A graph regularization based approach to transductive class-membership prediction

Considering the increasing availability of structured machine processable knowledge in the context of the Semantic Web, only relying on purely deductive inference may be limiting. This work proposes a new method for similarity-based class-membership prediction in Description Logic knowledge bases. The underlying idea is based on the concept of propagating class-membership information among similar individuals; it is non-parametric in nature and characterised by interesting complexity properties, making it a potential candidate for large-scale transductive inference. We also evaluate its effectiveness with respect to other approaches based on inductive inference in SW literature

Applications Of Machine Learning In Biology And Medicine

Machine learning as a field is defined to be the set of computational algorithms that improve their performance by assimilating data. As such, the field as a whole has found applications in many diverse disciplines from robotics and communication in engineering to economics and finance, and also biology and medicine. It should not come as a surprise that many popular methods in use today have completely different origins. Despite this heterogeneity, different methods can be divided into standard tasks, such as supervised, unsupervised, semi-supervised and reinforcement learning. Although machine learning as a field can be formalized as methods trying to solve certain standard tasks, applying these tasks on datasets from different fields comes with certain caveats, and sometimes is fraught with challenges. In this thesis, we develop general procedures and novel solutions, dealing with practical problems that arise when modeling biological and medical data. Cost sensitive learning is an important area of research in machine learning which addresses the widespread and practical problem of dealing with different costs during the learning and deployment of classification algorithms. In many applications such as credit fraud detection, network intrusion and specifically medical diagnosis domains, prior class distributions are highly skewed, which makes the training examples very much unbalanced. Combining this with uneven misclassification costs renders standard machine learning approaches useless in learning an acceptable decision function. We experimentally show the benefits and shortcomings of various methods that convert cost blind learning algorithms to cost sensitive ones. Using the results and best practices found for cost sensitive learning, we design and develop a machine learning approach to ontology mapping. Next, we present a novel approach to deal with uncertainty in classification when costs are unknown or otherwise hard to assign. Support Vector Machines (SVM) are considered to be among the most successful approaches for classification. However prediction of instances near the decision boundary depends more on the specific parameter selection or noise in data, rather than a clear difference in features. In many applications such as medical diagnosis, these regions should be labeled as uncertain rather than assigned to any particular class. Furthermore, instances may belong to novel disease subtypes that are not from any previously known class. In such applications, declining to make a prediction could be beneficial when more powerful but expensive tests are available. We develop a novel approach for optimal selection of the threshold and show its successful application on three biological and medical datasets. The last part of this thesis provides novel solutions for handling high dimensional data. Although high-dimensional data is ubiquitously found in many disciplines, current life science research almost always involves high-dimensional genomics/proteomics data. The ``omics\u27\u27 data provide a wealth of information and have changed the research landscape in biology and medicine. However, these data are plagued with noise, redundancy and collinearity, which makes the discovery process very difficult and costly. Any method that can accurately detect irrelevant and noisy variables in omics data would be highly valuable. We present Robust Feature Selection (RFS), a randomized feature selection approach dedicated to low-sample high-dimensional data. RFS combines an embedded feature selection method with a randomization procedure for stability. Recent advances in sparse recovery and estimation methods have provided efficient and asymptotically consistent feature selection algorithms. However, these methods lack finite sample error control due to instability. Furthermore, the chances of correct recovery diminish with more collinearity among features. To overcome these difficulties, RFS uses a randomization procedure to provide an accurate and stable feature selection method. We thoroughly evaluate RFS by comparing it to a number of popular univariate and multivariate feature selection methods and show marked prediction accuracy improvement of a diagnostic signature, while preserving a good stability

Machine Learning

Machine Learning can be defined in various ways related to a scientific domain concerned with the design and development of theoretical and implementation tools that allow building systems with some Human Like intelligent behavior. Machine learning addresses more specifically the ability to improve automatically through experience

