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

Molecular property prediction is a fundamental task in computational chemistry with critical applications in drug discovery and materials science. While recent works have explored Large Language Models (LLMs) for this task, they primarily rely on textual molecular representations such as SMILES/SELFIES, which can be ambiguous and structurally less informative. In this work, we introduce MolVision, a novel approach that leverages Vision-Language Models (VLMs) by integrating both molecular structure as images and textual descriptions to enhance property prediction. We construct a benchmark spanning ten diverse datasets, covering classification, regression and description tasks. Evaluating nine different VLMs in zero-shot, few-shot, and fine-tuned settings, we find that visual information improves prediction performance, particularly when combined with efficient fine-tuning strategies such as LoRA. Our results reveal that while visual information alone is insufficient, multimodal fusion significantly enhances generalization across molecular properties. Adaptation of vision encoder for molecular images in conjunction with LoRA further improves the performance.

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.