Toxicity remains a leading cause of early-stage drug development failure. Despite advances in molecular design and property prediction, the task of molecular toxicity repair, generating structurally valid molecular alternatives with reduced toxicity, has not yet been systematically defined or benchmarked. To fill this gap, we introduce ToxiMol, the first benchmark task for general-purpose Multimodal Large Language Models (MLLMs) focused on molecular toxicity repair. We construct a standardized dataset covering 11 primary tasks and 660 representative toxic molecules spanning diverse mechanisms and granularities. We design a prompt annotation pipeline with mechanism-aware and task-adaptive capabilities, informed by expert toxicological knowledge. In parallel, we propose an automated evaluation framework, ToxiEval, which integrates toxicity endpoint prediction, synthetic accessibility, drug-likeness, and structural similarity into a high-throughput evaluation chain for repair success. We systematically assess 43 mainstream general-purpose MLLMs and conduct multiple ablation studies to analyze key issues, including evaluation metrics, candidate diversity, and failure attribution. Experimental results show that although current MLLMs still face significant challenges on this task, they begin to demonstrate promising capabilities in toxicity understanding, semantic constraint adherence, and structure-aware editing.
Topological neural networks have emerged as powerful successors of graph neural networks. However, they typically involve higher-order message passing, which incurs significant computational expense. We circumvent this issue with a novel topological framework that introduces a Laplacian operator on combinatorial complexes (CCs), enabling efficient computation of heat kernels that serve as node descriptors. Our approach captures multiscale information and enables permutation-equivariant representations, allowing easy integration into modern transformer-based architectures. Theoretically, the proposed method is maximally expressive because it can distinguish arbitrary non-isomorphic CCs. Empirically, it significantly outperforms existing topological methods in terms of computational efficiency. Besides demonstrating competitive performance with the state-of-the-art descriptors on standard molecular datasets, it exhibits superior capability in distinguishing complex topological structures and avoiding blind spots on topological benchmarks. Overall, this work advances topological deep learning by providing expressive yet scalable representations, thereby opening up exciting avenues for molecular classification and property prediction tasks.
We present a modular framework powered by large language models (LLMs) that automates and streamlines key tasks across the early-stage computational drug discovery pipeline. By combining LLM reasoning with domain-specific tools, the framework performs biomedical data retrieval, domain-specific question answering, molecular generation, property prediction, property-aware molecular refinement, and 3D protein-ligand structure generation. In a case study targeting BCL-2 in lymphocytic leukemia, the agent autonomously retrieved relevant biomolecular information-including FASTA sequences, SMILES representations, and literature-and answered mechanistic questions with improved contextual accuracy over standard LLMs. It then generated chemically diverse seed molecules and predicted 67 ADMET-related properties, which guided iterative molecular refinement. Across two refinement rounds, the number of molecules with QED > 0.6 increased from 34 to 55, and those passing at least four out of five empirical drug-likeness rules rose from 29 to 52, within a pool of 194 molecules. The framework also employed Boltz-2 to generate 3D protein-ligand complexes and provide rapid binding affinity estimates for candidate compounds. These results demonstrate that the approach effectively supports molecular screening, prioritization, and structure evaluation. Its modular design enables flexible integration of evolving tools and models, providing a scalable foundation for AI-assisted therapeutic discovery.
