Machine Learning Approaches for Breast Cancer Survivability Prediction

Breast cancer is one of the leading causes of cancer death in women. If not diagnosed early, the 5-year survival rate of patients is just about 26\%. Furthermore, patients with similar phenotypes can respond differently to the same therapies, which means the therapies might not work well for some of them. Identifying biomarkers that can help predict a cancer class with high accuracy is at the heart of breast cancer studies because they are targets of the treatments and drug development. Genomics data have been shown to carry useful information for breast cancer diagnosis and prognosis, as well as uncovering the disease’s mechanism. Machine learning methods are powerful tools to find such information. Feature selection methods are often utilized in supervised learning and unsupervised learning tasks to deal with data containing a large number of features in which only a small portion of them are useful to the classification task. On the other hand, analyzing only one type of data, without reference to the existing knowledge about the disease and the therapies, might mislead the findings. Effective data integration approaches are necessary to uncover this complex disease. In this thesis, we apply and develop machine learning methods to identify meaningful biomarkers for breast cancer survivability prediction after a certain treatment. They include applying feature selection methods on gene-expression data to derived gene-signatures, where the initial genes are collected concerning the mechanism of some drugs used breast cancer therapies. We also propose a new feature selection method, named PAFS, and apply it to discover accurate biomarkers. In addition, it has been increasingly supported that, sub-network biomarkers are more robust and accurate than gene biomarkers. We proposed two network-based approaches to identify sub-network biomarkers for breast cancer survivability prediction after a treatment. They integrate gene-expression data with protein-protein interactions during the optimal sub-network searching process and use cancer-related genes and pathways to prioritize the extracted sub-networks. The sub-network search space is usually huge and many proteins interact with thousands of other proteins. Thus, we apply some heuristics to avoid generating and evaluating redundant sub-networks

Contributions à l’Optimisation de Requêtes Multidimensionnelles

Analyser les données consiste à choisir un sous-ensemble des dimensions qui les décriventafin d'en extraire des informations utiles. Or, il est rare que l'on connaisse a priori les dimensions"intéressantes". L'analyse se transforme alors en une activité exploratoire où chaque passe traduit par une requête. Ainsi, il devient primordiale de proposer des solutions d'optimisationde requêtes qui ont une vision globale du processus plutôt que de chercher à optimiser chaque requêteindépendamment les unes des autres. Nous présentons nos contributions dans le cadre de cette approcheexploratoire en nous focalisant sur trois types de requêtes: (i) le calcul de bordures,(ii) les requêtes dites OLAP (On Line Analytical Processing) dans les cubes de données et (iii) les requêtesde préférence type skyline

Non-Redundant Sequential Rules - Theory and Algorithm

A sequential rule expresses a relationship between two series of events happening one after another. Sequential rules are potentially useful for analyzing data in sequential format, ranging from purchase histories, network logs and program execution traces. In this work, we investigate and propose a syntactic characterization of a non-redundant set of sequential rules built upon past work on compact set of representative patterns. A rule is redundant if it can be inferred from another rule having the same support and confidence. When using the set of mined rules as a composite filter, replacing a full set of rules with a non-redundant subset of the rules does not impact the accuracy of the filter. We consider several rule sets based on composition of various types of pattern sets – generators, projected-database generators, closed patterns and projected-database closed patterns. We investigate the completeness and tightness of these rule sets. We characterize a tight and complete set of non

Mining iterative generators and representative rules for software specification discovery

10.1109/TKDE.2010.24IEEE Transactions on Knowledge and Data Engineering232282-296ITKE

Summarization Techniques for Pattern Collections in Data Mining

Discovering patterns from data is an important task in data mining. There exist techniques to find large collections of many kinds of patterns from data very efficiently. A collection of patterns can be regarded as a summary of the data. A major difficulty with patterns is that pattern collections summarizing the data well are often very large. In this dissertation we describe methods for summarizing pattern collections in order to make them also more understandable. More specifically, we focus on the following themes: 1) Quality value simplifications. 2) Pattern orderings. 3) Pattern chains and antichains. 4) Change profiles. 5) Inverse pattern discovery.Comment: PhD Thesis, Department of Computer Science, University of Helsink

