Carl Edwards


2022

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Translation between Molecules and Natural Language
Carl Edwards | Tuan Lai | Kevin Ros | Garrett Honke | Kyunghyun Cho | Heng Ji
Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing

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.

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RESIN-11: Schema-guided Event Prediction for 11 Newsworthy Scenarios
Xinya Du | Zixuan Zhang | Sha Li | Pengfei Yu | Hongwei Wang | Tuan Lai | Xudong Lin | Ziqi Wang | Iris Liu | Ben Zhou | Haoyang Wen | Manling Li | Darryl Hannan | Jie Lei | Hyounghun Kim | Rotem Dror | Haoyu Wang | Michael Regan | Qi Zeng | Qing Lyu | Charles Yu | Carl Edwards | Xiaomeng Jin | Yizhu Jiao | Ghazaleh Kazeminejad | Zhenhailong Wang | Chris Callison-Burch | Mohit Bansal | Carl Vondrick | Jiawei Han | Dan Roth | Shih-Fu Chang | Martha Palmer | Heng Ji
Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies: System Demonstrations

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.

2021

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Text2Mol: Cross-Modal Molecule Retrieval with Natural Language Queries
Carl Edwards | ChengXiang Zhai | Heng Ji
Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing

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.