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.

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.

FlexMS is a flexible framework for benchmarking deep learning-based mass spectrum prediction tools in metabolomics

The identification and property prediction of chemical molecules is of central importance in the advancement of drug discovery and material science, where the tandem mass spectrometry technology gives valuable fragmentation cues in the form of mass-to-charge ratio peaks. However, the lack of experimental spectra hinders the attachment of each molecular identification, and thus urges the establishment of prediction approaches for computational models. Deep learning models appear promising for predicting molecular structure spectra, but overall assessment remains challenging as a result of the heterogeneity in methods and the lack of well-defined benchmarks. To address this, our contribution is the creation of benchmark framework FlexMS for constructing and evaluating diverse model architectures in mass spectrum prediction. With its easy-to-use flexibility, FlexMS supports the dynamic construction of numerous distinct combinations of model architectures, while assessing their performance on preprocessed public datasets using different metrics. In this paper, we provide insights into factors influencing performance, including the structural diversity of datasets, hyperparameters like learning rate and data sparsity, pretraining effects, metadata ablation settings and cross-domain transfer learning analysis. This provides practical guidance in choosing suitable models. Moreover, retrieval benchmarks simulate practical identification scenarios and score potential matches based on predicted spectra.