PICO entity extraction for preclinical animal literature

BACKGROUND: Natural language processing could assist multiple tasks in systematic reviews to reduce workflow, including the extraction of PICO elements such as study populations, interventions, comparators and outcomes. The PICO framework provides a basis for the retrieval and selection for inclusion of evidence relevant to a specific systematic review question, and automatic approaches to PICO extraction have been developed particularly for reviews of clinical trial findings. Considering the difference between preclinical animal studies and clinical trials, developing separate approaches is necessary. Facilitating preclinical systematic reviews will inform the translation from preclinical to clinical research. METHODS: We randomly selected 400 abstracts from the PubMed Central Open Access database which described in vivo animal research and manually annotated these with PICO phrases for Species, Strain, methods of Induction of disease model, Intervention, Comparator and Outcome. We developed a two-stage workflow for preclinical PICO extraction. Firstly we fine-tuned BERT with different pre-trained modules for PICO sentence classification. Then, after removing the text irrelevant to PICO features, we explored LSTM-, CRF- and BERT-based models for PICO entity recognition. We also explored a self-training approach because of the small training corpus. RESULTS: For PICO sentence classification, BERT models using all pre-trained modules achieved an F1 score of over 80%, and models pre-trained on PubMed abstracts achieved the highest F1 of 85%. For PICO entity recognition, fine-tuning BERT pre-trained on PubMed abstracts achieved an overall F1 of 71% and satisfactory F1 for Species (98%), Strain (70%), Intervention (70%) and Outcome (67%). The score of Induction and Comparator is less satisfactory, but F1 of Comparator can be improved to 50% by applying self-training. CONCLUSIONS: Our study indicates that of the approaches tested, BERT pre-trained on PubMed abstracts is the best for both PICO sentence classification and PICO entity recognition in the preclinical abstracts. Self-training yields better performance for identifying comparators and strains

Template-Based Question Answering over Linked Data using Recursive Neural Networks

abstract: The Semantic Web contains large amounts of related information in the form of knowledge graphs such as DBpedia. These knowledge graphs are typically enormous and are not easily accessible for users as they need specialized knowledge in query languages (such as SPARQL) as well as deep familiarity of the ontologies used by these knowledge graphs. So, to make these knowledge graphs more accessible (even for non- experts) several question answering (QA) systems have been developed over the last decade. Due to the complexity of the task, several approaches have been undertaken that include techniques from natural language processing (NLP), information retrieval (IR), machine learning (ML) and the Semantic Web (SW). At a higher level, most question answering systems approach the question answering task as a conversion from the natural language question to its corresponding SPARQL query. These systems then utilize the query to retrieve the desired entities or literals. One approach to solve this problem, that is used by most systems today, is to apply deep syntactic and semantic analysis on the input question to derive the SPARQL query. This has resulted in the evolution of natural language processing pipelines that have common characteristics such as answer type detection, segmentation, phrase matching, part-of-speech-tagging, named entity recognition, named entity disambiguation, syntactic or dependency parsing, semantic role labeling, etc. This has lead to NLP pipeline architectures that integrate components that solve a specific aspect of the problem and pass on the results to subsequent components for further processing eg: DBpedia Spotlight for named entity recognition, RelMatch for relational mapping, etc. A major drawback in this approach is error propagation that is a common problem in NLP. This can occur due to mistakes early on in the pipeline that can adversely affect successive steps further down the pipeline. Another approach is to use query templates either manually generated or extracted from existing benchmark datasets such as Question Answering over Linked Data (QALD) to generate the SPARQL queries that is basically a set of predefined queries with various slots that need to be filled. This approach potentially shifts the question answering problem into a classification task where the system needs to match the input question to the appropriate template (class label). This thesis proposes a neural network approach to automatically learn and classify natural language questions into its corresponding template using recursive neural networks. An obvious advantage of using neural networks is the elimination for the need of laborious feature engineering that can be cumbersome and error prone. The input question would be encoded into a vector representation. The model will be trained and evaluated on the LC-QuAD Dataset (Large-scale Complex Question Answering Dataset). The dataset was created explicitly for machine learning based QA approaches for learning complex SPARQL queries. The dataset consists of 5000 questions along with their corresponding SPARQL queries over the DBpedia dataset spanning 5042 entities and 615 predicates. These queries were annotated based on 38 unique templates that the model will attempt to classify. The resulting model will be evaluated against both the LC-QuAD dataset and the Question Answering Over Linked Data (QALD-7) dataset. The recursive neural network achieves template classification accuracy of 0.828 on the LC-QuAD dataset and an accuracy of 0.618 on the QALD-7 dataset. When the top-2 most likely templates were considered the model achieves an accuracy of 0.945 on the LC-QuAD dataset and 0.786 on the QALD-7 dataset. After slot filling, the overall system achieves a macro F-score 0.419 on the LC- QuAD dataset and a macro F-score of 0.417 on the QALD-7 dataset.Dissertation/ThesisMasters Thesis Software Engineering 201

