HOLMES: A Hybrid Ontology-Learning Materials Engineering System

Designing and discovering novel materials is challenging problem in many domains such as fuel additives, composites, pharmaceuticals, and so on. At the core of all this are models that capture how the different domain-specific data, information, and knowledge regarding the structures and properties of the materials are related to one another. This dissertation explores the difficult task of developing an artificial intelligence-based knowledge modeling environment, called Hybrid Ontology-Learning Materials Engineering System (HOLMES) that can assist humans in populating a materials science and engineering ontology through automatic information extraction from journal article abstracts. While what we propose may be adapted for a generic materials engineering application, our focus in this thesis is on the needs of the pharmaceutical industry. We develop the Columbia Ontology for Pharmaceutical Engineering (COPE), which is a modification of the Purdue Ontology for Pharmaceutical Engineering. COPE serves as the basis for HOLMES. The HOLMES framework starts with journal articles that are in the Portable Document Format (PDF) and ends with the assignment of the entries in the journal articles into ontologies. While this might seem to be a simple task of information extraction, to fully extract the information such that the ontology is filled as completely and correctly as possible is not easy when considering a fully developed ontology. In the development of the information extraction tasks, we note that there are new problems that have not arisen in previous information extraction work in the literature. The first is the necessity to extract auxiliary information in the form of concepts such as actions, ideas, problem specifications, properties, etc. The second problem is in the existence of multiple labels for a single token due to the existence of the aforementioned concepts. These two problems are the focus of this dissertation. In this work, the HOLMES framework is presented as a whole, describing our successful progress as well as unsolved problems, which might help future research on this topic. The ontology is then presented to help in the identification of the relevant information that needs to be retrieved. The annotations are next developed to create the data sets necessary for the machine learning algorithms to perform. Then, the current level of information extraction for these concepts is explored and expanded. This is done through the introduction of entity feature sets that are based on previously extracted entities from the entity recognition task. And finally, the new task of handling multiple labels for tagging a single entity is also explored by the use of multiple-label algorithms used primarily in image processing

Adaptive Algorithms for Automated Processing of Document Images

Large scale document digitization projects continue to motivate interesting document understanding technologies such as script and language identification, page classification, segmentation and enhancement. Typically, however, solutions are still limited to narrow domains or regular formats such as books, forms, articles or letters and operate best on clean documents scanned in a controlled environment. More general collections of heterogeneous documents challenge the basic assumptions of state-of-the-art technology regarding quality, script, content and layout. Our work explores the use of adaptive algorithms for the automated analysis of noisy and complex document collections. We first propose, implement and evaluate an adaptive clutter detection and removal technique for complex binary documents. Our distance transform based technique aims to remove irregular and independent unwanted foreground content while leaving text content untouched. The novelty of this approach is in its determination of best approximation to clutter-content boundary with text like structures. Second, we describe a page segmentation technique called Voronoi++ for complex layouts which builds upon the state-of-the-art method proposed by Kise [Kise1999]. Our approach does not assume structured text zones and is designed to handle multi-lingual text in both handwritten and printed form. Voronoi++ is a dynamically adaptive and contextually aware approach that considers components' separation features combined with Docstrum [O'Gorman1993] based angular and neighborhood features to form provisional zone hypotheses. These provisional zones are then verified based on the context built from local separation and high-level content features. Finally, our research proposes a generic model to segment and to recognize characters for any complex syllabic or non-syllabic script, using font-models. This concept is based on the fact that font files contain all the information necessary to render text and thus a model for how to decompose them. Instead of script-specific routines, this work is a step towards a generic character and recognition scheme for both Latin and non-Latin scripts

EEG signal classification using wavelet feature extraction and neural networks

Decision support systems have been utilised since 1960, providing physicians with fast and accurate means towards more accurate diagnoses and increased tolerance when handling missing or incomplete data. This paper describes the application of neural network models for classification of electroencephalogram (EEG) signals. Decision making was performed in two stages: initially, a feature extraction scheme using the wavelet transform (WT) has been applied and then a learning-based algorithm classifier performed the classification. The performance of the neural model was evaluated in terms of training performance and classification accuracies and the results confirmed that the proposed scheme has potential in classifying the EEG signals

