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

Enhanced ontology-based text classification algorithm for structurally organized documents

Text classification (TC) is an important foundation of information retrieval and text mining. The main task of a TC is to predict the text‟s class according to the type of tag given in advance. Most TC algorithms used terms in representing the document which does not consider the relations among the terms. These algorithms represent documents in a space where every word is assumed to be a dimension. As a result such representations generate high dimensionality which gives a negative effect on the classification performance. The objectives of this thesis are to formulate algorithms for classifying text by creating suitable feature vector and reducing the dimension of data which will enhance the classification accuracy. This research combines the ontology and text representation for classification by developing five algorithms. The first and second algorithms namely Concept Feature Vector (CFV) and Structure Feature Vector (SFV), create feature vector to represent the document. The third algorithm is the Ontology Based Text Classification (OBTC) and is designed to reduce the dimensionality of training sets. The fourth and fifth algorithms, Concept Feature Vector_Text Classification (CFV_TC) and Structure Feature Vector_Text Classification (SFV_TC) classify the document to its related set of classes. These proposed algorithms were tested on five different scientific paper datasets downloaded from different digital libraries and repositories. Experimental obtained from the proposed algorithm, CFV_TC and SFV_TC shown better average results in terms of precision, recall, f-measure and accuracy compared against SVM and RSS approaches. The work in this study contributes to exploring the related document in information retrieval and text mining research by using ontology in TC

Modern considerations for the use of naive Bayes in the supervised classification of genetic sequence data

2021 Spring.Includes bibliographical references.Genetic sequence classification is the task of assigning a known genetic label to an unknown genetic sequence. Often, this is the first step in genetic sequence analysis and is critical to understanding data produced by molecular techniques like high throughput sequencing. Here, we explore an algorithm called naive Bayes that was historically successful in classifying 16S ribosomal gene sequences for microbiome analysis. We extend the naive Bayes classifier to perform the task of general sequence classification by leveraging advancements in computational parallelism and the statistical distributions that underlie naive Bayes. In Chapter 2, we show that our implementation of naive Bayes, called WarpNL, performs within a margin of error of modern classifiers like Kraken2 and local alignment. We discuss five crucial aspects of genetic sequence classification and show how these areas affect classifier performance: the query data, the reference sequence database, the feature encoding method, the classification algorithm, and access to computational resources. In Chapter 3, we cover the critical computational advancements introduced in WarpNL that make it efficient in a modern computing framework. This includes efficient feature encoding, introduction of a log-odds ratio for comparison of naive Bayes posterior estimates, description of schema for parallel and distributed naive Bayes architectures, and use of machine learning classifiers to perform outgroup sequence classification. Finally in Chapter 4, we explore a variant of the Dirichlet multinomial distribution that underlies the naive Bayes likelihood, called the beta-Liouville multinomial. We show that the beta-Liouville multinomial can be used to enhance classifier performance, and we provide mathematical proofs regarding its convergence during maximum likelihood estimation. Overall, this work explores the naive Bayes algorithm in a modern context and shows that it is competitive for genetic sequence classification

Semantics-based language models for information retrieval and text mining

The language modeling approach centers on the issue of estimating an accurate model by choosing appropriate language models as well as smoothing techniques. In the thesis, we propose a novel context-sensitive semantic smoothing method referred to as a topic signature language model. It extracts explicit topic signatures from a document and then statistically maps them into individual words in the vocabulary. In order to support the new language model, we developed two automated algorithms to extract multiword phrases and ontological concepts, respectively, and an EM-based algorithm to learn semantic mapping knowledge from co-occurrence data. The topic signature language model is applied to three applications: information retrieval, text classification, and text clustering. The evaluations on news collection and biomedical literature prove the effectiveness of the topic signature language model.In the experiment of information retrieval, the topic signature language model consistently outperforms the baseline two-stage language model as well as the context-insensitive semantic smoothing method in all configurations. It also beats the state-of-the-art Okapi models in all configurations. In the experiment of text classification, when the size of training documents is small, the Bayesian classifier with semantic smoothing not only outperforms the classifiers with background smoothing and Laplace smoothing, but it also beats the active learning classifiers and SVM classifiers. On the task of clustering, whether or not the dataset to cluster is small, the model-based k-means with semantic smoothing performs significantly better than both the model-based k-means with background smoothing and Laplace smoothing. It is also superior to the spherical k-means in terms of effectiveness.In addition, we empirically prove that, within the framework of topic signature language models, the semantic knowledge learned from one collection could be effectively applied to other collections. In the thesis, we also compare three types of topic signatures (i.e., words, multiword phrases, and ontological concepts), with respect to their effectiveness and efficiency for semantic smoothing. In general, it is more expensive to extract multiword phrases and ontological concepts than individual words, but semantic mapping based on multiword phrases and ontological concepts are more effective in handling data sparsity than on individual words.Ph.D., Information Science and Technology -- Drexel University, 200

