Large scale biomedical texts classification: a kNN and an ESA-based approaches

With the large and increasing volume of textual data, automated methods for identifying significant topics to classify textual documents have received a growing interest. While many efforts have been made in this direction, it still remains a real challenge. Moreover, the issue is even more complex as full texts are not always freely available. Then, using only partial information to annotate these documents is promising but remains a very ambitious issue. MethodsWe propose two classification methods: a k-nearest neighbours (kNN)-based approach and an explicit semantic analysis (ESA)-based approach. Although the kNN-based approach is widely used in text classification, it needs to be improved to perform well in this specific classification problem which deals with partial information. Compared to existing kNN-based methods, our method uses classical Machine Learning (ML) algorithms for ranking the labels. Additional features are also investigated in order to improve the classifiers' performance. In addition, the combination of several learning algorithms with various techniques for fixing the number of relevant topics is performed. On the other hand, ESA seems promising for this classification task as it yielded interesting results in related issues, such as semantic relatedness computation between texts and text classification. Unlike existing works, which use ESA for enriching the bag-of-words approach with additional knowledge-based features, our ESA-based method builds a standalone classifier. Furthermore, we investigate if the results of this method could be useful as a complementary feature of our kNN-based approach.ResultsExperimental evaluations performed on large standard annotated datasets, provided by the BioASQ organizers, show that the kNN-based method with the Random Forest learning algorithm achieves good performances compared with the current state-of-the-art methods, reaching a competitive f-measure of 0.55% while the ESA-based approach surprisingly yielded reserved results.ConclusionsWe have proposed simple classification methods suitable to annotate textual documents using only partial information. They are therefore adequate for large multi-label classification and particularly in the biomedical domain. Thus, our work contributes to the extraction of relevant information from unstructured documents in order to facilitate their automated processing. Consequently, it could be used for various purposes, including document indexing, information retrieval, etc.Comment: Journal of Biomedical Semantics, BioMed Central, 201

Analysis and Modular Approach for Text Extraction from Scientific Figures on Limited Data

Scientific figures are widely used as compact, comprehensible representations of important information. The re-usability of these figures is however limited, as one can rarely search directly for them, since they are mostly indexing by their surrounding text (e. g., publication or website) which often does not contain the full-message of the figure. In this thesis, the focus is on making the content of scientific figures accessible by extracting the text from these figures. A modular pipeline for unsupervised text extraction from scientific figures, based on a thorough analysis of the literature, was built to address the problem. This modular pipeline was used to build several unsupervised approaches, to evaluate different methods from the literature and new methods and method combinations. Some supervised approaches were built as well for comparison. One challenge, while evaluating the approaches, was the lack of annotated data, which especially needed to be considered when building the supervised approach. Three existing datasets were used for evaluation as well as two datasets of 241 scientific figures which were manually created and annotated. Additionally, two existing datasets for text extraction from other types of images were used for pretraining the supervised approach. Several experiments showed the superiority of the unsupervised pipeline over common Optical Character Recognition engines and identified the best unsupervised approach. This unsupervised approach was compared with the best supervised approach, which, despite of the limited amount of training data available, clearly outperformed the unsupervised approach.Infografiken sind ein viel verwendetes Medium zur kompakten Darstellung von Kernaussagen. Die Nachnutzbarkeit dieser Abbildungen ist jedoch häufig limitiert, da sie schlecht auffindbar sind, da sie meist über die umschließenden Medien, wie beispielsweise Publikationen oder Webseiten, und nicht über ihren Inhalt indexiert sind. Der Fokus dieser Arbeit liegt auf der Extraktion der textuellen Inhalte aus Infografiken, um deren Inhalt zu erschließen. Ausgehend von einer umfangreichen Analyse verwandter Arbeiten, wurde ein generalisierender, modularer Ansatz für die unüberwachte Textextraktion aus wissenschaftlichen Abbildungen entwickelt. Mit diesem modularen Ansatz wurden mehrere unüberwachte Ansätze und daneben auch noch einige überwachte Ansätze umgesetzt, um diverse Methoden aus der Literatur sowie neue und bisher noch nicht genutzte Methoden zu vergleichen. Eine Herausforderung bei der Evaluation war die geringe Menge an annotierten Abbildungen, was insbesondere beim überwachten Ansatz Methoden berücksichtigt werden musste. Für die Evaluation wurden drei existierende Datensätze verwendet und zudem wurden zusätzlich zwei Datensätze mit insgesamt 241 Infografiken erstellt und mit den nötigen Informationen annotiert, sodass insgesamt 5 Datensätze für die Evaluation verwendet werden konnten. Für das Pre-Training des überwachten Ansatzes wurden zudem zwei Datensätze aus verwandten Textextraktionsbereichen verwendet. In verschiedenen Experimenten wird gezeigt, dass der unüberwachte Ansatz besser funktioniert als klassische Texterkennungsverfahren und es wird aus den verschiedenen unüberwachten Ansätzen der beste ermittelt. Dieser unüberwachte Ansatz wird mit dem überwachten Ansatz verglichen, der trotz begrenzter Trainingsdaten die besten Ergebnisse liefert

