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This paper applies a structure-informed deep Q-network to decide when a small molecule needs further spectroscopic measurement and which measurement to request. On simulated MS/MS, IR, and NMR data, it raised Top-1 accuracy substantially with few extra measurements, but the results come from simulated spectra and fixed candidate sets, so real-world performance remains untested. For ML readers, the useful takeaway is the reward design that uses candidate-structure ambiguity to balance accuracy against acquisition cost.
From MS/MS evidence to adaptive spectroscopic characterization: Reinforcement learning guided by candidate molecular structures
arXiv:2610.40264v1 Announce Type: new Abstract: Small-molecule identification from tandem mass spectrometry (MS/MS) may require complementary measurements. Herein, we propose a structure-informed deep Q-network (SI-DQN) that uses existing MS/MS evidence to decide whether further characterization is needed, which measurement to request, and when to stop. The policy combines spectral representations and candidate rankings with score-weighted descriptors of the candidates' chemical features and structural differences. The policy was evaluated on 79,462 held-out samples with simulated MS/MS, infrared (IR), and nuclear magnetic resonance (NMR) spectra from the Multimodal Spectroscopic Dataset. Evaluation used fixed hard candidate sets containing the correct structure and equal normalized acquisition costs. Averaged across three training runs, SI-DQN increased Top-1 accuracy from 80.10% to 93.78% for positive-ion MS/MS starts and from 70.44% to 93.31% for negative-ion starts. The corresponding mean additional measurement counts were only 0.227 and 0.340 per sample, respectively. Complete acquisition achieved 97.72% accuracy with four additions, whereas SI-DQN reduced the additional measurement count by 94.3% and 91.5%. Relative to a rule-based policy, SI-DQN reduced the composite loss combining terminal ranking error and acquisition cost by 19.3% and 25.5%. Adding structural information to DQN further improved accuracy while reducing requests across all three training runs. At comparable ranking uncertainty, SI-DQN increased request rates relative to DQN more strongly in groups with high structural disagreement, where larger reductions in composite loss were also observed. Together, these results support using the ambiguity among candidate structures after MS/MS analysis to guide further characterization, providing a quantitative basis for balancing identification performance against subsequent measurement effort.
Abstract:Small-molecule identification from tandem mass spectrometry (MS/MS) may require complementary measurements. Herein, we propose a structure-informed deep Q-network (SI-DQN) that uses existing MS/MS evidence to decide whether further characterization is needed, which measurement to request, and when to stop. The policy combines spectral representations and candidate rankings with score-weighted descriptors of the candidates' chemical features and structural differences. The policy was evaluated on 79,462 held-out samples with simulated MS/MS, infrared (IR), and nuclear magnetic resonance (NMR) spectra from the Multimodal Spectroscopic Dataset. Evaluation used fixed hard candidate sets containing the correct structure and equal normalized acquisition costs. Averaged across three training runs, SI-DQN increased Top-1 accuracy from 80.10% to 93.78% for positive-ion MS/MS starts and from 70.44% to 93.31% for negative-ion starts. The corresponding mean additional measurement counts were only 0.227 and 0.340 per sample, respectively. Complete acquisition achieved 97.72% accuracy with four additions, whereas SI-DQN reduced the additional measurement count by 94.3% and 91.5%. Relative to a rule-based policy, SI-DQN reduced the composite loss combining terminal ranking error and acquisition cost by 19.3% and 25.5%. Adding structural information to DQN further improved accuracy while reducing requests across all three training runs. At comparable ranking uncertainty, SI-DQN increased request rates relative to DQN more strongly in groups with high structural disagreement, where larger reductions in composite loss were also observed. Together, these results support using the ambiguity among candidate structures after MS/MS analysis to guide further characterization, providing a quantitative basis for balancing identification performance against subsequent measurement effort.
17 pages, 5 figures, 2 tables. Supporting information: 10 pages, 3 figures and 7 tables, provided as an ancillary PDF
Machine Learning (cs.LG)
arXiv:2610.40264 [cs.LG]
(or arXiv:2610.40264v1 [cs.LG] for this version)
https://doi.org/10.48550/arXiv.2610.40264 Focus to learn more arXiv-issued DOI via DataCite (pending registration)
supplementary.pdf
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