Using Titles vs. Full-text as Source for Automated Semantic Document Annotation

We conduct the first systematic comparison of automated semantic annotation based on either the full-text or only on the title metadata of documents. Apart from the prominent text classification baselines kNN and SVM, we also compare recent techniques of Learning to Rank and neural networks and revisit the traditional methods logistic regression, Rocchio, and Naive Bayes. Across three of our four datasets, the performance of the classifications using only titles reaches over 90% of the quality compared to the performance when using the full-text

Semantic models as metrics for kernel-based interaction identification

Automatic detection of protein-protein interactions (PPIs) in biomedical publications is vital for efficient biological research. It also presents a host of new challenges for pattern recognition methodologies, some of which will be addressed by the research in this thesis. Proteins are the principal method of communication within a cell; hence, this area of research is strongly motivated by the needs of biologists investigating sub-cellular functions of organisms, diseases, and treatments. These researchers rely on the collaborative efforts of the entire field and communicate through experimental results published in reviewed biomedical journals. The substantial number of interactions detected by automated large-scale PPI experiments, combined with the ease of access to the digitised publications, has increased the number of results made available each day. The ultimate aim of this research is to provide tools and mechanisms to aid biologists and database curators in locating relevant information. As part of this objective this thesis proposes, studies, and develops new methodologies that go some way to meeting this grand challenge. Pattern recognition methodologies are one approach that can be used to locate PPI sentences; however, most accurate pattern recognition methods require a set of labelled examples to train on. For this particular task, the collection and labelling of training data is highly expensive. On the other hand, the digital publications provide a plentiful source of unlabelled data. The unlabelled data is used, along with word cooccurrence models, to improve classification using Gaussian processes, a probabilistic alternative to the state-of-the-art support vector machines. This thesis presents and systematically assesses the novel methods of using the knowledge implicitly encoded in biomedical texts and shows an improvement on the current approaches to PPI sentence detection

Protein interaction sentence detection using multiple semantic kernels

<p>Abstract</p> <p>Background</p> <p>Detection of sentences that describe protein-protein interactions (PPIs) in biomedical publications is a challenging and unresolved pattern recognition problem. Many state-of-the-art approaches for this task employ kernel classification methods, in particular support vector machines (SVMs). In this work we propose a novel data integration approach that utilises semantic kernels and a kernel classification method that is a probabilistic analogue to SVMs. Semantic kernels are created from statistical information gathered from large amounts of unlabelled text using lexical semantic models. Several semantic kernels are then fused into an overall composite classification space. In this initial study, we use simple features in order to examine whether the use of combinations of kernels constructed using word-based semantic models can improve PPI sentence detection.</p> <p>Results</p> <p>We show that combinations of semantic kernels lead to statistically significant improvements in recognition rates and receiver operating characteristic (ROC) scores over the plain Gaussian kernel, when applied to a well-known labelled collection of abstracts. The proposed kernel composition method also allows us to automatically infer the most discriminative kernels.</p> <p>Conclusions</p> <p>The results from this paper indicate that using semantic information from unlabelled text, and combinations of such information, can be valuable for classification of short texts such as PPI sentences. This study, however, is only a first step in evaluation of semantic kernels and probabilistic multiple kernel learning in the context of PPI detection. The method described herein is modular, and can be applied with a variety of feature types, kernels, and semantic models, in order to facilitate full extraction of interacting proteins.</p

Text Classification With Deep Neural Networks

The thesis explores different extensions of Deep Neural Networks in learning underlying natural language representations and how to apply them in Natural Language Processing tasks. Novel methods of learning lower or higher level features of natural languages are given in which word and phrase dense representations are derived from unlabelled corpora. Word representations are learned by training Deep Neural Networks to predict context from each sentence while phrase representations are learned by unsupervised learning with Convolutional Restricted Boltzmann Machine. It is shown that word representations learned from architectures which preserve text input as sequences have better word similarity and relatedness than bag-of-word approaches. Additionally phrase representations learned with Convolutional Restricted Boltzmann Machine when combined with bag-of-word features improve results of text classification tasks over only bag-of-word features. Beside learning word and phrase representations, to the best of my knowledge, the work in the thesis is first to explore Deep Neural Networks in Adverse Drug Reaction detection task where my architectures when used with pre-trained word representations significantly outperform the state-of-the-art models. In addition, outputs from my proposed attentional architecture can be used to highlight important word spans without explicit training labels. In the future I propose the learned representations to be used with the discussed Deep Neural Networks in different NLP tasks such as Dialog Systems, Machine Translation or Natural Language Inference