The ability to transfer knowledge from prior experiences to novel tasks stands as a pivotal capability of intelligent agents, including both humans and computational models. This principle forms the basis of transfer learning, where large pre-trained neural networks are fine-tuned to adapt to downstream tasks. Transfer learning has demonstrated tremendous success, both in terms of task adaptation speed and performance. However there are several domains where, due to lack of data, training such large pre-trained models or foundational models is not a possibility - computational chemistry, computational immunology, and medical imaging are examples. To address these challenges, our work focuses on designing architectures to enable efficient acquisition of priors when large amounts of data are unavailable. In particular, we demonstrate that we can use neural memory to enable adaptation on non-stationary distributions with only a few samples. Then we demonstrate that our hypernetwork designs (a network that generates another network) can acquire more generalizable priors than standard networks when trained with Model Agnostic Meta-Learning (MAML). Subsequently, we apply hypernetworks to 3D scene generation, demonstrating that they can acquire priors efficiently on just a handful of training scenes, thereby leading to faster text-to-3D generation. We then extend our hypernetwork framework to perform 3D segmentation on novel scenes with limited data by efficiently transferring priors from earlier viewed scenes. Finally, we repurpose an existing molecular generative method as a pre-training framework that facilitates improved molecular property prediction, addressing critical challenges in computational immunology
Recently, a novel two-phase framework named mol-infer for inference of chemical compounds with prescribed abstract structures and desired property values has been proposed. The framework mol-infer is primarily based on using mixed integer linear programming (MILP) to simulate the computational process of machine learning methods and describe the necessary and sufficient conditions to ensure such a chemical graph exists. The existing approaches usually first convert the chemical compounds into handcrafted feature vectors to construct prediction functions, but because of the limit on the kinds of descriptors originated from the need for tractability in the MILP formulation, the learning performances on datasets of some properties are not good enough. A lack of good learning performance can greatly lower the quality of the inferred chemical graphs, and thus improving learning performance is of great importance. On the other hand, graph neural networks (GNN) offer a promising machine learning method to directly utilize the chemical graphs as the input, and many existing GNN-based approaches to the molecular property prediction problem have shown that they can enjoy better learning performances compared to the traditional approaches that are based on feature vectors. In this study, we develop a molecular inference framework based on mol-infer, namely mol-infer-GNN, that utilizes GNN as the learning method while keeping the great flexibility originated from the two-layered model on the abstract structure of the chemical graph to be inferred. We conducted computational experiments on the QM9 dataset to show that our proposed GNN model can obtain satisfying learning performances for some properties despite its simple structure, and can infer small chemical graphs comprising up to 20 non-hydrogen atoms within reasonable computational time.
Molecular property prediction aims to learn representations that map chemical structures to functional properties. While multimodal learning has emerged as a powerful paradigm to learn molecular representations, prior works have largely overlooked textual and taxonomic information of molecules for representation learning. We introduce TRIDENT, a novel framework that integrates molecular SMILES, textual descriptions, and taxonomic functional annotations to learn rich molecular representations. To achieve this, we curate a comprehensive dataset of molecule-text pairs with structured, multi-level functional annotations. Instead of relying on conventional contrastive loss, TRIDENT employs a volume-based alignment objective to jointly align tri-modal features at the global level, enabling soft, geometry-aware alignment across modalities. Additionally, TRIDENT introduces a novel local alignment objective that captures detailed relationships between molecular substructures and their corresponding sub-textual descriptions. A momentum-based mechanism dynamically balances global and local alignment, enabling the model to learn both broad functional semantics and fine-grained structure-function mappings. TRIDENT achieves state-of-the-art performance on 11 downstream tasks, demonstrating the value of combining SMILES, textual, and taxonomic functional annotations for molecular property prediction.
Fast and accurate prediction of molecular properties with machine learning is pivotal to scientific advancements across myriad domains. Foundation models in particular have proven especially effective, enabling accurate training on small, real-world datasets. This study introduces CheMeleon, a novel molecular foundation model pre-trained on deterministic molecular descriptors from the Mordred package, leveraging a Directed Message-Passing Neural Network to predict these descriptors in a noise-free setting. Unlike conventional approaches relying on noisy experimental data or biased quantum mechanical simulations, CheMeleon uses low-noise molecular descriptors to learn rich molecular representations. Evaluated on 58 benchmark datasets from Polaris and MoleculeACE, CheMeleon achieves a win rate of 79% on Polaris tasks, outperforming baselines like Random Forest (46%), fastprop (39%), and Chemprop (36%), and a 97% win rate on MoleculeACE assays, surpassing Random Forest (63%) and other foundation models. However, it struggles to distinguish activity cliffs like many of the tested models. The t-SNE projection of CheMeleon's learned representations demonstrates effective separation of chemical series, highlighting its ability to capture structural nuances. These results underscore the potential of descriptor-based pre-training for scalable and effective molecular property prediction, opening avenues for further exploration of descriptor sets and unlabeled datasets.
