The ViT-L/14 encoder processes images into visual tokens, which the LLaMA-2-7B decoder converts into text.

Recent studies in Machine Learning (ML) for biological research focus on investigating molecular properties to accelerate drug discovery. However, limited labeled molecular data often hampers the performance of ML models. A common strategy to mitigate data scarcity is leveraging auxiliary learning tasks to provide additional supervision, but selecting effective auxiliary tasks requires substantial domain expertise and manual effort, and their inclusion does not always guarantee performance gains. To overcome these challenges, we introduce Automatic Auxiliary Task Selection (AUTAUT), a fully automated framework that seamlessly retrieves auxiliary tasks using large language models and adaptively integrates them through a novel gradient alignment weighting mechanism. By automatically emphasizing auxiliary tasks aligned with the primary objective, AUTAUT significantly enhances predictive accuracy while reducing negative impacts from irrelevant tasks. Extensive evaluations demonstrate that AUTAUT outperforms 10 auxiliary task-based approaches and 18 advanced molecular property prediction models.

Molecular Relational Learning (MRL) is a rapidly growing field that focuses on understanding the interaction dynamics between molecules, which is crucial for applications ranging from catalyst engineering to drug discovery. Despite recent progress, ture of molecules, earlier MRL as obtaining approaches the are 3D limited interaction to using geometry only the remains 2D topological prohibiti strucvely expensive. This paper introduces a novel 3D geometric pre-training strategy for MRL (3DMRL) that incorporates a 3D virtual interaction environment, overcoming the the constructe limitations d of 3D costly virtual tradit interaction ional quantum environment, mechanical 3DMRL calculation trains 2D methods. MRL model With to learn the global and local 3D geometric information of molecular interaction. Extensive experiments on various tasks using real-world datasets, including out-ofdistribution and extrapolation scenarios, demonstrate the effectiveness of 3DMRL, sho publicly wing a up vailable to a 24.93% at https://github.com/

Molecular Property Prediction (MPP) is a crucial task in the AI-driven Drug Discovery (AIDD) pipeline, which has recently gained considerable attention thanks to advancements in deep learning. However, recent research has revealed that deep models struggle to beat traditional non-deep ones on MPP.

Predicting molecular properties with data-driven methods has drawn much attention in recent years. Particularly, Graph Neural Networks (GNNs) have demonstrated remarkable success in various molecular generation and prediction tasks. In cases where labeled data is scarce, GNNs can be pre-trained on unlabeled molecular data to first learn the general semantic and structural information before being finetuned for specific tasks. However, most existing self-supervised pretraining frameworks for GNNs only focus on node-level or graph-level tasks.

Graph Neural Networks (GNNs) typically scale with the number of graph edges, making them well suited for sparse graphs but less efficient on dense graphs, such as point clouds or molecular interactions. A common remedy is to sparsify the graph via similarity thresholding or distance pruning, but this forces an arbitrary choice of a single interaction scale and discards crucial information from other scales. To overcome this limitation, we introduce a multi-view graph-tuple framework. Instead of a single graph, our graph-tuple framework partitions the graph into disjoint subgraphs, capturing primary local interactions and weaker, long-range connections. We then learn multi-view representations from the graph-tuple via a heterogeneous message-passing architecture inspired by the theory of non-commuting operators, which we formally prove is strictly more expressive and guarantees a lower oracle risk compared to single-graph message-passing models. We instantiate our framework on two scientific domains: molecular property prediction from feature-scarce Coulomb matrices and cosmological parameter inference from geometric point clouds. On both applications, our multi-view graph-tuple models demonstrate better performance than single-graph baselines, highlighting the power and versatility of our multi-view approach.

The discovery of next-generation photoinitiators for two-photon polymerization (TPP) is hindered by the absence of large, open datasets containing the quantum-chemical and photophysical properties required to model photodissociation and excited-state behavior. Existing molecular datasets typically provide only basic physicochemical descriptors and therefore cannot support data-driven screening or AI-assisted design of photoinitiators. To address this gap, we introduce QuantumChem-200K, a large-scale dataset of over 200,000 organic molecules annotated with eleven quantum-chemical properties, including two-photon absorption (TPA) cross sections, TPA spectral ranges, singlet-triplet intersystem crossing (ISC) energies, toxicity and synthetic accessibility scores, hydrophilicity, solubility, boiling point, molecular weight, and aromaticity. These values are computed using a hybrid workflow that integrates density function theory (DFT), semi-empirical excited-state methods, atomistic quantum solvers, and neural-network predictors. Using QuantumChem-200K, we fine tune the open-source Qwen2.5-32B large language model to create a chemistry AI assistant capable of forward property prediction from SMILES. Benchmarking on 3000 unseen molecules from VQM24 and ZINC20 demonstrates that domain-specific fine-tuning significantly improves accuracy over GPT-4o, Llama-3.1-70B, and the base Qwen2.5-32B model, particularly for TPA and ISC predictions central to photoinitiator design. QuantumChem-200K and the corresponding AI assistant together provide the first scalable platform for high-throughput, LLM-driven photoinitiator screening and accelerated discovery of photosensitive materials.