arXiv:2606. 11868v1 Announce Type: new Abstract: De novo peptide sequencing from tandem mass spectrometry is pivotal in proteomics, enabling identification of novel peptides without reference databases.
arXiv:2602. 22822v3 Announce Type: replace Abstract: 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.
arXiv:2607. 23607v1 Announce Type: new Abstract: Molecular structure elucidation from tandem mass spectra (MS/MS) is a central inverse problem in analytical chemistry.
arXiv:2608. 01924v2 Announce Type: replace-cross Abstract: Personalized neoantigen prediction is challenging due to the scarcity of positive samples, the noise of the experimental data, the severe class imbalance trait and the complex of immunogenicity features.
arXiv:2606. 18302v1 Announce Type: cross Abstract: Correct identification of fish species is highly significant for food security, economic development, and climate resilience in Bangladesh.
arXiv:2606. 05139v1 Announce Type: new Abstract: The rapid advancement of high-throughput sequencing has led to large, high-dimensional omics datasets.
arXiv:2606. 05225v1 Announce Type: cross Abstract: Untargeted liquid chromatography-high-resolution mass spectrometry (LC-HRMS) detects thousands of molecular features per sample, yet only 2-20% receive confident structural annotations.
arXiv:2606. 08191v1 Announce Type: cross Abstract: Token aggregation is a common bottleneck in models that map token representations to sample-level predictions, yet most pooling methods operate only in the original token domain.
arXiv:2607. 04774v1 Announce Type: new Abstract: Untargeted tandem mass spectrometry (MS/MS) detects thousands of small molecules per biological sample, yet most go unidentified because they are absent from spectral libraries.
arXiv:2608. 08182v1 Announce Type: cross Abstract: Machine learning models for MALDI-TOF mass spectrometry have shown considerable promise for clinical microbiology tasks such as microbial identification and antimicrobial resistance prediction.
arXiv:2604. 16648v2 Announce Type: replace Abstract: Tandem mass spectrometry is prominent in scientific discovery workflows for identifying unknown small molecules, yet high-throughput structural elucidation remains challenging.
arXiv:2607. 14070v1 Announce Type: cross Abstract: Genomic foundation models such as Evo 2 learn rich sequence representations, but their value for biosecurity screening is largely unexplored.
arXiv:2606. 08100v1 Announce Type: new Abstract: Multimodal $\Delta\Delta G$ predictors integrating protein language models with inverse-folding representations achieve strong in-distribution accuracy on the Megascale dataset but exhibit limited robustness on out-of-distribution (OOD) proteins, persistent forward-reverse bias on paired-mutation benchmarks, and under-representation of rare stabilizing mutations.