4 papers
Breaking the Correlation Plateau: On the Optimization and Capacity Limits of Attention-Based Regressors
Jingquan Yan, Yuwei Miao, Peiran Yu +1
Attention-based regression models are often trained by jointly optimizing Mean Squared Error (MSE) loss and Pearson correlation coefficient (PCC) loss, emphasizing the magnitude of…
GenePheno: Interpretable Gene Knockout-Induced Phenotype Abnormality Prediction from Gene Sequences
Jingquan Yan, Yuwei Miao, Lei Yu +4
Exploring how genetic sequences shape phenotypes is a fundamental challenge in biology and a key step toward scalable, hypothesis-driven experimentation. The task is complicated by…
GoBERT: Gene Ontology Graph Informed BERT for Universal Gene Function Prediction
Yuwei Miao, Yuzhi Guo, Hehuan Ma +4
Exploring the functions of genes and gene products is crucial to a wide range of fields, including medical research, evolutionary biology, and environmental science. However, disco…
UniEntrezDB: Large-scale Gene Ontology Annotation Dataset and Evaluation Benchmarks with Unified Entrez Gene Identifiers
Yuwei Miao, Yuzhi Guo, Hehuan Ma +5
Gene studies are crucial for fields such as protein structure prediction, drug discovery, and cancer genomics, yet they face challenges in fully utilizing the vast and diverse info…