Co-Learning: Code Learning for Multi-Agent Reinforcement Collaborative Framework with Conversational Natural Language Interfaces

Online question-and-answer (Q\&A) systems based on the Large Language Model (LLM) have progressively diverged from recreational to professional use. This paper proposed a Multi-Agent framework with environmentally reinforcement learning (E-RL) for code correction called Code Learning (Co-Learning) community, assisting beginners to correct code errors independently. It evaluates the performance of multiple LLMs from an original dataset with 702 error codes, uses it as a reward or punishment criterion for E-RL; Analyzes input error codes by the current agent; selects the appropriate LLM-based agent to achieve optimal error correction accuracy and reduce correction time. Experiment results showed that 3\% improvement in Precision score and 15\% improvement in time cost as compared with no E-RL method respectively. Our source code is available at: https://github.com/yuqian2003/Co_Learning

Deep Feature Embedding for Tabular Data

Tabular data learning has extensive applications in deep learning but its existing embedding techniques are limited in numerical and categorical features such as the inability to capture complex relationships and engineering. This paper proposes a novel deep embedding framework with leverages lightweight deep neural networks to generate effective feature embeddings for tabular data in machine learning research. For numerical features, a two-step feature expansion and deep transformation technique is used to capture copious semantic information. For categorical features, a unique identification vector for each entity is referred by a compact lookup table with a parameterized deep embedding function to uniform the embedding size dimensions, and transformed into a embedding vector using deep neural network. Experiments are conducted on real-world datasets for performance evaluation.

AMPCliff: quantitative definition and benchmarking of activity cliffs in antimicrobial peptides

Activity cliff (AC) is a phenomenon that a pair of similar molecules differ by a small structural alternation but exhibit a large difference in their biochemical activities. The AC of small molecules has been extensively investigated but limited knowledge is accumulated about the AC phenomenon in peptides with canonical amino acids. This study introduces a quantitative definition and benchmarking framework AMPCliff for the AC phenomenon in antimicrobial peptides (AMPs) composed by canonical amino acids. A comprehensive analysis of the existing AMP dataset reveals a significant prevalence of AC within AMPs. AMPCliff quantifies the activities of AMPs by the metric minimum inhibitory concentration (MIC), and defines 0.9 as the minimum threshold for the normalized BLOSUM62 similarity score between a pair of aligned peptides with at least two-fold MIC changes. This study establishes a benchmark dataset of paired AMPs in Staphylococcus aureus from the publicly available AMP dataset GRAMPA, and conducts a rigorous procedure to evaluate various AMP AC prediction models, including nine machine learning, four deep learning algorithms, four masked language models, and four generative language models. Our analysis reveals that these models are capable of detecting AMP AC events and the pre-trained protein language ESM2 model demonstrates superior performance across the evaluations. The predictive performance of AMP activity cliffs remains to be further improved, considering that ESM2 with 33 layers only achieves the Spearman correlation coefficient=0.50 for the regression task of the MIC values on the benchmark dataset. Source code and additional resources are available at https://www.healthinformaticslab.org/supp/ or https://github.com/Kewei2023/AMPCliff-generation.

PepHarmony: A Multi-View Contrastive Learning Framework for Integrated Sequence and Structure-Based Peptide Encoding

Recent advances in protein language models have catalyzed significant progress in peptide sequence representation. Despite extensive exploration in this field, pre-trained models tailored for peptide-specific needs remain largely unaddressed due to the difficulty in capturing the complex and sometimes unstable structures of peptides. This study introduces a novel multi-view contrastive learning framework PepHarmony for the sequence-based peptide encoding task. PepHarmony innovatively combines both sequence- and structure-level information into a sequence-level encoding module through contrastive learning. We carefully select datasets from the Protein Data Bank (PDB) and AlphaFold database to encompass a broad spectrum of peptide sequences and structures. The experimental data highlights PepHarmony's exceptional capability in capturing the intricate relationship between peptide sequences and structures compared with the baseline and fine-tuned models. The robustness of our model is confirmed through extensive ablation studies, which emphasize the crucial roles of contrastive loss and strategic data sorting in enhancing predictive performance. The proposed PepHarmony framework serves as a notable contribution to peptide representations, and offers valuable insights for future applications in peptide drug discovery and peptide engineering. We have made all the source code utilized in this study publicly accessible via GitHub at https://github.com/zhangruochi/PepHarmony or http://www.healthinformaticslab.org/supp/.