Electron density (ED), which describes the probability distribution of electrons in space, is crucial for accurately understanding the energy and force distribution in molecular force fields (MFF). Existing machine learning force fields (MLFF) focus on mining appropriate physical quantities from the
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
Accurate prediction of ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties is crucial in drug development, as these properties directly impact a drug's efficacy and safety. However, existing multi-task learning models often face challenges related to noise interference 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…
In single-cell perturbation prediction, a central task is to forecast the effects of perturbing a gene unseen in the training data. The efficacy of such predictions depends on two factors: (1) the similarity of the target gene to those covered in the training data, which informs model (epistemic) un…
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…
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…
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…
Extracting rich molecular representation is a crucial prerequisite for accurate drug discovery. Recent molecular representation learning methods achieve impressive progress, but the paradigm of learning from a single modality gradually encounters the bottleneck of limited representation capabilities…
In robot-assisted retinal surgery, a Remote Center of Motion (Rcm) allows the surgical instrument to rotate around a distal fixed point without any lateral translations. The Rcm point should be perfectly aligned inside the trocar. Otherwise, unexpected tool translations at the expected remote center…
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…
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…
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…
Intent learning, which aims to learn users' intents for user understanding and item recommendation, has become a hot research spot in recent years. However, existing methods suffer from complex and cumbersome alternating optimization, limiting performance and scalability. To this end, we propose a n…
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…
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…
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…
In this paper, we address the challenge of accurately modeling and predicting Gibbs free energy in solute-solvent interactions, a pivotal yet complex aspect in the field of chemical modeling. Traditional approaches, primarily relying on deep learning models, face limitations in capturing the intrica…
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…
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…
Due to the increasing popularity of Artificial Intelligence (AI), more and more backdoor attacks are designed to mislead Deep Neural Network (DNN) predictions by manipulating training samples or processes. Although backdoor attacks have been investigated in various scenarios, they still suffer from…
Deep learning has achieved remarkable success in learning representations for molecules, which is crucial for various biochemical applications, ranging from property prediction to drug design. However, training Deep Neural Networks (DNNs) from scratch often requires abundant labeled molecules, which…
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…
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…
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…
The linear sequence of amino acids determines protein structure and function. Protein design, known as the inverse of protein structure prediction, aims to obtain a novel protein sequence that will fold into the defined structure. Recent works on computational protein design have studied designing s…
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)…
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…
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…
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…
Due to the prosperity of Artificial Intelligence (AI) techniques, more and more backdoors are designed by adversaries to attack Deep Neural Networks (DNNs). Although the state-of-the-art method Neural Attention Distillation (NAD) can effectively erase backdoor triggers from DNNs, it still suffers fr…
Datasets with noisy labels present challenges for training Deep Neural Networks (DNNs) with high generalization ability. An direct idea is to correct the noisy labels for robust learning. However, existing label correction methods can not handle with heavy noise or datasets with samples of many cate…
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…
Deep convolutional networks (CNNs) show their potential in image colorization for producing plausible results. Recently, the attention mechanism further boosts the performances of CNNs by constructing channel and spatial interactions. However, existing attention methods are performed in a single-sca…
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…
Image colorization recovers a colorful image from a grayscale one. Trained by large-scale datasets, recent deep neural networks based methods can produce impressive colorful images. However, they usually directly train a single network using training images of fixed resolution. It is hard for such a…
Clear Corneal Incision, a challenging step in cataract surgery, and important to the overall quality of the surgery. New surgeons usually spend one full year trying to perfect their incision, but even after such rigorous training deficient incisions can still occur. This paper proposes an autonomous…