Semantic Biclustering

Tato disertační práce se zaměřuje na problém hledání interpretovatelných a prediktivních vzorů, které jsou vyjádřeny formou dvojshluků, se specializací na biologická data. Prezentované metody jsou souhrnně označovány jako sémantické dvojshlukování, jedná se o podobor dolování dat. Termín sémantické dvojshlukování je použit z toho důvodu, že zohledňuje proces hledání koherentních podmnožin řádků a sloupců, tedy dvojshluků, v 2-dimensionální binární matici a zárove ň bere také v potaz sémantický význam prvků v těchto dvojshlucích. Ačkoliv byla práce motivována biologicky orientovanými daty, vyvinuté algoritmy jsou obecně aplikovatelné v jakémkoli jiném výzkumném oboru. Je nutné pouze dodržet požadavek na formát vstupních dat. Disertační práce představuje dva originální a v tomto ohledu i základní přístupy pro hledání sémantických dvojshluků, jako je Bicluster enrichment analysis a Rule a tree learning. Jelikož tyto metody nevyužívají vlastní hierarchické uspořádání termů v daných ontologiích, obecně je běh těchto algoritmů dlouhý čin může docházet k indukci hypotéz s redundantními termy. Z toho důvodu byl vytvořen nový operátor zjemnění. Tento operátor byl včleněn do dobře známého algoritmu CN2, kde zavádí dvě redukční procedury: Redundant Generalization a Redundant Non-potential. Obě procedury pomáhají dramaticky prořezat prohledávaný prostor pravidel a tím umožňují urychlit proces indukce pravidel v porovnání s tradičním operátorem zjemnění tak, jak je původně prezentován v CN2. Celý algoritmus spolu s redukčními metodami je publikován ve formě R balííčku, který jsme nazvali sem1R. Abychom ukázali i možnost praktického užití metody sémantického dvojshlukování na reálných biologických problémech, v disertační práci dále popisujeme a specificky upravujeme algoritmus sem1R pro dv+ úlohy. Zaprvé, studujeme praktickou aplikaci algoritmu sem1R v analýze E-3 ubikvitin ligázy v trávicí soustavě s ohledem na potenciál regenerace tkáně. Zadruhé, kromě objevování dvojshluků v dat ech genové exprese, adaptujeme algoritmus sem1R pro hledání potenciálne patogenních genetických variant v kohortě pacientů.This thesis focuses on the problem of finding interpretable and predic tive patterns, which are expressed in the form of biclusters, with an orientation to biological data. The presented methods are collectively called semantic biclustering, as a subfield of data mining. The term semantic biclustering is used here because it reflects both a process of finding coherent subsets of rows and columns in a 2-dimensional binary matrix and simultaneously takes into account a mutual semantic meaning of elements in such biclusters. In spite of focusing on applications of algorithms in biological data, the developed algorithms are generally applicable to any other research field, there are only limitations on the format of the input data. The thesis introduces two novel, and in that context basic, approaches for finding semantic biclusters, as Bicluster enrichment analysis and Rule and tree learning. Since these methods do not exploit the native hierarchical order of terms of input ontologies, the run-time of algorithms is relatively long in general or an induced hypothesis might have terms that are redundant. For this reason, a new refinement operator has been invented. The refinement operator was incorporated into the well-known CN2 algorithm and uses two reduction procedures: Redundant Generalization and Redundant Non-potential, both of which help to dramatically prune the rule space and consequently, speed-up the entire process of rule induction in comparison with the traditional refinement operator as is presented in CN2. The reduction procedures were published as an R package that we called sem1R. To show a possible practical usage of semantic biclustering in real biological problems, the thesis also describes and specifically adapts the algorithm for two real biological problems. Firstly, we studied a practical application of sem1R algorithm in an analysis of E-3 ubiquitin ligase in the gastrointestinal tract with respect to tissue regeneration potential. Secondly, besides discovering biclusters in gene expression data, we adapted the sem1R algorithm for a different task, concretely for finding potentially pathogenic genetic variants in a cohort of patients

