MolCap-Arena: A Comprehensive Captioning Benchmark on Language-Enhanced Molecular Property Prediction

Bridging biomolecular modeling with natural language information, particularly through large language models (LLMs), has recently emerged as a promising interdisciplinary research area. LLMs, having been trained on large corpora of scientific documents, demonstrate significant potential in understanding and reasoning about biomolecules by providing enriched contextual and domain knowledge. However, the extent to which LLM-driven insights can improve performance on complex predictive tasks (e.g., toxicity) remains unclear. Further, the extent to which relevant knowledge can be extracted from LLMs also remains unknown. In this study, we present Molecule Caption Arena: the first comprehensive benchmark of LLM-augmented molecular property prediction. We evaluate over twenty LLMs, including both general-purpose and domain-specific molecule captioners, across diverse prediction tasks. To this goal, we introduce a novel, battle-based rating system. Our findings confirm the ability of LLM-extracted knowledge to enhance state-of-the-art molecular representations, with notable model-, prompt-, and dataset-specific variations. Code, resources, and data are available at github.com/Genentech/molcap-arena.

Geometry Informed Tokenization of Molecules for Language Model Generation

We consider molecule generation in 3D space using language models (LMs), which requires discrete tokenization of 3D molecular geometries. Although tokenization of molecular graphs exists, that for 3D geometries is largely unexplored. Here, we attempt to bridge this gap by proposing the Geo2Seq, which converts molecular geometries into $SE(3)$-invariant 1D discrete sequences. Geo2Seq consists of canonical labeling and invariant spherical representation steps, which together maintain geometric and atomic fidelity in a format conducive to LMs. Our experiments show that, when coupled with Geo2Seq, various LMs excel in molecular geometry generation, especially in controlled generation tasks.

GLaD: Synergizing Molecular Graphs and Language Descriptors for Enhanced Power Conversion Efficiency Prediction in Organic Photovoltaic Devices

This paper presents a novel approach for predicting Power Conversion Efficiency (PCE) of Organic Photovoltaic (OPV) devices, called GLaD: synergizing molecular Graphs and Language Descriptors for enhanced PCE prediction. Due to the lack of high-quality experimental data, we collect a dataset consisting of 500 pairs of OPV donor and acceptor molecules along with their corresponding PCE values, which we utilize as the training data for our predictive model. In this low-data regime, GLaD leverages properties learned from large language models (LLMs) pretrained on extensive scientific literature to enrich molecular structural representations, allowing for a multimodal representation of molecules. GLaD achieves precise predictions of PCE, thereby facilitating the synthesis of new OPV molecules with improved efficiency. Furthermore, GLaD showcases versatility, as it applies to a range of molecular property prediction tasks (BBBP, BACE, ClinTox, and SIDER), not limited to those concerning OPV materials. Especially, GLaD proves valuable for tasks in low-data regimes within the chemical space, as it enriches molecular representations by incorporating molecular property descriptions learned from large-scale pretraining. This capability is significant in real-world scientific endeavors like drug and material discovery, where access to comprehensive data is crucial for informed decision-making and efficient exploration of the chemical space.

$\textit{L+M-24}$: Building a Dataset for Language + Molecules @ ACL 2024

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the $\textit{L+M-24}$ dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, $\textit{L+M-24}$ is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction.

ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback

The discovery of new catalysts is essential for the design of new and more efficient chemical processes in order to transition to a sustainable future. We introduce an AI-guided computational screening framework unifying linguistic reasoning with quantum-chemistry based feedback from 3D atomistic representations. Our approach formulates catalyst discovery as an uncertain environment where an agent actively searches for highly effective catalysts via the iterative combination of large language model (LLM)-derived hypotheses and atomistic graph neural network (GNN)-derived feedback. Identified catalysts in intermediate search steps undergo structural evaluation based on spatial orientation, reaction pathways, and stability. Scoring functions based on adsorption energies and barriers steer the exploration in the LLM's knowledge space toward energetically favorable, high-efficiency catalysts. We introduce planning methods that automatically guide the exploration without human input, providing competitive performance against expert-enumerated chemical descriptor-based implementations. By integrating language-guided reasoning with computational chemistry feedback, our work pioneers AI-accelerated, trustworthy catalyst discovery.

Defining a New NLP Playground

The recent explosion of performance of large language models (LLMs) has changed the field of Natural Language Processing (NLP) more abruptly and seismically than any other shift in the field's 80-year history. This has resulted in concerns that the field will become homogenized and resource-intensive. The new status quo has put many academic researchers, especially PhD students, at a disadvantage. This paper aims to define a new NLP playground by proposing 20+ PhD-dissertation-worthy research directions, covering theoretical analysis, new and challenging problems, learning paradigms, and interdisciplinary applications.

