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 L+M-24 dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, L+M-24 is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction

Climate change, access to food and water, pandemics–the world faces an enormous number of problems in the coming decades on scales of complexity never-before-seen. To address these issues, development of scientific solutions which are scalable, flexible, and inexpensive are critical. Over the last couple years, considerable interest has arisen for applying natural language-driven solutions to these problems. Particularly, the chemistry field is posed to be substantially accelerated by language+molecule models. This tutorial is designed to provide an introduction to this area of research. It requires no knowledge outside mainstream NLP, and it will enable participants to begin exploring relevant research. By discussing cutting-edge work, we will highlight the key roles language can fill for 1) abstract, compositional control of generative models, 2) bridging different biochemical modalities, 3) planning experimental procedures, and 4) broadening access to computational approaches. Beyond this, language models have also seen considerable success when applied to proteins or molecule structures, which can be considered as ‘exotic’ languages, and computational linguistics researchers’ expertise can be highly valuable for these impactful, possibly life-saving tasks.

Due to the rapid growth of publications varying in quality, there exists a pressing need to help scientists digest and evaluate relevant papers, thereby facilitating scientific discovery. This creates a number of urgent questions; however, computer-human collaboration in the scientific paper lifecycle is still in the exploratory stage and lacks a unified framework for analyzing the relevant tasks. Additionally, with the recent significant success of large language models (LLMs), they have increasingly played an important role in academic writing. In this cutting-edge tutorial, we aim to provide an all-encompassing overview of the paper lifecycle, detailing how machines can augment every stage of the research process for the scientist, including scientific literature understanding, experiment development, manuscript draft writing, and finally draft evaluation. This tutorial is devised for researchers interested in this rapidly-developing field of NLP-augmented paper writing. The tutorial will also feature a session of hands-on exercises during which participants can guide machines in generating ideas and automatically composing key paper elements. Furthermore, we will address current challenges, explore future directions, and discuss potential ethical issues. A toolkit designed for human-computer collaboration throughout the paper lifecycle will also be made publically available.

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.

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. This 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.

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 achieve an adjusted rand index score of 48.85%. 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.

We introduce RESIN-11, a new schema-guided event extraction&prediction framework that can be applied to a large variety of newsworthy scenarios. The framework consists of two parts: (1) an open-domain end-to-end multimedia multilingual information extraction system with weak-supervision and zero-shot learningbased techniques. (2) schema matching and schema-guided event prediction based on our curated schema library. We build a demo website based on our dockerized system and schema library publicly available for installation (https://github.com/RESIN-KAIROS/RESIN-11). We also include a video demonstrating the system.

We present MolT5 - a self-supervised learning framework for pretraining models on a vast amount of unlabeled natural language text and molecule strings. 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. Since MolT5 pretrains models on single-modal data, it helps overcome the chemistry domain shortcoming of data scarcity. Furthermore, we consider several metrics, including a new cross-modal embedding-based metric, to evaluate the tasks of molecule captioning and text-based molecule generation. Our results show that MolT5-based models are able to generate outputs, both molecules and captions, which in many cases are high quality.

We propose a new task, Text2Mol, to retrieve molecules using natural language descriptions as queries. Natural language and molecules encode information in very different ways, which leads to the exciting but challenging problem of integrating these two very different modalities. Although some work has been done on text-based retrieval and structure-based retrieval, this new task requires integrating molecules and natural language more directly. Moreover, this can be viewed as an especially challenging cross-lingual retrieval problem by considering the molecules as a language with a very unique grammar. We construct a paired dataset of molecules and their corresponding text descriptions, which we use to learn an aligned common semantic embedding space for retrieval. We extend this to create a cross-modal attention-based model for explainability and reranking by interpreting the attentions as association rules. We also employ an ensemble approach to integrate our different architectures, which significantly improves results from 0.372 to 0.499 MRR. This new multimodal approach opens a new perspective on solving problems in chemistry literature understanding and molecular machine learning.