Geometric Inference in Bayesian Hierarchical Models with Applications to Topic Modeling

Unstructured data is available in abundance with the rapidly growing size of digital information. Labeling such data is expensive and impractical, making unsupervised learning an increasingly important field. Big data collections often have rich latent structure that statistical modeler is challenged to uncover. Bayesian hierarchical modeling is a particularly suitable approach for complex latent patterns. Graphical model formalism has been prominent in developing various procedures for inference in Bayesian models, however the corresponding computational limits often fall behind the demands of the modern data sizes. In this thesis we develop new approaches for scalable approximate Bayesian inference. In particular, our approaches are driven by the analysis of latent geometric structures induced by the models. Our specific contributions include the following. We develop full geometric recipe of the Latent Dirichlet Allocation topic model. Next, we study several approaches for exploiting the latent geometry to first arrive at a fast weighted clustering procedure augmented with geometric corrections for topic inference, and then a nonparametric approach based on the analysis of the concentration of mass and angular geometry of the topic simplex, a convex polytope constructed by taking the convex hull of vertices representing the latent topics. Estimates produced by our methods are shown to be statistically consistent under some conditions. Finally, we develop a series of models for temporal dynamics of the latent geometric structures where inference can be performed in online and distributed fashion. All our algorithms are evaluated with extensive experiments on simulated and real datasets, culminating at a method several orders of magnitude faster than existing state-of-the-art topic modeling approaches, as demonstrated by experiments working with several million documents in a dozen minutes.PHDStatisticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/146051/1/moonfolk_1.pd

Finding Optimal Diverse Feature Sets with Alternative Feature Selection

Feature selection is popular for obtaining small, interpretable, yet highly accurate prediction models. Conventional feature-selection methods typically yield one feature set only, which might not suffice in some scenarios. For example, users might be interested in finding alternative feature sets with similar prediction quality, offering different explanations of the data. In this article, we introduce alternative feature selection and formalize it as an optimization problem. In particular, we define alternatives via constraints and enable users to control the number and dissimilarity of alternatives. Next, we analyze the complexity of this optimization problem and show NP-hardness. Further, we discuss how to integrate conventional feature-selection methods as objectives. Finally, we evaluate alternative feature selection with 30 classification datasets. We observe that alternative feature sets may indeed have high prediction quality, and we analyze several factors influencing this outcome

Finding Optimal Diverse Feature Sets with Alternative Feature Selection

Feature selection is popular for obtaining small, interpretable, yet highly accurate prediction models. Conventional feature-selection methods typically yield one feature set only, which might not suffice in some scenarios. For example, users might be interested in finding alternative feature sets with similar prediction quality, offering different explanations of the data. In this article, we introduce alternative feature selection and formalize it as an optimization problem. In particular, we define alternatives via constraints and enable users to control the number and dissimilarity of alternatives. Next, we analyze the complexity of this optimization problem and show NP-hardness. Further, we discuss how to integrate conventional feature-selection methods as objectives. Finally, we evaluate alternative feature selection with 30 classification datasets. We observe that alternative feature sets may indeed have high prediction quality, and we analyze several factors influencing this outcome

Discovering Higher-order SNP Interactions in High-dimensional Genomic Data

In this thesis, a multifactor dimensionality reduction based method on associative classification is employed to identify higher-order SNP interactions for enhancing the understanding of the genetic architecture of complex diseases. Further, this thesis explored the application of deep learning techniques by providing new clues into the interaction analysis. The performance of the deep learning method is maximized by unifying deep neural networks with a random forest for achieving reliable interactions in the presence of noise

Logic learning and optimized drawing: two hard combinatorial problems

Nowadays, information extraction from large datasets is a recurring operation in countless fields of applications. The purpose leading this thesis is to ideally follow the data flow along its journey, describing some hard combinatorial problems that arise from two key processes, one consecutive to the other: information extraction and representation. The approaches here considered will focus mainly on metaheuristic algorithms, to address the need for fast and effective optimization methods. The problems studied include data extraction instances, as Supervised Learning in Logic Domains and the Max Cut-Clique Problem, as well as two different Graph Drawing Problems. Moreover, stemming from these main topics, other additional themes will be discussed, namely two different approaches to handle Information Variability in Combinatorial Optimization Problems (COPs), and Topology Optimization of lightweight concrete structures