The prediction of crystal properties is essential for understanding structure-property relationships and accelerating the discovery of functional materials. However, conventional approaches relying on experimental measurements or density functional theory (DFT) calculations are often resource-intensive, limiting their scalability. Machine learning (ML) models offer a promising alternative by learning complex structure-property relationships from data, enabling faster predictions. Yet, existing ML models often rely on labeled data, adopt representations that poorly capture essential structural characteristics, and lack integration with physical principles--factors that limit their generalizability and interpretability. Here, we introduce CLOUD (Crystal Language mOdel for Unified and Differentiable materials modeling), a transformer-based framework trained on a novel Symmetry-Consistent Ordered Parameter Encoding (SCOPE) that encodes crystal symmetry, Wyckoff positions, and composition in a compact, coordinate-free string representation. Pre-trained on over six million crystal structures, CLOUD is fine-tuned on multiple downstream tasks and achieves competitive performance in predicting a wide range of material properties, demonstrating strong scaling performance. Furthermore, as proof of concept of differentiable materials modeling, CLOUD is applied to predict the phonon internal energy and heat capacity, which integrates the Debye model to preserve thermodynamic consistency. The CLOUD-DEBYE framework enforces thermodynamic consistency and enables temperature-dependent property prediction without requiring additional data. These results demonstrate the potential of CLOUD as a scalable and physics-informed foundation model for crystalline materials, unifying symmetry-consistent representations with physically grounded learning for property prediction and materials discovery.
Foundation models (FMs) are catalyzing a transformative shift in materials science (MatSci) by enabling scalable, general-purpose, and multimodal AI systems for scientific discovery. Unlike traditional machine learning models, which are typically narrow in scope and require task-specific engineering, FMs offer cross-domain generalization and exhibit emergent capabilities. Their versatility is especially well-suited to materials science, where research challenges span diverse data types and scales. This survey provides a comprehensive overview of foundation models, agentic systems, datasets, and computational tools supporting this growing field. We introduce a task-driven taxonomy encompassing six broad application areas: data extraction, interpretation and Q\&A; atomistic simulation; property prediction; materials structure, design and discovery; process planning, discovery, and optimization; and multiscale modeling. We discuss recent advances in both unimodal and multimodal FMs, as well as emerging large language model (LLM) agents. Furthermore, we review standardized datasets, open-source tools, and autonomous experimental platforms that collectively fuel the development and integration of FMs into research workflows. We assess the early successes of foundation models and identify persistent limitations, including challenges in generalizability, interpretability, data imbalance, safety concerns, and limited multimodal fusion. Finally, we articulate future research directions centered on scalable pretraining, continual learning, data governance, and trustworthiness.
Machine learning has revolutionized materials design, yet predicting complex properties like alloy ductility remains challenging due to the influence of processing conditions and microstructural features that resist quantification through traditional reductionist approaches. Here, we present an innovative information fusion architecture that integrates domain-specific texts from materials science literature with quantitative physical descriptors to overcome these limitations. Our framework employs MatSciBERT for advanced textual comprehension and incorporates contrastive learning to automatically extract implicit knowledge regarding processing parameters and microstructural characteristics. Through rigorous ablation studies and comparative experiments, the model demonstrates superior performance, achieving coefficient of determination (R2) values of 0.849 and 0.680 on titanium alloy validation set and refractory multi-principal-element alloy test set. This systematic approach provides a holistic framework for property prediction in complex material systems where quantitative descriptors are incomplete and establishes a foundation for knowledge-guided materials design and informatics-driven materials discovery.
A widely recognized limitation of molecular prediction models is their reliance on structures observed in the training data, resulting in poor generalization to out-of-distribution compounds. Yet in drug discovery, the compounds most critical for advancing research often lie beyond the training set, making the bias toward the training data particularly problematic. This mismatch introduces substantial covariate shift, under which standard deep learning models produce unstable and inaccurate predictions. Furthermore, the scarcity of labeled data, stemming from the onerous and costly nature of experimental validation, further exacerbates the difficulty of achieving reliable generalization. To address these limitations, we propose a novel meta-learning-based approach that leverages unlabeled data to interpolate between in-distribution (ID) and out-of-distribution (OOD) data, enabling the model to meta-learn how to generalize beyond the training distribution. We demonstrate significant performance gains over state-of-the-art methods on challenging real-world datasets that exhibit substantial covariate shift.
