Investigating Genotype-Phenotype relationship extraction from biomedical text

During the last decade biomedicine has developed at a tremendous pace. Every day a lot of biomedical papers are published and a large amount of new information is produced. To help enable automated and human interaction in the multitude of applications of this biomedical data, the need for Natural Language Processing systems to process the vast amount of new information is increasing. Our main purpose in this research project is to extract the relationships between genotypes and phenotypes mentioned in the biomedical publications. Such a system provides important and up-to-date data for database construction and updating, and even text summarization. To achieve this goal we had to solve three main problems: finding genotype names, finding phenotype names, and finally extracting phenotype--genotype interactions. We consider all these required modules in a comprehensive system and propose a promising solution for each of them taking into account available tools and resources. BANNER, an open source biomedical named entity recognition system, which has achieved good results in detecting genotypes, has been used for the genotype name recognition task. We were the first group to start working on phenotype name recognition. We have developed two different systems (rule-based and machine-learning based) for extracting phenotype names from text. These systems incorporated the available knowledge from the Unified Medical Language System metathesaurus and the Human Phenotype Onotolgy (HPO). As there was no available annotated corpus for phenotype names, we created a valuable corpus with annotated phenotype names using information available in HPO and a self-training method which can be used for future research. To solve the final problem of this project i.e. , phenotype--genotype relationship extraction, a machine learning method has been proposed. As there was no corpus available for this task and it was not possible for us to annotate a sufficiently large corpus manually, a semi-automatic approach has been used to annotate a small corpus and a self-training method has been proposed to annotate more sentences and enlarge this corpus. A test set was manually annotated by an expert. In addition to having phenotype-genotype relationships annotated, the test set contains important comments about the nature of these relationships. The evaluation results related to each system demonstrate the significantly good performance of all the proposed methods

Text-to-picture tools, systems, and approaches: a survey

Text-to-picture systems attempt to facilitate high-level, user-friendly communication between humans and computers while promoting understanding of natural language. These systems interpret a natural language text and transform it into a visual format as pictures or images that are either static or dynamic. In this paper, we aim to identify current difficulties and the main problems faced by prior systems, and in particular, we seek to investigate the feasibility of automatic visualization of Arabic story text through multimedia. Hence, we analyzed a number of well-known text-to-picture systems, tools, and approaches. We showed their constituent steps, such as knowledge extraction, mapping, and image layout, as well as their performance and limitations. We also compared these systems based on a set of criteria, mainly natural language processing, natural language understanding, and input/output modalities. Our survey showed that currently emerging techniques in natural language processing tools and computer vision have made promising advances in analyzing general text and understanding images and videos. Furthermore, important remarks and findings have been deduced from these prior works, which would help in developing an effective text-to-picture system for learning and educational purposes. - 2019, The Author(s).This work was made possible by NPRP grant #10-0205-170346 from the Qatar National Research Fund (a member of Qatar Foundation). The statements made herein are solely the responsibility of the authors

Towards Communicating Simple Sentence using Pictorial Representations

Language can sometimes be an impediment in communication. Whether we are talking about people who speak different languages, students who are learning a new language, or people with language disorders, the understanding of linguistic representations in a given language requires a certain amount of knowledge that not everybody has. In this thesis, we propose "translation through pictures" as a means for conveying simple pieces of information across language barriers, and describe a system that can automatically generate pictorial representations for simple sentences. Comparative experiments conducted on visual and linguistic representations of information show that a considerable amount of understanding can be achieved through pictorial descriptions, with results within a comparable range of those obtained with current machine translation techniques. Moreover, a user study conducted around the pictorial translation system reveals that users found the system to generally produce correct word/image associations, and rate the system as interactive and intelligent

Theory and Applications for Advanced Text Mining

Due to the growth of computer technologies and web technologies, we can easily collect and store large amounts of text data. We can believe that the data include useful knowledge. Text mining techniques have been studied aggressively in order to extract the knowledge from the data since late 1990s. Even if many important techniques have been developed, the text mining research field continues to expand for the needs arising from various application fields. This book is composed of 9 chapters introducing advanced text mining techniques. They are various techniques from relation extraction to under or less resourced language. I believe that this book will give new knowledge in the text mining field and help many readers open their new research fields