Modelling the Structure and Dynamics of Science Using Books

Scientific research is a major driving force in a knowledge based economy. Income, health and wellbeing depend on scientific progress. The better we understand the inner workings of the scientific enterprise, the better we can prompt, manage, steer, and utilize scientific progress. Diverse indicators and approaches exist to evaluate and monitor research activities, from calculating the reputation of a researcher, institution, or country to analyzing and visualizing global brain circulation. However, there are very few predictive models of science that are used by key decision makers in academia, industry, or government interested to improve the quality and impact of scholarly efforts. We present a novel 'bibliographic bibliometric' analysis which we apply to a large collection of books relevant for the modelling of science. We explain the data collection together with the results of the data analyses and visualizations. In the final section we discuss how the analysis of books that describe different modelling approaches can inform the design of new models of science.Comment: data and large scale maps http://cns.iu.edu/2015-ModSci.html, Ginda, Michael, Andrea Scharnhorst, and Katy B\"orner. "Modelling Science". In Theories of Informetrics: A Festschrift in Honor of Blaise Cronin, edited by Sugimoto, Cassidy. Munich: De Gruyter Sau

Scalable Text Mining with Sparse Generative Models

The information age has brought a deluge of data. Much of this is in text form, insurmountable in scope for humans and incomprehensible in structure for computers. Text mining is an expanding field of research that seeks to utilize the information contained in vast document collections. General data mining methods based on machine learning face challenges with the scale of text data, posing a need for scalable text mining methods. This thesis proposes a solution to scalable text mining: generative models combined with sparse computation. A unifying formalization for generative text models is defined, bringing together research traditions that have used formally equivalent models, but ignored parallel developments. This framework allows the use of methods developed in different processing tasks such as retrieval and classification, yielding effective solutions across different text mining tasks. Sparse computation using inverted indices is proposed for inference on probabilistic models. This reduces the computational complexity of the common text mining operations according to sparsity, yielding probabilistic models with the scalability of modern search engines. The proposed combination provides sparse generative models: a solution for text mining that is general, effective, and scalable. Extensive experimentation on text classification and ranked retrieval datasets are conducted, showing that the proposed solution matches or outperforms the leading task-specific methods in effectiveness, with a order of magnitude decrease in classification times for Wikipedia article categorization with a million classes. The developed methods were further applied in two 2014 Kaggle data mining prize competitions with over a hundred competing teams, earning first and second places

Training Datasets for Machine Reading Comprehension and Their Limitations

Neural networks are a powerful model class to learn machine Reading Comprehen- sion (RC), yet they crucially depend on the availability of suitable training datasets. In this thesis we describe methods for data collection, evaluate the performance of established models, and examine a number of model behaviours and dataset limita- tions. We first describe the creation of a data resource for the science exam QA do- main, and compare existing models on the resulting dataset. The collected ques- tions are plausible – non-experts can distinguish them from real exam questions with 55% accuracy – and using them as additional training data leads to improved model scores on real science exam questions. Second, we describe and apply a distant supervision dataset construction method for multi-hop RC across documents. We identify and mitigate several dataset assembly pitfalls – a lack of unanswerable candidates, label imbalance, and spurious correlations between documents and particular candidates – which often leave shallow predictive cues for the answer. Furthermore we demonstrate that se- lecting relevant document combinations is a critical performance bottleneck on the datasets created. We thus investigate Pseudo-Relevance Feedback, which leads to improvements compared to TF-IDF-based document combination selection both in retrieval metrics and answer accuracy. Third, we investigate model undersensitivity: model predictions do not change when given adversarially altered questions in SQUAD2.0 and NEWSQA, even though they should. We characterise affected samples, and show that the phe- nomenon is related to a lack of structurally similar but unanswerable samples during training: data augmentation reduces the adversarial error rate, e.g. from 51.7% to 20.7% for a BERT model on SQUAD2.0, and improves robustness also in other settings. Finally we explore efficient formal model verification via Interval Bound Propagation (IBP) to measure and address model undersensitivity, and show that using an IBP-derived auxiliary loss can improve verification rates, e.g. from 2.8% to 18.4% on the SNLI test set