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

Document analysis by means of data mining techniques

The huge amount of textual data produced everyday by scientists, journalists and Web users, allows investigating many different aspects of information stored in the published documents. Data mining and information retrieval techniques are exploited to manage and extract information from huge amount of unstructured textual data. Text mining also known as text data mining is the processing of extracting high quality information (focusing relevance, novelty and interestingness) from text by identifying patterns etc. Text mining typically involves the process of structuring input text by means of parsing and other linguistic features or sometimes by removing extra data and then finding patterns from structured data. Patterns are then evaluated at last and interpretation of output is performed to accomplish the desired task. Recently, text mining has got attention in several fields such as in security (involves analysis of Internet news), for commercial (for search and indexing purposes) and in academic departments (such as answering query). Beyond searching the documents consisting the words given in a user query, text mining may provide direct answer to user by semantic web for content based (content meaning and its context). It can also act as intelligence analyst and can also be used in some email spam filters for filtering out unwanted material. Text mining usually includes tasks such as clustering, categorization, sentiment analysis, entity recognition, entity relation modeling and document summarization. In particular, summarization approaches are suitable for identifying relevant sentences that describe the main concepts presented in a document dataset. Furthermore, the knowledge existed in the most informative sentences can be employed to improve the understanding of user and/or community interests. Different approaches have been proposed to extract summaries from unstructured text documents. Some of them are based on the statistical analysis of linguistic features by means of supervised machine learning or data mining methods, such as Hidden Markov models, neural networks and Naive Bayes methods. An appealing research field is the extraction of summaries tailored to the major user interests. In this context, the problem of extracting useful information according to domain knowledge related to the user interests is a challenging task. The main topics have been to study and design of novel data representations and data mining algorithms useful for managing and extracting knowledge from unstructured documents. This thesis describes an effort to investigate the application of data mining approaches, firmly established in the subject of transactional data (e.g., frequent itemset mining), to textual documents. Frequent itemset mining is a widely exploratory technique to discover hidden correlations that frequently occur in the source data. Although its application to transactional data is well-established, the usage of frequent itemsets in textual document summarization has never been investigated so far. A work is carried on exploiting frequent itemsets for the purpose of multi-document summarization so a novel multi-document summarizer, namely ItemSum (Itemset-based Summarizer) is presented, that is based on an itemset-based model, i.e., a framework comprise of frequent itemsets, taken out from the document collection. Highly representative and not redundant sentences are selected for generating summary by considering both sentence coverage, with respect to a sentence relevance score, based on tf-idf statistics, and a concise and highly informative itemset-based model. To evaluate the ItemSum performance a suite of experiments on a collection of news articles has been performed. Obtained results show that ItemSum significantly outperforms mostly used previous summarizers in terms of precision, recall, and F-measure. We also validated our approach against a large number of approaches on the DUC’04 document collection. Performance comparisons, in terms of precision, recall, and F-measure, have been performed by means of the ROUGE toolkit. In most cases, ItemSum significantly outperforms the considered competitors. Furthermore, the impact of both the main algorithm parameters and the adopted model coverage strategy on the summarization performance are investigated as well. In some cases, the soundness and readability of the generated summaries are unsatisfactory, because the summaries do not cover in an effective way all the semantically relevant data facets. A step beyond towards the generation of more accurate summaries has been made by semantics-based summarizers. Such approaches combine the use of general-purpose summarization strategies with ad-hoc linguistic analysis. The key idea is to also consider the semantics behind the document content to overcome the limitations of general-purpose strategies in differentiating between sentences based on their actual meaning and context. Most of the previously proposed approaches perform the semantics-based analysis as a preprocessing step that precedes the main summarization process. Therefore, the generated summaries could not entirely reflect the actual meaning and context of the key document sentences. In contrast, we aim at tightly integrating the ontology-based document analysis into the summarization process in order to take the semantic meaning of the document content into account during the sentence evaluation and selection processes. With this in mind, we propose a new multi-document summarizer, namely Yago-based Summarizer, that integrates an established ontology-based entity recognition and disambiguation step. Named Entity Recognition from Yago ontology is being used for the task of text summarization. The Named Entity Recognition (NER) task is concerned with marking occurrences of a specific object being mentioned. These mentions are then classified into a set of predefined categories. Standard categories include “person”, “location”, “geo-political organization”, “facility”, “organization”, and “time”. The use of NER in text summarization improved the summarization process by increasing the rank of informative sentences. To demonstrate the effectiveness of the proposed approach, we compared its performance on the DUC’04 benchmark document collections with that of a large number of state-of-the-art summarizers. Furthermore, we also performed a qualitative evaluation of the soundness and readability of the generated summaries and a comparison with the results that were produced by the most effective summarizers. A parallel effort has been devoted to integrating semantics-based models and the knowledge acquired from social networks into a document summarization model named as SociONewSum. The effort addresses the sentence-based generic multi-document summarization problem, which can be formulated as follows: given a collection of news articles ranging over the same topic, the goal is to extract a concise yet informative summary, which consists of most salient document sentences. An established ontological model has been used to improve summarization performance by integrating a textual entity recognition and disambiguation step. Furthermore, the analysis of the user-generated content coming from Twitter has been exploited to discover current social trends and improve the appealing of the generated summaries. An experimental evaluation of the SociONewSum performance was conducted on real English-written news article collections and Twitter posts. The achieved results demonstrate the effectiveness of the proposed summarizer, in terms of different ROUGE scores, compared to state-of-the-art open source summarizers as well as to a baseline version of the SociONewSum summarizer that does not perform any UGC analysis. Furthermore, the readability of the generated summaries has also been analyzed