Saber Akhondi


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NLP for Chemistry – Introduction and Recent Advances
Camilo Thorne | Saber Akhondi
Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024): Tutorial Summaries

In this half-day tutorial we will be giving an introductory overview to a number of recent applications of natural language processing to a relatively underrepresented application domain: chemistry. Specifically, we will see how neural language models (transformers) can be applied (oftentimes with near-human performance) to chemical text mining, reaction extraction, or more importantly computational chemistry (forward and backward synthesis of chemical compounds). At the same time, a number of gold standards for experimentation have been made available to the research –academic and otherwise– community. Theoretical results will be, whenever possible, supported by system demonstrations in the form of Jupyter notebooks. This tutorial targets an audience interested in bioinformatics and biomedical applications, but pre-supposes no advanced knowledge of either.


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Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings
Zenan Zhai | Dat Quoc Nguyen | Saber Akhondi | Camilo Thorne | Christian Druckenbrodt | Trevor Cohn | Michelle Gregory | Karin Verspoor
Proceedings of the 18th BioNLP Workshop and Shared Task

Chemical patents are an important resource for chemical information. However, few chemical Named Entity Recognition (NER) systems have been evaluated on patent documents, due in part to their structural and linguistic complexity. In this paper, we explore the NER performance of a BiLSTM-CRF model utilising pre-trained word embeddings, character-level word representations and contextualized ELMo word representations for chemical patents. We compare word embeddings pre-trained on biomedical and chemical patent corpora. The effect of tokenizers optimized for the chemical domain on NER performance in chemical patents is also explored. The results on two patent corpora show that contextualized word representations generated from ELMo substantially improve chemical NER performance w.r.t. the current state-of-the-art. We also show that domain-specific resources such as word embeddings trained on chemical patents and chemical-specific tokenizers, have a positive impact on NER performance.