Sentence Simplification for Text Processing

A thesis submitted in partial fulfilment of the requirement of the University of Wolverhampton for the degree of Doctor of Philosophy.Propositional density and syntactic complexity are two features of sentences which affect the ability of humans and machines to process them effectively. In this thesis, I present a new approach to automatic sentence simplification which processes sentences containing compound clauses and complex noun phrases (NPs) and converts them into sequences of simple sentences which contain fewer of these constituents and have reduced per sentence propositional density and syntactic complexity. My overall approach is iterative and relies on both machine learning and handcrafted rules. It implements a small set of sentence transformation schemes, each of which takes one sentence containing compound clauses or complex NPs and converts it one or two simplified sentences containing fewer of these constituents (Chapter 5). The iterative algorithm applies the schemes repeatedly and is able to simplify sentences which contain arbitrary numbers of compound clauses and complex NPs. The transformation schemes rely on automatic detection of these constituents, which may take a variety of forms in input sentences. In the thesis, I present two new shallow syntactic analysis methods which facilitate the detection process. The first of these identifies various explicit signs of syntactic complexity in input sentences and classifies them according to their specific syntactic linking and bounding functions. I present the annotated resources used to train and evaluate this sign tagger (Chapter 2) and the machine learning method used to implement it (Chapter 3). The second syntactic analysis method exploits the sign tagger and identifies the spans of compound clauses and complex NPs in input sentences. In Chapter 4 of the thesis, I describe the development and evaluation of a machine learning approach performing this task. This chapter also presents a new annotated dataset supporting this activity. In the thesis, I present two implementations of my approach to sentence simplification. One of these exploits handcrafted rule activation patterns to detect different parts of input sentences which are relevant to the simplification process. The other implementation uses my machine learning method to identify compound clauses and complex NPs for this purpose. Intrinsic evaluation of the two implementations is presented in Chapter 6 together with a comparison of their performance with several baseline systems. The evaluation includes comparisons of system output with human-produced simplifications, automated estimations of the readability of system output, and surveys of human opinions on the grammaticality, accessibility, and meaning of automatically produced simplifications. Chapter 7 presents extrinsic evaluation of the sentence simplification method exploiting handcrafted rule activation patterns. The extrinsic evaluation involves three NLP tasks: multidocument summarisation, semantic role labelling, and information extraction. Finally, in Chapter 8, conclusions are drawn and directions for future research considered

Proceedings of the Eighth Italian Conference on Computational Linguistics CliC-it 2021

The eighth edition of the Italian Conference on Computational Linguistics (CLiC-it 2021) was held at Università degli Studi di Milano-Bicocca from 26th to 28th January 2022. After the edition of 2020, which was held in fully virtual mode due to the health emergency related to Covid-19, CLiC-it 2021 represented the first moment for the Italian research community of Computational Linguistics to meet in person after more than one year of full/partial lockdown

Shape analysis of the human brain.

Autism is a complex developmental disability that has dramatically increased in prevalence, having a decisive impact on the health and behavior of children. Methods used to detect and recommend therapies have been much debated in the medical community because of the subjective nature of diagnosing autism. In order to provide an alternative method for understanding autism, the current work has developed a 3-dimensional state-of-the-art shape based analysis of the human brain to aid in creating more accurate diagnostic assessments and guided risk analyses for individuals with neurological conditions, such as autism. Methods: The aim of this work was to assess whether the shape of the human brain can be used as a reliable source of information for determining whether an individual will be diagnosed with autism. The study was conducted using multi-center databases of magnetic resonance images of the human brain. The subjects in the databases were analyzed using a series of algorithms consisting of bias correction, skull stripping, multi-label brain segmentation, 3-dimensional mesh construction, spherical harmonic decomposition, registration, and classification. The software algorithms were developed as an original contribution of this dissertation in collaboration with the BioImaging Laboratory at the University of Louisville Speed School of Engineering. The classification of each subject was used to construct diagnoses and therapeutic risk assessments for each patient. Results: A reliable metric for making neurological diagnoses and constructing therapeutic risk assessment for individuals has been identified. The metric was explored in populations of individuals having autism spectrum disorders, dyslexia, Alzheimers disease, and lung cancer. Conclusion: Currently, the clinical applicability and benefits of the proposed software approach are being discussed by the broader community of doctors, therapists, and parents for use in improving current methods by which autism spectrum disorders are diagnosed and understood

Proceedings of the Fifth Italian Conference on Computational Linguistics CLiC-it 2018 : 10-12 December 2018, Torino