Geometric graph neural networks (GNNs) that respect E(3) symmetries have achieved strong performance on small molecule modeling, but they face scalability and expressiveness challenges when applied to large biomolecules such as RNA and proteins. These systems require models that can simultaneously capture fine-grained atomic interactions, long-range dependencies across spatially distant components, and biologically relevant hierarchical structure, such as atoms forming residues, which in turn form higher-order domains. Existing geometric GNNs, which typically operate exclusively in either Euclidean or Spherical Harmonics space, are limited in their ability to capture both the fine-scale atomic details and the long-range, symmetry-aware dependencies required for modeling the multi-scale structure of large biomolecules. We introduce DualEquiNet, a Dual-Space Hierarchical Equivariant Network that constructs complementary representations in both Euclidean and Spherical Harmonics spaces to capture local geometry and global symmetry-aware features. DualEquiNet employs bidirectional cross-space message passing and a novel Cross-Space Interaction Pooling mechanism to hierarchically aggregate atomic features into biologically meaningful units, such as residues, enabling efficient and expressive multi-scale modeling for large biomolecular systems. DualEquiNet achieves state-of-the-art performance on multiple existing benchmarks for RNA property prediction and protein modeling, and outperforms prior methods on two newly introduced 3D structural benchmarks demonstrating its broad effectiveness across a range of large biomolecule modeling tasks.
Accurate geological modeling is critical for reservoir characterization, yet traditional methods struggle with complex subsurface heterogeneity, and they have problems with conditioning to observed data. This study introduces Pix2Geomodel, a novel conditional generative adversarial network (cGAN) framework based on Pix2Pix, designed to predict reservoir properties (facies, porosity, permeability, and water saturation) from the Rotliegend reservoir of the Groningen gas field. Utilizing a 7.6 million-cell dataset from the Nederlandse Aardolie Maatschappij, accessed via EPOS-NL, the methodology included data preprocessing, augmentation to generate 2,350 images per property, and training with a U-Net generator and PatchGAN discriminator over 19,000 steps. Evaluation metrics include pixel accuracy (PA), mean intersection over union (mIoU), frequency weighted intersection over union (FWIoU), and visualizations assessed performance in masked property prediction and property-to-property translation tasks. Results demonstrated high accuracy for facies (PA 0.88, FWIoU 0.85) and water saturation (PA 0.96, FWIoU 0.95), with moderate success for porosity (PA 0.70, FWIoU 0.55) and permeability (PA 0.74, FWIoU 0.60), and robust translation performance (e.g., facies-to-facies PA 0.98, FWIoU 0.97). The framework captured spatial variability and geological realism, as validated by variogram analysis, and calculated the training loss curves for the generator and discriminator for each property. Compared to traditional methods, Pix2Geomodel offers enhanced fidelity in direct property mapping. Limitations include challenges with microstructural variability and 2D constraints, suggesting future integration of multi-modal data and 3D modeling (Pix2Geomodel v2.0). This study advances the application of generative AI in geoscience, supporting improved reservoir management and open science initiatives.
Graph machine learning architectures are typically tailored to specific tasks on specific datasets, which hinders their broader applicability. This has led to a new quest in graph machine learning: how to build graph foundation models capable of generalizing across arbitrary graphs and features? In this work, we present a recipe for designing graph foundation models for node-level tasks from first principles. The key ingredient underpinning our study is a systematic investigation of the symmetries that a graph foundation model must respect. In a nutshell, we argue that label permutation-equivariance alongside feature permutation-invariance are necessary in addition to the common node permutation-equivariance on each local neighborhood of the graph. To this end, we first characterize the space of linear transformations that are equivariant to permutations of nodes and labels, and invariant to permutations of features. We then prove that the resulting network is a universal approximator on multisets that respect the aforementioned symmetries. Our recipe uses such layers on the multiset of features induced by the local neighborhood of the graph to obtain a class of graph foundation models for node property prediction. We validate our approach through extensive experiments on 29 real-world node classification datasets, demonstrating both strong zero-shot empirical performance and consistent improvement as the number of training graphs increases.
The pretraining-and-finetuning paradigm has driven significant advances across domains, such as natural language processing and computer vision, with representative pretraining paradigms such as masked language modeling and next-token prediction. However, in molecular representation learning, the task design remains largely limited to node-level denoising, which is effective at modeling local atomic environments, yet maybe insufficient for capturing the global molecular structure required by graph-level property prediction tasks, such as energy estimation and molecular regression. In this work, we present GeoRecon, a novel graph-level pretraining framework that shifts the focus from individual atoms to the molecule as an integrated whole. GeoRecon introduces a graph-level reconstruction task: during pretraining, the model is trained to generate an informative graph representation capable of accurately guiding reconstruction of the molecular geometry. This encourages the model to learn coherent, global structural features rather than isolated atomic details. Without relying on additional supervision or external data, GeoRecon outperforms node-centric baselines on multiple molecular benchmarks (e.g., QM9, MD17), demonstrating the benefit of incorporating graph-level reconstruction for learning more holistic and geometry-aware molecular embeddings.