Dynamic causal mining

Causality plays a central role in human reasoning, in particular, in common human decision-making, by providing a basis for strategy selection. The main aim of the research reported in this thesis is to develop a new way to identify dynamic causal relationships between attributes of a system. The first part of the thesis introduces the development of a new data mining algorithm, called Dynamic Causal Mining (DCM), which extracts rules from data sets based on simultaneous time stamps. The rules derived can be combined into policies, which can simulate the future behaviour of systems. New rules can be added to the policies depending on the degree of accuracy. In addition, facilities to process categorical or numerical attributes directly and approaches to prune the rule set efficiently are implemented in the DCM algorithm. The second part of the thesis discusses how to improve the DCM algorithm in order to identify delay and feedback relationships. Fuzzy logic is applied to manage the rules and policies flexibly and accurately during the learning process and help the algorithm to find feasible solutions. The third part of the thesis describes the application of the suggested algorithm to a problem in the game-theoretic domain. This part concludes with the suggestion to use concept lattices as a method to represent and structure the discovered knowledge

On Pattern Mining in Graph Data to Support Decision-Making

In recent years graph data models became increasingly important in both research and industry. Their core is a generic data structure of things (vertices) and connections among those things (edges). Rich graph models such as the property graph model promise an extraordinary analytical power because relationships can be evaluated without knowledge about a domain-specific database schema. This dissertation studies the usage of graph models for data integration and data mining of business data. Although a typical company's business data implicitly describes a graph it is usually stored in multiple relational databases. Therefore, we propose the first semi-automated approach to transform data from multiple relational databases into a single graph whose vertices represent domain objects and whose edges represent their mutual relationships. This transformation is the base of our conceptual framework BIIIG (Business Intelligence with Integrated Instance Graphs). We further proposed a graph-based approach to data integration. The process is executed after the transformation. In established data mining approaches interrelated input data is mostly represented by tuples of measure values and dimension values. In the context of graphs these values must be attached to the graph structure and aggregated measure values are graph attributes. Since the latter was not supported by any existing model, we proposed the use of collections of property graphs. They act as data structure of the novel Extended Property Graph Model (EPGM). The model supports vertices and edges that may appear in different graphs as well as graph properties. Further on, we proposed some operators that benefit from this data structure, for example, graph-based aggregation of measure values. A primitive operation of graph pattern mining is frequent subgraph mining (FSM). However, existing algorithms provided no support for directed multigraphs. We extended the popular gSpan algorithm to overcome this limitation. Some patterns might not be frequent while their generalizations are. Generalized graph patterns can be mined by attaching vertices to taxonomies. We proposed a novel approach to Generalized Multidimensional Frequent Subgraph Mining (GM-FSM), in particular the first solution to generalized FSM that supports not only directed multigraphs but also multiple dimensional taxonomies. In scenarios that compare patterns of different categories, e.g., fraud or not, FSM is not sufficient since pattern frequencies may differ by category. Further on, determining all pattern frequencies without frequency pruning is not an option due to the computational complexity of FSM. Thus, we developed an FSM extension to extract patterns that are characteristic for a specific category according to a user-defined interestingness function called Characteristic Subgraph Mining (CSM). Parts of this work were done in the context of GRADOOP, a framework for distributed graph analytics. To make the primitive operation of frequent subgraph mining available to this framework, we developed Distributed In-Memory gSpan (DIMSpan), a frequent subgraph miner that is tailored to the characteristics of shared-nothing clusters and distributed dataflow systems. Finally, the results of use case evaluations in cooperation with a large scale enterprise will be presented. This includes a report of practical experiences gained in implementation and application of the proposed algorithms

The evaluation of occupational accident with sequential pattern mining

Accidents in manufacturing systems greatly affect productivity and efficiency, which are well known perfor-mance indicaters in practice. Therefore, it is very important to know the sequential patterns among the accidents to avode possible losses decrasing performance of the manufacturing systems. In order to reduce accidents, it is necessary to determine the patterns that cause the accident first. The associations among the causes of the occurrence of accidents is rarely investigated in the literature. To fill this gap, the patterns of causes among the accidents in the manufacturing system are revealed by using sequential pattern mining in this study. The most important contribution of this study is the discovery of sequential patterns formed by accident characteristics of pre-accident, moment of accident and post-accident stages unlike traditional accident investigation methods. Additionally, knowing the patterns of causes among the accidents can help decision makers to prepare a more proactive security program in real life. The CloFast algorithm is performed to go into the details of accidents in manufacturing systems. Accident records induding data between 2013 and 2019 are used to discover the sequential patterns. The results of this study showed that each accidents has its own sequential accident patterns and it is also posible to prevent possible accidents and reduce losses due to accidents considering sequential patterns in real life. Safety engineers and occupational safety specialists should take into account the sequential patterns among the accidents to avoid similar accident in the near future