On behalf of the Program Committee, a very warm welcome to the Fifth Italian Conference on Computational Linguistics (CLiC-­‐it 2018). This edition of the conference is held in Torino. The conference is locally organised by the University of Torino and hosted into its prestigious main lecture hall “Cavallerizza Reale”. The CLiC-­‐it conference series is an initiative of the Italian Association for Computational Linguistics (AILC) which, after five years of activity, has clearly established itself as the premier national forum for research and development in the fields of Computational Linguistics and Natural Language Processing, where leading researchers and practitioners from academia and industry meet to share their research results, experiences, and challenges

Tipping the scales: exploring the added value of deep semantic processing on readability prediction and sentiment analysis

Applications which make use of natural language processing (NLP) are said to benefit more from incorporating a rich model of text meaning than from a basic representation in the form of bag-of-words. This thesis set out to explore the added value of incorporating deep semantic information in two end-user applications that normally rely mostly on superficial and lexical information, viz. readability prediction and aspect-based sentiment analysis. For both applications we apply supervised machine learning techniques and focus on the incorporation of coreference and semantic role information. To this purpose, we adapted a Dutch coreference resolution system and developed a semantic role labeler for Dutch. We tested the cross-genre robustness of both systems and in a next phase retrained them on a large corpus comprising a variety of text genres. For the readability prediction task, we first built a general-purpose corpus consisting of a large variety of text genres which was then assessed on readability. Moreover, we proposed an assessment technique which has not previously been used in readability assessment, namely crowdsourcing, and revealed that crowdsourcing is a viable alternative to the more traditional assessment technique of having experts assign labels. We built the first state-of-the-art classification-based readability prediction system relying on a rich feature space of traditional, lexical, syntactic and shallow semantic features. Furthermore, we enriched this tool by introducing new features based on coreference resolution and semantic role labeling. We then explored the added value of incorporating this deep semantic information by performing two different rounds of experiments. In the first round these features were manually in- or excluded and in the second round joint optimization experiments were performed using a wrapper-based feature selection system based on genetic algorithms. In both setups, we investigated whether there was a difference in performance when these features were derived from gold standard information compared to when they were automatically generated, which allowed us to assess the true upper bound of incorporating this type of information. Our results revealed that readability classification definitely benefits from the incorporation of semantic information in the form of coreference and semantic role features. More precisely, we found that the best results for both tasks were achieved after jointly optimizing the hyperparameters and semantic features using genetic algorithms. Contrary to our expectations, we observed that our system achieved its best performance when relying on the automatically predicted deep semantic features. This is an interesting result, as our ultimate goal is to predict readability based exclusively on automatically-derived information sources. For the aspect-based sentiment analysis task, we developed the first Dutch end-to-end system. We therefore collected a corpus of Dutch restaurant reviews and annotated each review with aspect term expressions and polarity. For the creation of our system, we distinguished three individual subtasks: aspect term extraction, aspect category classification and aspect polarity classification. We then investigated the added value of our two semantic information layers in the second subtask of aspect category classification. In a first setup, we focussed on investigating the added value of performing coreference resolution prior to classification in order to derive which implicit aspect terms (anaphors) could be linked to which explicit aspect terms (antecedents). In these experiments, we explored how the performance of a baseline classifier relying on lexical information alone would benefit from additional semantic information in the form of lexical-semantic and semantic role features. We hypothesized that if coreference resolution was performed prior to classification, more of this semantic information could be derived, i.e. for the implicit aspect terms, which would result in a better performance. In this respect, we optimized our classifier using a wrapper-based approach for feature selection and we compared a setting where we relied on gold-standard anaphor-antecedent pairs to a setting where these had been predicted. Our results revealed a very moderate performance gain and underlined that incorporating coreference information only proves useful when integrating gold-standard coreference annotations. When coreference relations were derived automatically, this led to an overall decrease in performance because of semantic mismatches. When comparing the semantic role to the lexical-semantic features, it seemed that especially the latter features allow for a better performance. In a second setup, we investigated how to resolve implicit aspect terms. We compared a setting where gold-standard coreference resolution was used for this purpose to a setting where the implicit aspects were derived from a simple subjectivity heuristic. Our results revealed that using this heuristic results in a better coverage and performance, which means that, overall, it was difficult to find an added value in resolving coreference first. Does deep semantic information help tip the scales on performance? For Dutch readability prediction, we found that it does, when integrated in a state-of-the-art classifier. By using such information for Dutch aspect-based sentiment analysis, we found that this approach adds weight to the scales, but cannot make them tip