Machine Learning in Automated Text Categorization

The automated categorization (or classification) of texts into predefined categories has witnessed a booming interest in the last ten years, due to the increased availability of documents in digital form and the ensuing need to organize them. In the research community the dominant approach to this problem is based on machine learning techniques: a general inductive process automatically builds a classifier by learning, from a set of preclassified documents, the characteristics of the categories. The advantages of this approach over the knowledge engineering approach (consisting in the manual definition of a classifier by domain experts) are a very good effectiveness, considerable savings in terms of expert manpower, and straightforward portability to different domains. This survey discusses the main approaches to text categorization that fall within the machine learning paradigm. We will discuss in detail issues pertaining to three different problems, namely document representation, classifier construction, and classifier evaluation.Comment: Accepted for publication on ACM Computing Survey

Feature Extraction Methods for Character Recognition

Not Include

Integrating in silico models and read-across methods for predicting toxicity of chemicals: A step-wise strategy

Abstract In silico methods and models are increasingly used for predicting properties of chemicals for hazard identification and hazard characterisation in the absence of experimental toxicity data. Many in silico models are available and can be used individually or in an integrated fashion. Whilst such models offer major benefits to toxicologists, risk assessors and the global scientific community, the lack of a consistent framework for the integration of in silico results can lead to uncertainty and even contradictions across models and users, even for the same chemicals. In this context, a range of methods for integrating in silico results have been proposed on a statistical or case-specific basis. Read-across constitutes another strategy for deriving reference points or points of departure for hazard characterisation of untested chemicals, from the available experimental data for structurally-similar compounds, mostly using expert judgment. Recently a number of software systems have been developed to support experts in this task providing a formalised and structured procedure. Such a procedure could also facilitate further integration of the results generated from in silico models and read-across. This article discusses a framework on weight of evidence published by EFSA to identify the stepwise approach for systematic integration of results or values obtained from these "non-testing methods". Key criteria and best practices for selecting and evaluating individual in silico models are also described, together with the means to combining the results, taking into account any limitations, and identifying strategies that are likely to provide consistent results

Text localization and recognition in natural scene images

Text localization and recognition (text spotting) in natural scene images is an interesting task that finds many practical applications. Algorithms for text spotting may be used in helping visually impaired subjects during navigation in unknown environments; building autonomous driving systems that automatically avoid collisions with pedestrians or automatically identify speed limits and warn the driver about possible infractions that are being committed; and to ease or solve some tedious and repetitive data entry tasks that are still manually carried out by humans. While Optical Character Recognition (OCR) from scanned documents is a solved problem, the same cannot be said for text spotting in natural images. In fact, this latest class of images contains plenty of difficult situations that algorithms for text spotting need to deal with in order to reach acceptable recognition rates. During my PhD research I focused my studies on the development of novel systems for text localization and recognition in natural scene images. The two main works that I have presented during these three years of PhD studies are presented in this thesis: (i) in my first work I propose a hybrid system which exploits the key ideas of region-based and connected components (CC)-based text localization approaches to localize uncommon fonts and writings in natural images; (ii) in my second work I describe a novel deep-based system which exploits Convolutional Neural Networks and enhanced stable CC to achieve good text spotting results on challenging data sets. During the development of both these methods, my focus has always been on maintaining an acceptable computational complexity and a high reproducibility of the achieved results

Text localization and recognition in natural scene images

Text localization and recognition (text spotting) in natural scene images is an interesting task that finds many practical applications. Algorithms for text spotting may be used in helping visually impaired subjects during navigation in unknown environments; building autonomous driving systems that automatically avoid collisions with pedestrians or automatically identify speed limits and warn the driver about possible infractions that are being committed; and to ease or solve some tedious and repetitive data entry tasks that are still manually carried out by humans. While Optical Character Recognition (OCR) from scanned documents is a solved problem, the same cannot be said for text spotting in natural images. In fact, this latest class of images contains plenty of difficult situations that algorithms for text spotting need to deal with in order to reach acceptable recognition rates. During my PhD research I focused my studies on the development of novel systems for text localization and recognition in natural scene images. The two main works that I have presented during these three years of PhD studies are presented in this thesis: (i) in my first work I propose a hybrid system which exploits the key ideas of region-based and connected components (CC)-based text localization approaches to localize uncommon fonts and writings in natural images; (ii) in my second work I describe a novel deep-based system which exploits Convolutional Neural Networks and enhanced stable CC to achieve good text spotting results on challenging data sets. During the development of both these methods, my focus has always been on maintaining an acceptable computational complexity and a high reproducibility of the achieved results