pharmaceutical data engineers

Abstract: A frontier language model was recently reported to solve 1D NMR structural elucidation without tools. We ask whether this capability transfers to tandem mass spectrometry (MS/MS) in the de novo setting, where the model must propose a structure directly from the spectrum without a candidate list or reference library. To separate reasoning from recall, we build a 100-analyte benchmark from MassSpecGym, split by each analyte's textual footprint into in-distribution (well documented in literature) and out-of-distribution (essentially undocumented) arms. We hold the model, harness, and output format fixed and vary only the LLM's access to domain-specific tools. Without tools, a frontier LLM reaches 52% Top-1 accuracy in-distribution but only 2% out-of-distribution. Only access to de novo structure generators improves out-of-distribution accuracy, raising it to as much as 38% Top-1, and the resulting agent outperforms the standalone de novo models both in and out of distribution. These results suggest that LLMs are not effective at de novo MS/MS structural elucidation on their own, and that further gains depend on the specialist tools available to the agent rather than on the LLM itself.

Abstract: Graph-level out-of-distribution (OOD) generalization is critical for deploying graph neural networks in real-world applications where distribution shifts are inevitable. Existing approaches typically require class labels during representation learning to decide which substructures are predictive, limiting their applicability. We propose SCARCE, a label-free representation-learning framework that yields distribution-shift-robust graph representations from an environment partition of the training graphs alone, whether that partition comes from dataset metadata or, when none is available, from clustering a self-supervised embedding. Our method operates in two stages: (1) a variational graph autoencoder is warm-started for graph reconstruction; and (2) an adversarial confusion mechanism forces the encoder to produce representations from which a discriminator cannot distinguish environments, while preserving graph-reconstruction fidelity. We provide theoretical analysis showing that environment confusion contracts environment-discriminative directions in the representation space, which, under regularized downstream classifiers, is equivalent to imposing a stronger directional penalty on environment-associated features. This feature-reweighting mechanism reduces reliance on spurious correlations without erasing information, offering a label-free, continuous relaxation of last-layer reweighting methods. Experiments on a controlled synthetic datasets and the DrugOOD datasets show that SCARCE achieves state-of-the-art OOD generalization among label-free methods, using no class labels during representation learning.