26 accepted papers
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…
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…
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…
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…
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
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
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…
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…
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
The Retrieval-Augmented Language Model (RALM) has demonstrated remarkable performance on knowledge-intensive tasks by integrating external knowledge during inference, which mitigates the factual hallucinations inherited in large language models (LLMs). Despite these advancements, challenges persist…
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…
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…
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…
Origin-destination (OD) crowd flow, if more accurately inferred at a fine-grained level, has the potential to enhance the efficacy of various urban applications. While in practice for mining OD crowd flow with effect, the problem of spatially interpolating OD crowd flow occurs since the ineluctable…
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…
We consider a problem of placing generators of rewards to be collected by randomly moving agents in a network. In many settings, the precise mobility pattern may be one of several possible, based on parameters outside our control, such as weather conditions. The placement should be robust to this un…
Visualization recommendations, which aim to automatically match proper visual charts for specific data tables, can significantly simplify the data analysis process. Traditional approaches in this domain have primarily relied on rule-based or machine learning-based methodologies. These methods often…
The essential task of urban planning is to generate the optimal land-use configuration of a target area. However, traditional urban planning is time-consuming and labor-intensive. Deep generative learning gives us hope that we can automate this planning process and come up with the ideal urban plans…
Recently, efficient fine-tuning of large-scale pre-trained models has attracted increasing research interests, where linear probing (LP) as a fundamental module is involved in exploiting the final representations for task-dependent classification. However, most of the existing methods focus on how t…
With the development of medical digitization, the extraction and structuring of Electronic Medical Records (EMRs) have become challenging but fundamental tasks. How to accurately and automatically extract structured information from medical dialogues is especially difficult because the information n…
Recent years have witnessed a large amount of decentralized data in multiple (edge) devices of end-users, while the aggregation of the decentralized data remains difficult for machine learning jobs due to laws or regulations. Federated Learning (FL) emerges as an effective approach to handling decen…
Recently many efforts have been devoted to applying graph neural networks (GNNs) to molecular property prediction which is a fundamental task for computational drug and material discovery. One of major obstacles to hinder the successful prediction of molecular property by GNNs is the scarcity of lab…
The novel coronavirus disease (COVID-19) has crushed daily routines and is still rampaging through the world. Existing solution for nonpharmaceutical interventions usually needs to timely and precisely select a subset of residential urban areas for containment or even quarantine, where the spatial d…
The task of multi-turn text-to-SQL semantic parsing aims to translate natural language utterances in an interaction into SQL queries in order to answer them using a database which normally contains multiple table schemas. Previous studies on this task usually utilized contextual information to enric…