In this paper, we review recent developments and the role of Graph Neural Networks (GNNs) in computational drug discovery, including molecule generation, molecular property prediction, and drug-drug interaction prediction. By summarizing the most recent developments in this area, we underscore the capabilities of GNNs to comprehend intricate molecular patterns, while exploring both their current and prospective applications. We initiate our discussion by examining various molecular representations, followed by detailed discussions and categorization of existing GNN models based on their input types and downstream application tasks. We also collect a list of commonly used benchmark datasets for a variety of applications. We conclude the paper with brief discussions and summarize common trends in this important research area.
Machine learning has promised to change the landscape of laboratory chemistry, with impressive results in molecular property prediction and reaction retro-synthesis. However, chemical datasets are often inaccessible to the machine learning community as they tend to require cleaning, thorough understanding of the chemistry, or are simply not available. In this paper, we introduce a novel dataset for yield prediction, providing the first-ever transient flow dataset for machine learning benchmarking, covering over 1200 process conditions. While previous datasets focus on discrete parameters, our experimental set-up allow us to sample a large number of continuous process conditions, generating new challenges for machine learning models. We focus on solvent selection, a task that is particularly difficult to model theoretically and therefore ripe for machine learning applications. We showcase benchmarking for regression algorithms, transfer-learning approaches, feature engineering, and active learning, with important applications towards solvent replacement and sustainable manufacturing.
Small molecules are essential to drug discovery, and graph-language models hold promise for learning molecular properties and functions from text. However, existing molecule-text datasets are limited in scale and informativeness, restricting the training of generalizable multimodal models. We present MolTextNet, a dataset of 2.5 million high-quality molecule-text pairs designed to overcome these limitations. To construct it, we propose a synthetic text generation pipeline that integrates structural features, computed properties, bioactivity data, and synthetic complexity. Using GPT-4o-mini, we create structured descriptions for 2.5 million molecules from ChEMBL35, with text over 10 times longer than prior datasets. MolTextNet supports diverse downstream tasks, including property prediction and structure retrieval. Pretraining CLIP-style models with Graph Neural Networks and ModernBERT on MolTextNet yields improved performance, highlighting its potential for advancing foundational multimodal modeling in molecular science. Our dataset is available at https://huggingface.co/datasets/liuganghuggingface/moltextnet.
Pretrained molecular encoders have become indispensable in computational chemistry for tasks such as property prediction and molecular generation. However, the standard practice of relying solely on final-layer embeddings for downstream tasks may discard valuable information. In this work, we challenge this convention by conducting a comprehensive layer-wise analysis of five diverse molecular encoders across 22 ADMET property prediction tasks. Our results demonstrate that embeddings from intermediate layers consistently outperform final-layer representations. Specifically, using fixed embeddings from the optimal intermediate layers improved downstream performance by an average of 5.4%, reaching gains up to 28.6%. Furthermore, finetuning up to these intermediate layers yielded even greater average improvements of 8.5%, with performance increases as high as 40.8%, achieving new state-of-the-art results on several benchmarks. Additionally, a strong positive correlation between fixed embedding performance and finetuning outcomes supports an efficient evaluate-then-finetune approach, enabling identification of optimal layers with reduced computational cost. These findings highlight the importance of exploring the full representational depth of molecular encoders to achieve substantial performance improvements and computational efficiency. The code is made publicly available at https://github.com/luispintoc/Unlocking-Chemical-Insights.
The local inductive bias of message-passing graph neural networks (GNNs) hampers their ability to exploit key structural information (e.g., connectivity and cycles). Positional encoding (PE) and Persistent Homology (PH) have emerged as two promising approaches to mitigate this issue. PE schemes endow GNNs with location-aware features, while PH methods enhance GNNs with multiresolution topological features. However, a rigorous theoretical characterization of the relative merits and shortcomings of PE and PH has remained elusive. We bridge this gap by establishing that neither paradigm is more expressive than the other, providing novel constructions where one approach fails but the other succeeds. Our insights inform the design of a novel learnable method, PiPE (Persistence-informed Positional Encoding), which is provably more expressive than both PH and PE. PiPE demonstrates strong performance across a variety of tasks (e.g., molecule property prediction, graph classification, and out-of-distribution generalization), thereby advancing the frontiers of graph representation learning. Code is available at https://github.com/Aalto-QuML/PIPE.