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Register a new userAI- and HPC-enabled Lead Generation for SARS-CoV-2: Models and Processes to Extract Druglike Molecules Contained in Natural Language Text
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Added by
Zhi Hong
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Researchers worldwide are seeking to repurpose existing drugs or discover new drugs to counter the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A promising source of candidates for such studies is molecules that have been reported in the scientific literature to be drug-like in the context of coronavirus research. We report here on a project that leverages both human and artificial intelligence to detect references to drug-like molecules in free text. We engage non-expert humans to create a corpus of labeled text, use this labeled corpus to train a named entity recognition model, and employ the trained model to extract 10912 drug-like molecules from the COVID-19 Open Research Dataset Challenge (CORD-19) corpus of 198875 papers. Performance analyses show that our automated extraction model can achieve performance on par with that of non-expert humans.
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Researchers across the globe are seeking to rapidly repurpose existing drugs or discover new drugs to counter the the novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). One promising approach is to train machine learning (ML) and artificial intelligence (AI) tools to screen large numbers of small molecules. As a contribution to that effort, we are aggregating numerous small molecules from a variety of sources, using high-performance computing (HPC) to computer diverse properties of those molecules, using the computed properties to train ML/AI models, and then using the resulting models for screening. In this first data release, we make available 23 datasets collected from community sources representing over 4.2 B molecules enriched with pre-computed: 1) molecular fingerprints to aid similarity searches, 2) 2D images of molecules to enable exploration and application of image-based deep learning methods, and 3) 2D and 3D molecular descriptors to speed development of machine learning models. This data release encompasses structural information on the 4.2 B molecules and 60 TB of pre-computed data. Future releases will expand the data to include more detailed molecular simulations, computed models, and other products.
In Natural Language Generation (NLG), End-to-End (E2E) systems trained through deep learning have recently gained a strong interest. Such deep models need a large amount of carefully annotated data to reach satisfactory performance. However, acquiring such datasets for every new NLG application is a tedious and time-consuming task. In this paper, we propose a semi-supervised deep learning scheme that can learn from non-annotated data and annotated data when available. It uses an NLG and a Natural Language Understanding (NLU) sequence-to-sequence models which are learned jointly to compensate for the lack of annotation. Experiments on two benchmark datasets show that, with limited amount of annotated data, the method can achieve very competitive results while not using any pre-processing or re-scoring tricks. These findings open the way to the exploitation of non-annotated datasets which is the current bottleneck for the E2E NLG system development to new applications.
We introduce Texygen, a benchmarking platform to support research on open-domain text generation models. Texygen has not only implemented a majority of text generation models, but also covered a set of metrics that evaluate the diversity, the quality and the consistency of the generated texts. The Texygen platform could help standardize the research on text generation and facilitate the sharing of fine-tuned open-source implementations among researchers for their work. As a consequence, this would help in improving the reproductivity and reliability of future research work in text generation.
Large transformer-based language models (LMs) trained on huge text corpora have shown unparalleled generation capabilities. However, controlling attributes of the generated language (e.g. switching topic or sentiment) is difficult without modifying the model architecture or fine-tuning on attribute-specific data and entailing the significant cost of retraining. We propose a simple alternative: the Plug and Play Language Model (PPLM) for controllable language generation, which combines a pretrained LM with one or more simple attribute classifiers that guide text generation without any further training of the LM. In the canonical scenario we present, the attribute models are simple classifiers consisting of a user-specified bag of words or a single learned layer with 100,000 times fewer parameters than the LM. Sampling entails a forward and backward pass in which gradients from the attribute model push the LMs hidden activations and thus guide the generation. Model samples demonstrate control over a range of topics and sentiment styles, and extensive automated and human annotated evaluations show attribute alignment and fluency. PPLMs are flexible in that any combination of differentiable attribute models may be used to steer text generation, which will allow for diverse and creative applications beyond the examples given in this paper.
In the era of big data, the advancement, improvement, and application of algorithms in academic research have played an important role in promoting the development of different disciplines. Academic papers in various disciplines, especially computer science, contain a large number of algorithms. Identifying the algorithms from the full-text content of papers can determine popular or classical algorithms in a specific field and help scholars gain a comprehensive understanding of the algorithms and even the field. To this end, this article takes the field of natural language processing (NLP) as an example and identifies algorithms from academic papers in the field. A dictionary of algorithms is constructed by manually annotating the contents of papers, and sentences containing algorithms in the dictionary are extracted through dictionary-based matching. The number of articles mentioning an algorithm is used as an indicator to analyze the influence of that algorithm. Our results reveal the algorithm with the highest influence in NLP papers and show that classification algorithms represent the largest proportion among the high-impact algorithms. In addition, the evolution of the influence of algorithms reflects the changes in research tasks and topics in the field, and the changes in the influence of different algorithms show different trends. As a preliminary exploration, this paper conducts an analysis of the impact of algorithms mentioned in the academic text, and the results can be used as training data for the automatic extraction of large-scale algorithms in the future. The methodology in this paper is domain-independent and can be applied to other domains.
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