We consider the problem of crystal materials generation using language models (LMs). A key step is to convert 3D crystal structures into 1D sequences to be processed by LMs. Prior studies used the crystallographic information framework (CIF) file stream, which fails to ensure SE(3) and periodic invariance and may not lead to unique sequence representations for a given crystal structure. Here, we propose a novel method, known as Mat2Seq, to tackle this challenge. Mat2Seq converts 3D crystal structures into 1D sequences and ensures that different mathematical descriptions of the same crystal are represented in a single unique sequence, thereby provably achieving SE(3) and periodic invariance. Experimental results show that, with language models, Mat2Seq achieves promising performance in crystal structure generation as compared with prior methods.

Existing work within transfer learning often follows a two-step process -- pre-training over a large-scale source domain and then finetuning over limited samples from the target domain. Yet, despite its popularity, this methodology has been shown to suffer in the presence of distributional shift -- specifically when the output spaces diverge. Previous work has focused on increasing model performance within this setting by identifying and classifying only the shared output classes between distributions. However, these methods are inherently limited as they ignore classes outside the shared class set, disregarding potential information relevant to the model transfer. This paper proposes a new process for few-shot transfer learning that selects and weighs classes from the source domain to optimize the transfer between domains. More concretely, we use Wasserstein distance to choose a set of source classes and their weights that minimize the distance between the source and target domain. To justify our proposed algorithm, we provide a generalization analysis of the performance of the learned classifier over the target domain and show that our method corresponds to a bound minimization algorithm. We empirically demonstrate the effectiveness of our approach (WaSS) by experimenting on several different datasets and presenting superior performance within various label shift settings, including the extreme case where the label spaces are disjoint.

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.

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.

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 reaction energy 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.

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.

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 work 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.

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.

Predicting synergistic drug combinations can help accelerate discovery of cancer treatments, particularly therapies personalized to a patient's specific tumor via biopsied cells. In this paper, we propose a novel setting and models for in-context drug synergy learning. We are given a small "personalized dataset" of 10-20 drug synergy relationships in the context of specific cancer cell targets. Our goal is to predict additional drug synergy relationships in that context. Inspired by recent work that pre-trains a GPT language model (LM) to "in-context learn" common function classes, we devise novel pre-training schemes that enable a GPT model to in-context learn "drug synergy functions". Our model -- which does not use any textual corpora, molecular fingerprints, protein interaction or any other domain-specific knowledge -- is able to achieve competitive results. We further integrate our in-context approach with a genetic algorithm to optimize model prompts and select synergy candidates to test after conducting a patient biopsy. Finally, we explore a novel task of inverse drug design which can potentially enable the design of drugs that synergize specifically to target a given patient's "personalized dataset". Our findings can potentially have an important impact on precision cancer medicine, and also raise intriguing questions on non-textual pre-training for LMs.

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.