DeepVar: An End-to-End Deep Learning Approach for Genomic Variant Recognition in Biomedical Literature

We consider the problem of Named Entity Recognition (NER) on biomedical scientific literature, and more specifically the genomic variants recognition in this work. Significant success has been achieved for NER on canonical tasks in recent years where large data sets are generally available. However, it remains a challenging problem on many domain-specific areas, especially the domains where only small gold annotations can be obtained. In addition, genomic variant entities exhibit diverse linguistic heterogeneity, differing much from those that have been characterized in existing canonical NER tasks. The state-of-the-art machine learning approaches in such tasks heavily rely on arduous feature engineering to characterize those unique patterns. In this work, we present the first successful end-to-end deep learning approach to bridge the gap between generic NER algorithms and low-resource applications through genomic variants recognition. Our proposed model can result in promising performance without any hand-crafted features or post-processing rules. Our extensive experiments and results may shed light on other similar low-resource NER applications.Comment: accepted by AAAI 202

Data augmentation for named entity recognition in the German legal domain

Named Entity Recognition over texts from the legal domain aims to recognize legal entities such as references to legal norms or court decisions. This task is commonly approached with supervised deep learning techniques that require large amounts of training data. However, especially for low-resource languages and specific domains, such training data is often scarce. In this work, we focus on the German legal domain because it is of interest to the Canarėno project, which deals with information extraction from and analysis of legal norms. The objective of the work presented in this thesis is the implementation, evaluation, and comparison of different data augmentation techniques that can be used to expand the available data and thereby improve model performance. Through experiments on different dataset fractions, we show that Mention Replacement and Synonym Replacement can effectively enhance the performance of both recurrent and transformer-based NER models in low-resource environments.Die Anwendung von Named Entity Recognition auf Texte aus dem juristischen Bereich zielt darauf ab, juristische Entitäten wie Referenzen auf Rechtsnormen oder Gerichtsentscheidungen zu erkennen. Diese Aufgabe wird in der Regel mit überwachten Deep-Learning-Techniken angegangen, die große Mengen an Trainingsdaten erfordern. Vor allem für Sprachen mit geringen Ressourcen und für bestimmte Domänen sind solche Trainingsdaten jedoch oft rar. In dieser Arbeit konzentrieren wir uns auf die deutsche Rechtsdomäne, da sie für das Canarėno-Projekt von Interesse ist, das sich mit der Informationsextraktion aus und Analyse von Rechtsnormen beschäftigt. Das Ziel dieser Arbeit ist die Implementierung, Bewertung und der Vergleich verschiedener Techniken, die zur Erweiterung von verfügbaren Daten und damit zur Verbesserung der Modellleistung eingesetzt werden können. Durch Experimente mit verschiedenen Datensatzanteilen zeigen wir, dass Mention Replacement und Synonym Replacement die Leistung von sowohl rekurrenten als auch von transformatorischen NERModellen in ressourcenarmen Umgebungen effektiv verbessern können

A review on Natural Language Processing Models for COVID-19 research

This survey paper reviews Natural Language Processing Models and their use in COVID-19 research in two main areas. Firstly, a range of transformer-based biomedical pretrained language models are evaluated using the BLURB benchmark. Secondly, models used in sentiment analysis surrounding COVID-19 vaccination are evaluated. We filtered literature curated from various repositories such as PubMed and Scopus and reviewed 27 papers. When evaluated using the BLURB benchmark, the novel T-BPLM BioLinkBERT gives groundbreaking results by incorporating document link knowledge and hyperlinking into its pretraining. Sentiment analysis of COVID-19 vaccination through various Twitter API tools has shown the public’s sentiment towards vaccination to be mostly positive. Finally, we outline some limitations and potential solutions to drive the research community to improve the models used for NLP tasks

A word-building method based on neural network for text classification

Text classification is a foundational task in many natural language processing applications. All traditional text classifiers take words as the basic units and conduct the pre-training process (like word2vec) to directly generate word vectors at the first step. However, none of them have considered the information contained in word structure which is proved to be helpful for text classification. In this paper, we propose a word-building method based on neural network model that can decompose a Chinese word to a sequence of radicals and learn structure information from these radical level features which is a key difference from the existing models. Then, the convolutional neural network is applied to extract structure information of words from radical sequence to generate a word vector, and the long short-term memory is applied to generate the sentence vector for the prediction purpose. The experimental results show that our model outperforms other existing models on Chinese dataset. Our model is also applicable to English as well where an English word can be decomposed down to character level, which demonstrates the excellent generalisation ability of our model. The experimental results have proved that our model also outperforms others on English dataset