Monte Carlo Thought Search: Large Language Model Querying for Complex Scientific Reasoning in Catalyst Design

Discovering novel catalysts requires complex reasoning involving multiple chemical properties and resultant trade-offs, leading to a combinatorial growth in the search space. While large language models (LLM) have demonstrated novel capabilities for chemistry through complex instruction following capabilities and high quality reasoning, a goal-driven combinatorial search using LLMs has not been explored in detail. In this work, we present a Monte Carlo Tree Search-based approach that improves beyond state-of-the-art chain-of-thought prompting variants to augment scientific reasoning. We introduce two new reasoning datasets: 1) a curation of computational chemistry simulations, and 2) diverse questions written by catalysis researchers for reasoning about novel chemical conversion processes. We improve over the best baseline by 25.8\% and find that our approach can augment scientist's reasoning and discovery process with novel insights.

Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems

Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences. Today, AI has started to advance natural sciences by improving, accelerating, and enabling our understanding of natural phenomena at a wide range of spatial and temporal scales, giving rise to a new area of research known as AI for science (AI4Science). Being an emerging research paradigm, AI4Science is unique in that it is an enormous and highly interdisciplinary area. Thus, a unified and technical treatment of this field is needed yet challenging. This paper aims to provide a technically thorough account of a subarea of AI4Science; namely, AI for quantum, atomistic, and continuum systems. These areas aim at understanding the physical world from the subatomic (wavefunctions and electron density), atomic (molecules, proteins, materials, and interactions), to macro (fluids, climate, and subsurface) scales and form an important subarea of AI4Science. A unique advantage of focusing on these areas is that they largely share a common set of challenges, thereby allowing a unified and foundational treatment. A key common challenge is how to capture physics first principles, especially symmetries, in natural systems by deep learning methods. We provide an in-depth yet intuitive account of techniques to achieve equivariance to symmetry transformations. We also discuss other common technical challenges, including explainability, out-of-distribution generalization, knowledge transfer with foundation and large language models, and uncertainty quantification. To facilitate learning and education, we provide categorized lists of resources that we found to be useful. We strive to be thorough and unified and hope this initial effort may trigger more community interests and efforts to further advance AI4Science.

Translation between Molecules and Natural Language

Joint representations between images and text have been deeply investigated in the literature. In computer vision, the benefits of incorporating natural language have become clear for enabling semantic-level control of images. In this work, we present $\textbf{MolT5}-$a self-supervised learning framework for pretraining models on a vast amount of unlabeled natural language text and molecule strings. $\textbf{MolT5}$ allows for new, useful, and challenging analogs of traditional vision-language tasks, such as molecule captioning and text-based de novo molecule generation (altogether: translation between molecules and language), which we explore for the first time. Furthermore, since $\textbf{MolT5}$ pretrains models on single-modal data, it helps overcome the chemistry domain shortcoming of data scarcity. Additionally, we consider several metrics, including a new cross-modal embedding-based metric, to evaluate the tasks of molecule captioning and text-based molecule generation. By interfacing molecules with natural language, we enable a higher semantic level of control over molecule discovery and understanding--a critical task for scientific domains such as drug discovery and material design. Our results show that $\textbf{MolT5}$-based models are able to generate outputs, both molecule and text, which in many cases are high quality and match the input modality. On molecule generation, our best model achieves 30% exact matching test accuracy (i.e., it generates the correct structure for about one-third of the captions in our held-out test set).

Semi-supervised New Event Type Induction and Description via Contrastive Loss-Enforced Batch Attention

Most event extraction methods have traditionally relied on an annotated set of event types. However, creating event ontologies and annotating supervised training data are expensive and time-consuming. Previous work has proposed semi-supervised approaches which leverage seen (annotated) types to learn how to automatically discover new event types. State-of-the-art methods, both semi-supervised or fully unsupervised, use a form of reconstruction loss on specific tokens in a context. In contrast, we present a novel approach to semi-supervised new event type induction using a masked contrastive loss, which learns similarities between event mentions by enforcing an attention mechanism over the data minibatch. We further disentangle the discovered clusters by approximating the underlying manifolds in the data, which allows us to increase normalized mutual information and Fowlkes-Mallows scores by over 20% absolute. Building on these clustering results, we extend our approach to two new tasks: predicting the type name of the discovered clusters and linking them to FrameNet frames.