arXiv subjects

Xiaohu Zhu

Publications and source records attributed to Xiaohu Zhu.

3 recordsLinked to original sources

arXiv2026

AMPBench-MT: A Homology-Controlled Benchmark for Antimicrobial Peptide Potency, Spectrum, and Safety Prediction

Computational AMP discovery is often evaluated through AMP/non-AMP recognition, yet follow-up decisions depend on assay-derived evidence such as target-species potency, hemolysis, toxicity, and selectivity. Existing AMP and peptide benchmarks cover binary recognition, multilabel annotation, assay regression, or broader peptide-model comparison, but they do not jointly place AMP recognition, species-conditioned potency, spectrum, safety-facing proxy endpoints, and cross-endpoint behavior within one sequence-homology-controlled protocol. To address this problem, we introduce AMPBench-MT, a provenance-preserving benchmark that standardizes canonical peptide records and organizes them into binary recognition, species-conditioned pMIC regression, and endpoint-specific potency and safety-facing readouts. Across 161 endpoint-specific model evaluations, high binary performance does not reliably indicate assay-endpoint behavior. Frozen protein-language-model embeddings form the leading pMIC error cluster, while graph and classical regressors remain close. Spectrum labels further reveal that PR-oriented metrics can be misleading under scarce observed negatives, whereas low-toxicity, HC50 hemolysis, and selectivity expose smaller but more assay-facing signals. AMPBench-MT shows that AMP evaluation should move beyond recognition leaderboards toward endpoint-aware evidence auditing. Our proposed benchmark is available at https://huggingface.co/datasets/ZihengZhou06/AMPBench-MT.

cs.LG↗

arXiv2024

Large Language Model Enhanced Text-to-SQL Generation: A Survey

Text-to-SQL translates natural language queries into Structured Query Language (SQL) commands, enabling users to interact with databases using natural language. Essentially, the text-to-SQL task is a text generation task, and its development is primarily dependent on changes in language models. Especially with the rapid development of Large Language Models (LLMs), the pattern of text-to-SQL has undergone significant changes. Existing survey work mainly focuses on rule-based and neural-based approaches, but it still lacks a survey of Text-to-SQL with LLMs. In this paper, we survey the large language model enhanced text-to-SQL generations, classifying them into prompt engineering, fine-tuning, pre-trained, and Agent groups according to training strategies. We also summarize datasets and evaluation metrics comprehensively. This survey could help people better understand the pattern, research status, and challenges of LLM-based text-to-SQL generations.

cs.DB↗

arXiv2022

GAFX: A General Audio Feature eXtractor

Most machine learning models for audio tasks are dealing with a handcrafted feature, the spectrogram. However, it is still unknown whether the spectrogram could be replaced with deep learning based features. In this paper, we answer this question by comparing the different learnable neural networks extracting features with a successful spectrogram model and proposed a General Audio Feature eXtractor (GAFX) based on a dual U-Net (GAFX-U), ResNet (GAFX-R), and Attention (GAFX-A) modules. We design experiments to evaluate this model on the music genre classification task on the GTZAN dataset and perform a detailed ablation study of different configurations of our framework and our model GAFX-U, following the Audio Spectrogram Transformer (AST) classifier achieves competitive performance.

eess.AS↗