arXiv subjects

Yunhua Zhong

Publications and source records attributed to Yunhua Zhong.

4 recordsLinked to original sources

arXiv2026

Transferable Mass Spectrum Prediction via Reference-Guided Test-time Specialization

Tandem mass spectrum prediction supports compound identification across metabolomics, natural-product discovery, and environmental analysis. However, pretrained predictors often degrade under shifts in chemical space and acquisition conditions, while retraining domain-specific models from scratch is costly. We introduce SPARC, a retrieval-guided test-time specialization framework that adapts a pretrained predictor using a spectral reference library without accessing test-query spectra. For each target query, SPARC retrieves chemically related reference spectra to recalibrate fragment intensities within the learned fragmentation space. During Transfer, SPARC combines reference-guided spectral adaptation with reliability-aware consistency, using reconstruction behavior on retrieved spectra to selectively preserve trustworthy predictions during continual specialization. Across MassSpecGym, NPLIB1 and application-specific GNPS libraries, SPARC improves spectral prediction under multiple transfer settings. These results establish retrieval-guided test-time specialization as a practical strategy for extending pretrained MS/MS predictors to specific chemical and acquisition domains, with continual test-time training providing further refinement during deployment.

cs.LG↗

arXiv2026

FlexMS: A Unified Public Benchmark for Molecule Tandem Mass Spectrum Prediction

Tandem mass spectrometry (MS/MS) is central to small molecule identification, but current deep learning systems for spectrum prediction still remain difficult to evaluate and deploy in practice. While novel architectures constantly claim state-of-the-art performance, inconsistent metadata conditioning and entangled preprocessing pipelines hinder fair architectural comparisons. Besides, existing evaluations are often restricted to curated datasets, failing to capture the heterogeneity and cross-domain shifts of real-world metabolomics. Furthermore, current benchmarks lack difficulty-aware diagnostics and leave blind to how models behave under specific compute or data constraints. To address this, we present FlexMS, a modular public-data benchmark framework that standardizes MS/MS prediction across public resources while keeping molecular encoders, metadata conditioning, predictor heads, and downstream retrieval under one protocol. FlexMS establishes a fair evaluation playground which significantly lowers the barrier for integrating new predictive tools. Rather than solely optimizing for average scores, FlexMS augments aggregate accuracy with difficulty-aware diagnostics, providing actionable guidance on model selection across different compute constraints, data scales, and downstream retrieval objectives. Ultimately, FlexMS provides the community with a reproducible standard to identify which algorithmic conclusions are stable and which operating points are most viable in practice.

cs.AI↗

arXiv2026

PepSpecBench: A Unified Evaluation Benchmark for Peptide Tandem Mass Spectrometry Prediction

Tandem mass spectrometry provides a high-throughput framework for identifying and quantifying proteins in complex biological samples. In computational proteomics, predicting peptide MS/MS spectra is a critical task, enabling downstream applications such as large-scale peptide identification and quantification. While deep learning architectures have substantially improved prediction accuracy, three evaluation challenges obscure the true progress of the field. First, inconsistent data preprocessing and incompatible model output spaces hinder fair model comparison. Second, flawed data splitting strategies can permit hidden sequence leakage and inflate reported performance. Third, existing evaluations typically lack comprehensive cross-species benchmarking and systematic assessment of model robustness to influential experimental conditions. To address these challenges, we propose PepSpecBench, a unified benchmark for peptide MS/MS spectrum prediction. PepSpecBench standardizes data preprocessing across complementary public datasets, enforces a strict backbone-disjoint splitting strategy to eliminate sequence leakage, and evaluates diverse architectures within a shared fragment-ion representation space. It further introduces a comprehensive multi-species evaluation suite and physically grounded metadata perturbation probes to assess model robustness and instrument awareness. We uncover previously unrecognized performance discrepancies and robustness limitations across six representative models, providing actionable insights for future model design, evaluation and practical deployment.

cs.LG↗

arXiv2026

Unlocking the Potential of Grounding DINO in Videos: Parameter-Efficient Adaptation for Limited-Data Spatial-Temporal Localization

Spatio-temporal video grounding (STVG) aims to localize queried objects within dynamic video segments. Prevailing fully-trained approaches are notoriously data-hungry. However, gathering large-scale STVG data is exceptionally challenging: dense frame-level bounding boxes and complex temporal language alignments are prohibitively expensive to annotate, especially for specialized video domains. Consequently, conventional models suffer from severe overfitting on these inherently limited datasets, while zero-shot foundational models lack the task-specific temporal awareness needed for precise localization. To resolve this small-data challenge, we introduce ST-GD, a data-efficient framework that adapts pre-trained 2D visual-language models (e.g., Grounding DINO) to video tasks. To avoid destroying pre-trained priors on small datasets, ST-GD keeps the base model frozen and strategically injects lightweight adapters (~10M trainable parameters) to instill spatio-temporal awareness, alongside a novel temporal decoder for boundary prediction. This design naturally counters data scarcity. Consequently, ST-GD excels in data-scarce scenarios, achieving highly competitive performance on the limited-scale HC-STVG v1/v2 benchmarks, while maintaining robust generalization on the VidSTG dataset. This validates ST-GD as a powerful paradigm for complex video understanding under strict small-data constraints.

cs.CV↗