Molecular structure elucidation from tandem mass spectra (MS/MS) is a central inverse problem in analytical chemistry. Most existing approaches to MS/MS identification remain tied to reference libraries or predefined candidate sets, whereas de novo methods aim to generate structures directly from spectra. A common de novo route predicts a molecular fingerprint from the spectrum and then decodes structures from it, enabling decoder pretraining on large molecule-only corpora. However, this paradigm creates a training-inference mismatch: the decoder is trained on oracle fingerprints computed from molecules, but at inference it is queried with a noisy spectrum-induced fingerprint posterior that is typically collapsed to a single thresholded fingerprint. We introduce MS-GPT, which recasts fingerprint-mediated de novo elucidation as spectrum-induced posterior querying of a conditional molecule-language model. MS-GPT conditions a molecule-language model on fingerprints and formulas, then converts the spectrum-induced posterior into a band of fingerprint queries near the oracle-fingerprint manifold through active-bit density calibration. Candidates sampled across this band are pooled and ranked by generation-frequency consensus. A lightweight LoRA adapter further mitigates domain-specific posterior bias while preserving the pretrained molecular prior. On NPLIB1 and MassSpecGym, MS-GPT sets a new state of the art, reaching Top-1/Top-10 exact-match accuracy of 29.8\%/41.1\% and 23.9\%/28.7\%, respectively. Candidate-pool scaling shows that efficient autoregressive molecular generation continues to improve recall with a little additional inference cost. The source code and model checkpoints are available at https://github.com/VIKI623/MS-GPT.
Xin Zhao, Yumin Liu, Zhuowei Li et al.· 0 citations
Analytic Continual Learning (ACL) offers a computationally efficient alternative to gradient-based approaches. Recent ACL methods are based on Recursive Least Squares (RLS) and have achieved the state-of-the-art results compared to other alternatives. However, they falter significantly in Class-Incremental Learning scenarios characterized by Long-Tailed distributions. While the ill-conditioning of the autocorrelation (Gram) matrix is a known limitation of RLS, we demonstrate that class imbalance exacerbates this issue into a distinct spectral pathology:"tail"classes suffer from severe spectral collapse, rendering their subspaces numerically indistinguishable from noise. Standard Ridge Regression ($L_2$) fails to address this effectively as it applies isotropic regularization - a uniform penalty that is insufficient to stabilize the tail without over-shrinking the head. To address this, we propose Geometry-Spectral Rectification (GSR), a theoretically grounded framework that treats long-tailed learning as a spectral regularization problem. Unlike standard isotropic regularization (Ridge) which uniformly penalizes all eigenvalues, GSR acts as an anisotropic spectral filter, selectively inflating the collapsed eigenvalues of tail classes. We construct a structured, data-dependent spectral perturbation matrix $\Delta$ that selectively inflates collapsed tail eigen-directions of the Gram matrix. Theoretical analysis proves that GSR guarantees an improved stable rank for the Gram matrix, ensuring numerical stability. Extensive experiments show that GSR establishes a new state-of-the-art for analytic CIL, offering a superior trade-off between computational efficiency and robust generalization in long-tailed settings.
Q. Tran, Ngoc-Hai Nguyen, Quan Dao et al.· arXiv.org· 0 citations
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