7 citations · 20 across the 15 of their papers we have counts for
15 papers
SAVE: A Generalizable Framework for Multi-Condition Single-Cell Generation with Gene Block Attention
Jiahao Li, Jiayi Dong, Peng Ye +3
Modeling single-cell gene expression across diverse biological and technical conditions is crucial for characterizing cellular states and simulating unseen scenarios. Existing meth…
Fair splits flip the leaderboard: CHANRG reveals limited generalization in RNA secondary-structure prediction
Zhiyuan Chen, Zhenfeng Deng, Pan Deng +4
Accurate prediction of RNA secondary structure underpins transcriptome annotation, mechanistic analysis of non-coding RNAs, and RNA therapeutic design. Recent gains from deep learn…
scMRDR: A scalable and flexible framework for unpaired single-cell multi-omics data integration
Jianle Sun, Chaoqi Liang, Ran Wei +5
Advances in single-cell sequencing have enabled high-resolution profiling of diverse molecular modalities, while integrating unpaired multi-omics single-cell data remains challengi…
The Avengers: A Simple Recipe for Uniting Smaller Language Models to Challenge Proprietary Giants
Yiqun Zhang, Hao Li, Chenxu Wang +11
Proprietary giants are increasingly dominating the race for ever-larger language models. Can open-source, smaller models remain competitive across a broad range of tasks? In this p…
Attention Reallocation: Towards Zero-cost and Controllable Hallucination Mitigation of MLLMs
Chongjun Tu, Peng Ye, Dongzhan Zhou +4
Multi-Modal Large Language Models (MLLMs) stand out in various tasks but still struggle with hallucinations. While recent training-free mitigation methods mostly introduce addition…
Nature-Inspired Population-Based Evolution of Large Language Models
Yiqun Zhang, Peng Ye, Xiaocui Yang +5
Evolution, the engine behind the survival and growth of life on Earth, operates through the population-based process of reproduction. Inspired by this principle, this paper formall…
Revisiting Convolution Architecture in the Realm of DNA Foundation Models
Yu Bo, Weian Mao, Yanjun Shao +6
In recent years, a variety of methods based on Transformer and state space model (SSM) architectures have been proposed, advancing foundational DNA language models. However, there…
Model Decides How to Tokenize: Adaptive DNA Sequence Tokenization with MxDNA
Lifeng Qiao, Peng Ye, Yuchen Ren +5
Foundation models have made significant strides in understanding the genomic language of DNA sequences. However, previous models typically adopt the tokenization methods designed f…
Biology-Instructions: A Dataset and Benchmark for Multi-Omics Sequence Understanding Capability of Large Language Models
Haonan He, Yuchen Ren, Yining Tang +12
Large language models (LLMs) have shown remarkable capabilities in general domains, but their application to multi-omics biology remains underexplored. To address this gap, we intr…
Critic-V: VLM Critics Help Catch VLM Errors in Multimodal Reasoning
Di Zhang, Junxian Li, Jingdi Lei +10
Vision-language models (VLMs) have shown remarkable advancements in multimodal reasoning tasks. However, they still often generate inaccurate or irrelevant responses due to issues…
A CLIP-Powered Framework for Robust and Generalizable Data Selection
Suorong Yang, Peng Ye, Wanli Ouyang +2
Large-scale datasets have been pivotal to the advancements of deep learning models in recent years, but training on such large datasets invariably incurs substantial storage and co…
FNP: Fourier Neural Processes for Arbitrary-Resolution Data Assimilation
Kun Chen, Tao Chen, Peng Ye +5
Data assimilation is a vital component in modern global medium-range weather forecasting systems to obtain the best estimation of the atmospheric state by combining the short-term…
BEACON: Benchmark for Comprehensive RNA Tasks and Language Models
Yuchen Ren, Zhiyuan Chen, Lifeng Qiao +10
RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emerg…
CasCast: Skillful High-resolution Precipitation Nowcasting via Cascaded Modelling
Junchao Gong, Lei Bai, Peng Ye +5
Precipitation nowcasting based on radar data plays a crucial role in extreme weather prediction and has broad implications for disaster management. Despite progresses have been mad…
Toward Understanding BERT-Like Pre-Training for DNA Foundation Models
Chaoqi Liang, Lifeng Qiao, Peng Ye +9
With the success of large-scale pre-training in language tasks, there is an increasing trend of applying it to the domain of life sciences. In particular, pre-training methods base…