arXiv subjects

Boming Kang

Publications and source records attributed to Boming Kang.

3 recordsLinked to original sources

arXiv2026

LC-SEPLM: long-range contact-supervised adaptation for sequence-only protein representation learning

Protein language models learn transferable sequence representations. However, because they primarily model contextual dependencies along amino-acid sequences, their training objectives do not explicitly constrain the model to learn three-dimensional residue contacts formed after folding . Here, we introduce LC-SEPLM (Long-range Contact-supervised ESM Protein Language Model), which adapts ESM2 with LoRA and long-range residue-pair contact supervision while retaining sequence-only downstream inference. Pair-specific queries use cross-attention over the complete sequence to extract global sequence context associated with long-range spatial contacts. To expose the model to diverse structural information, we trained LC-SEPLM on 500,000 AlphaFold Swiss-Prot proteins. In downstream evaluation, LC-SEPLM improved all eight protein-level tasks relative to ESM2. The largest gain occurred in remote-homology recognition, where macro-F1 increased from 0.6122 to 0.6769 (+0.0647, or 6.47 percentage points). On the official ESM-S EC benchmark, LC-SEPLM also outperformed ESM-S with a maximum absolute gain of 0.1771. These results support residue-pair contact supervision as a bounded route for introducing structural information into protein sequence representations while preserving sequence-only inference.

cs.LG↗

arXiv2024

Ratio law: mathematical descriptions for a universal relationship between AI performance and input samples

Artificial intelligence based on machine learning and deep learning has made significant advances in various fields such as protein structure prediction and climate modeling. However, a central challenge remains: the "black box" nature of AI, where precise quantitative relationships between inputs and outputs are often lacking. Here, by analyzing 323 AI models trained to predict human essential proteins, we uncovered a ratio law showing that model performance and the ratio of minority to majority samples can be closely linked by two concise equations. Moreover, we mathematically proved that an AI model achieves its optimal performance on a balanced dataset. More importantly, we next explore whether this finding can further guide us to enhance AI models' performance. Therefore, we divided the imbalanced dataset into several balanced subsets to train base classifiers, and then applied a bagging-based ensemble learning strategy to combine these base models. As a result, the equation-guided strategy substantially improved model performance, with increases of 4.06% and 5.28%, respectively, outperforming traditional dataset balancing techniques. Finally, we confirmed the broad applicability and generalization of these equations using different types of classifiers and 10 additional, diverse binary classification tasks. In summary, this study reveals two equations precisely linking AI's input and output, which could be helpful for unboxing the mysterious "black box" of AI.

cs.LG↗

arXiv2024

ProLLM: Protein Chain-of-Thoughts Enhanced LLM for Protein-Protein Interaction Prediction

The prediction of protein-protein interactions (PPIs) is crucial for understanding biological functions and diseases. Previous machine learning approaches to PPI prediction mainly focus on direct physical interactions, ignoring the broader context of nonphysical connections through intermediate proteins, thus limiting their effectiveness. The emergence of Large Language Models (LLMs) provides a new opportunity for addressing this complex biological challenge. By transforming structured data into natural language prompts, we can map the relationships between proteins into texts. This approach allows LLMs to identify indirect connections between proteins, tracing the path from upstream to downstream. Therefore, we propose a novel framework ProLLM that employs an LLM tailored for PPI for the first time. Specifically, we propose Protein Chain of Thought (ProCoT), which replicates the biological mechanism of signaling pathways as natural language prompts. ProCoT considers a signaling pathway as a protein reasoning process, which starts from upstream proteins and passes through several intermediate proteins to transmit biological signals to downstream proteins. Thus, we can use ProCoT to predict the interaction between upstream proteins and downstream proteins. The training of ProLLM employs the ProCoT format, which enhances the model's understanding of complex biological problems. In addition to ProCoT, this paper also contributes to the exploration of embedding replacement of protein sites in natural language prompts, and instruction fine-tuning in protein knowledge datasets. We demonstrate the efficacy of ProLLM through rigorous validation against benchmark datasets, showing significant improvement over existing methods in terms of prediction accuracy and generalizability. The code is available at: https://github.com/MingyuJ666/ProLLM.

q-bio.BM↗