On the Nature and Types of Anomalies: A Review

Anomalies are occurrences in a dataset that are in some way unusual and do not fit the general patterns. The concept of the anomaly is generally ill-defined and perceived as vague and domain-dependent. Moreover, despite some 250 years of publications on the topic, no comprehensive and concrete overviews of the different types of anomalies have hitherto been published. By means of an extensive literature review this study therefore offers the first theoretically principled and domain-independent typology of data anomalies, and presents a full overview of anomaly types and subtypes. To concretely define the concept of the anomaly and its different manifestations, the typology employs five dimensions: data type, cardinality of relationship, anomaly level, data structure and data distribution. These fundamental and data-centric dimensions naturally yield 3 broad groups, 9 basic types and 61 subtypes of anomalies. The typology facilitates the evaluation of the functional capabilities of anomaly detection algorithms, contributes to explainable data science, and provides insights into relevant topics such as local versus global anomalies.Comment: 38 pages (30 pages content), 10 figures, 3 tables. Preprint; review comments will be appreciated. Improvements in version 2: Explicit mention of fifth anomaly dimension; Added section on explainable anomaly detection; Added section on variations on the anomaly concept; Various minor additions and improvement

Contribution à la construction d’ontologies et à la recherche d’information : application au domaine médical

This work aims at providing efficient access to relevant information among the increasing volume of digital data. Towards this end, we studied the benefit from using ontology to support an information retrieval (IR) system.We first described a methodology for constructing ontologies. Thus, we proposed a mixed method which combines natural language processing techniques for extracting knowledge from text and the reuse of existing semantic resources for the conceptualization step. We have also developed a method for aligning terms in English and French in order to enrich terminologically the resulting ontology. The application of our methodology resulted in a bilingual ontology dedicated to Alzheimer’s disease.We then proposed algorithms for supporting ontology-based semantic IR. Thus, we used concepts from ontology for describing documents automatically and for query reformulation. We were particularly interested in: 1) the extraction of concepts from texts, 2) the disambiguation of terms, 3) the vectorial weighting schema adapted to concepts and 4) query expansion. These algorithms have been used to implement a semantic portal about Alzheimer’s disease. Further, because the content of documents are not always fully available, we exploited incomplete information for identifying the concepts, which are relevant for indexing the whole content of documents. Toward this end, we have proposed two classification methods: the first is based on the k nearest neighbors’ algorithm and the second on the explicit semantic analysis. The two methods have been evaluated on large standard collections of biomedical documents within an international challenge.Ce travail vise à permettre un accès efficace à des informations pertinentes malgré le volume croissant des données disponibles au format électronique. Pour cela, nous avons étudié l’apport d’une ontologie au sein d’un système de recherche d'information (RI).Nous avons tout d’abord décrit une méthodologie de construction d’ontologies. Ainsi, nous avons proposé une méthode mixte combinant des techniques de traitement automatique des langues pour extraire des connaissances à partir de textes et la réutilisation de ressources sémantiques existantes pour l’étape de conceptualisation. Nous avons par ailleurs développé une méthode d’alignement de termes français-anglais pour l’enrichissement terminologique de l’ontologie. L’application de notre méthodologie a permis de créer une ontologie bilingue de la maladie d’Alzheimer.Ensuite, nous avons élaboré des algorithmes pour supporter la RI sémantique guidée par une ontologie. Les concepts issus d’une ontologie ont été utilisés pour décrire automatiquement les documents mais aussi pour reformuler les requêtes. Nous nous sommes intéressés à : 1) l’identification de concepts représentatifs dans des corpus, 2) leur désambiguïsation, 3), leur pondération selon le modèle vectoriel, adapté aux concepts et 4) l’expansion de requêtes. Ces propositions ont permis de mettre en œuvre un portail de RI sémantique dédié à la maladie d’Alzheimer. Par ailleurs, le contenu des documents à indexer n’étant pas toujours accessible dans leur ensemble, nous avons exploité des informations incomplètes pour déterminer les concepts pertinents permettant malgré tout de décrire les documents. Pour cela, nous avons proposé deux méthodes de classification de documents issus d’un large corpus, l’une basée sur l’algorithme des k plus proches voisins et l’autre sur l’analyse sémantique explicite. Ces méthodes ont été évaluées sur de larges collections de documents biomédicaux fournies lors d’un challenge international