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Register a new userDrug Repurposing for Cancer: An NLP Approach to Identify Low-Cost Therapies
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Ioana Baldini
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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More than 200 generic drugs approved by the U.S. Food and Drug Administration for non-cancer indications have shown promise for treating cancer. Due to their long history of safe patient use, low cost, and widespread availability, repurposing of generic drugs represents a major opportunity to rapidly improve outcomes for cancer patients and reduce healthcare costs worldwide. Evidence on the efficacy of non-cancer generic drugs being tested for cancer exists in scientific publications, but trying to manually identify and extract such evidence is intractable. In this paper, we introduce a system to automate this evidence extraction from PubMed abstracts. Our primary contribution is to define the natural language processing pipeline required to obtain such evidence, comprising the following modules: querying, filtering, cancer type entity extraction, therapeutic association classification, and study type classification. Using the subject matter expertise on our team, we create our own datasets for these specialized domain-specific tasks. We obtain promising performance in each of the modules by utilizing modern language modeling techniques and plan to treat them as baseline approaches for future improvement of individual components.
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Objective: To discover candidate drugs to repurpose for COVID-19 using literature-derived knowledge and knowledge graph completion methods. Methods: We propose a novel, integrative, and neural network-based literature-based discovery (LBD) approach to identify drug candidates from both PubMed and COVID-19-focused research literature. Our approach relies on semantic triples extracted using SemRep (via SemMedDB). We identified an informative subset of semantic triples using filtering rules and an accuracy classifier developed on a BERT variant, and used this subset to construct a knowledge graph. Five SOTA, neural knowledge graph completion algorithms were used to predict drug repurposing candidates. The models were trained and assessed using a time slicing approach and the predicted drugs were compared with a list of drugs reported in the literature and evaluated in clinical trials. These models were complemented by a discovery pattern-based approach. Results: Accuracy classifier based on PubMedBERT achieved the best performance (F1= 0.854) in classifying semantic predications. Among five knowledge graph completion models, TransE outperformed others (MR = 0.923, Hits@1=0.417). Some known drugs linked to COVID-19 in the literature were identified, as well as some candidate drugs that have not yet been studied. Discovery patterns enabled generation of plausible hypotheses regarding the relationships between the candidate drugs and COVID-19. Among them, five highly ranked and novel drugs (paclitaxel, SB 203580, alpha 2-antiplasmin, pyrrolidine dithiocarbamate, and butylated hydroxytoluene) with their mechanistic explanations were further discussed. Conclusion: We show that an LBD approach can be feasible for discovering drug candidates for COVID-19, and for generating mechanistic explanations. Our approach can be generalized to other diseases as well as to other clinical questions.
We review the cost of training large-scale language models, and the drivers of these costs. The intended audience includes engineers and scientists budgeting their model-training experiments, as well as non-practitioners trying to make sense of the economics of modern-day Natural Language Processing (NLP).
With the rapid development of NLP research, leaderboards have emerged as one tool to track the performance of various systems on various NLP tasks. They are effective in this goal to some extent, but generally present a rather simplistic one-dimensional view of the submitted systems, communicated only through holistic accuracy numbers. In this paper, we present a new conceptualization and implementation of NLP evaluation: the ExplainaBoard, which in addition to inheriting the functionality of the standard leaderboard, also allows researchers to (i) diagnose strengths and weaknesses of a single system (e.g.~what is the best-performing system bad at?) (ii) interpret relationships between multiple systems. (e.g.~where does system A outperform system B? What if we combine systems A, B, and C?) and (iii) examine prediction results closely (e.g.~what are common errors made by multiple systems, or in what contexts do particular errors occur?). So far, ExplainaBoard covers more than 400 systems, 50 datasets, 40 languages, and 12 tasks. ExplainaBoard keeps updated and is recently upgraded by supporting (1) multilingual multi-task benchmark, (2) meta-evaluation, and (3) more complicated task: machine translation, which reviewers also suggested.} We not only released an online platform on the website url{http://explainaboard.nlpedia.ai/} but also make our evaluation tool an API with MIT Licence at Github url{https://github.com/neulab/explainaBoard} and PyPi url{https://pypi.org/project/interpret-eval/} that allows users to conveniently assess their models offline. We additionally release all output files from systems that we have run or collected to motivate output-driven research in the future.
Speech-enabled systems typically first convert audio to text through an automatic speech recognition (ASR) model and then feed the text to downstream natural language processing (NLP) modules. The errors of the ASR system can seriously downgrade the performance of the NLP modules. Therefore, it is essential to make them robust to the ASR errors. Previous work has shown it is effective to employ data augmentation methods to solve this problem by injecting ASR noise during the training process. In this paper, we utilize the prevalent pre-trained language model to generate training samples with ASR-plausible noise. Compare to the previous methods, our approach generates ASR noise that better fits the real-world error distribution. Experimental results on spoken language translation(SLT) and spoken language understanding (SLU) show that our approach effectively improves the system robustness against the ASR errors and achieves state-of-the-art results on both tasks.
To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations, and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence.
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