CoRe-Gen: Robust Spectrum-to-Structure Generation under Imperfect Fingerprint Conditions

Molecular structure elucidation from tandem mass spectra (MS/MS) remains challenging, particularly for de novo generation beyond database coverage. A common approach decomposes the task into spectrum-to-fingerprint prediction followed by fingerprint-to-structure decoding, enabling the use of large-scale molecular corpora. However, at deployment, the decoder relies on predicted rather than oracle fingerprints, introducing structured errors that propagate into generation. This results in a fundamental condition mismatch, where models trained on clean inputs must operate under noisy, biased predictions, especially for long-tail substructures. We present CoRe-Gen that explicitly addresses this gap. CoRe-Gen improves the intermediate condition via synthetic-spectrum pretraining of the encoder, matches deployment-time noise through frequency-aware fingerprint corruption during decoder training, and mitigates residual errors using structure-aware autoregressive decoding with compositional SELFIES representations, auxiliary structural supervision, and lightweight chemical constraints. Experiments on standard benchmarks show that CoRe-Gen establishes a new state of the art on NPLIB1, achieving 19.54\% Top-1 and 29.92\% Top-10 exact-match accuracy, while remaining competitive on the more challenging MassSpecGym benchmark. Importantly, CoRe-Gen preserves the efficiency advantages of autoregressive decoding, providing a practical and scalable solution for robust spectrum-to-structure generation under realistic conditions.

AI-Powered Prediction of Nanoparticle Pharmacokinetics: A Multi-View Learning Approach

The clinical translation of nanoparticle-based treatments remains limited due to the unpredictability of (nanoparticle) NP pharmacokinetics$\unicode{x2014}$how they distribute, accumulate, and clear from the body. Predicting these behaviours is challenging due to complex biological interactions and the difficulty of obtaining high-quality experimental datasets. Existing AI-driven approaches rely heavily on data-driven learning but fail to integrate crucial knowledge about NP properties and biodistribution mechanisms. We introduce a multi-view deep learning framework that enhances pharmacokinetic predictions by incorporating prior knowledge of key NP properties such as size and charge into a cross-attention mechanism, enabling context-aware feature selection and improving generalization despite small datasets. To further enhance prediction robustness, we employ an ensemble learning approach, combining deep learning with XGBoost (XGB) and Random Forest (RF), which significantly outperforms existing AI models. Our interpretability analysis reveals key physicochemical properties driving NP biodistribution, providing biologically meaningful insights into possible mechanisms governing NP behaviour in vivo rather than a black-box model. Furthermore, by bridging machine learning with physiologically based pharmacokinetic (PBPK) modelling, this work lays the foundation for data-efficient AI-driven drug discovery and precision nanomedicine.