4 papers
Inter-Residue Geometry Attention for Antibody-Specific Epitope Prediction
Chuanliu Fan, Nan Yu, Junjie Wu +1
Antibody-specific epitope prediction aims to identify which antigen residues are recognized by a given antibody, a task that depends on the three-dimensional complementarity betwee…
Interleaved Tool-Call Reasoning for Protein Function Understanding
Chuanliu Fan, Zicheng Ma, Huanran Meng +6
Recent advances in large language models (LLMs) have highlighted the effectiveness of chain-of-thought reasoning in symbolic domains such as mathematics and programming. However, o…
ProtTeX-CC: Activating In-Context Learning in Protein LLM via Two-Stage Instruction Compression
Chuanliu Fan, Zicheng Ma, Jun Gao +5
Recent advances in protein large language models, such as ProtTeX, represent both side-chain amino acids and backbone structure as discrete token sequences of residue length. While…
Adaptive Sparse Softmax: An Effective and Efficient Softmax Variant
Qi Lv, Lei Geng, Ziqiang Cao +4
Softmax with the cross entropy loss is the standard configuration for current neural classification models. The gold score for a target class is supposed to be 1, but it is never r…