Efficient Storage of Genomic Sequences in High Performance Computing Systems

ABSTRACT: In this dissertation, we address the challenges of genomic data storage in high performance computing systems. In particular, we focus on developing a referential compression approach for Next Generation Sequence data stored in FASTQ format files. The amount of genomic data available for researchers to process has increased exponentially, bringing enormous challenges for its efficient storage and transmission. General-purpose compressors can only offer limited performance for genomic data, thus the need for specialized compression solutions. Two trends have emerged as alternatives to harness the particular properties of genomic data: non-referential and referential compression. Non-referential compressors offer higher compression rations than general purpose compressors, but still below of what a referential compressor could theoretically achieve. However, the effectiveness of referential compression depends on selecting a good reference and on having enough computing resources available. This thesis presents one of the first referential compressors for FASTQ files. We first present a comprehensive analytical and experimental evaluation of the most relevant tools for genomic raw data compression, which led us to identify the main needs and opportunities in this field. As a consequence, we propose a novel compression workflow that aims at improving the usability of referential compressors. Subsequently, we discuss the implementation and performance evaluation for the core of the proposed workflow: a referential compressor for reads in FASTQ format that combines local read-to-reference alignments with a specialized binary-encoding strategy. The compression algorithm, named UdeACompress, achieved very competitive compression ratios when compared to the best compressors in the current state of the art, while showing reasonable execution times and memory use. In particular, UdeACompress outperformed all competitors when compressing long reads, typical of the newest sequencing technologies. Finally, we study the main aspects of the data-level parallelism in the Intel AVX-512 architecture, in order to develop a parallel version of the UdeACompress algorithms to reduce the runtime. Through the use of SIMD programming, we managed to significantly accelerate the main bottleneck found in UdeACompress, the Suffix Array Construction

A framework for dynamic heterogeneous information networks change discovery based on knowledge engineering and data mining methods

Information Networks are collections of data structures that are used to model interactions in social and living phenomena. They can be either homogeneous or heterogeneous and static or dynamic depending upon the type and nature of relations between the network entities. Static, homogeneous and heterogenous networks have been widely studied in data mining but recently, there has been renewed interest in dynamic heterogeneous information networks (DHIN) analysis because the rich temporal, structural and semantic information is hidden in this kind of network. The heterogeneity and dynamicity of the real-time networks offer plenty of prospects as well as a lot of challenges for data mining. There has been substantial research undertaken on the exploration of entities and their link identification in heterogeneous networks. However, the work on the formal construction and change mining of heterogeneous information networks is still infant due to its complex structure and rich semantics. Researchers have used clusters-based methods and frequent pattern-mining techniques in the past for change discovery in dynamic heterogeneous networks. These methods only work on small datasets, only provide the structural change discovery and fail to consider the quick and parallel process on big data. The problem with these methods is also that cluster-based approaches provide the structural changes while the pattern-mining provide semantic characteristics of changes in a dynamic network. Another interesting but challenging problem that has not been considered by past studies is to extract knowledge from these semantically richer networks based on the user-specific constraint.This study aims to develop a new change mining system ChaMining to investigate dynamic heterogeneous network data, using knowledge engineering with semantic web technologies and data mining to overcome the problems of previous techniques, this system and approach are important in academia as well as real-life applications to support decision-making based on temporal network data patterns. This research has designed a novel framework “ChaMining” (i) to find relational patterns in dynamic networks locally and globally by employing domain ontologies (ii) extract knowledge from these semantically richer networks based on the user-specific (meta-paths) constraints (iii) Cluster the relational data patterns based on structural properties of nodes in the dynamic network (iv) Develop a hybrid approach using knowledge engineering, temporal rule mining and clustering to detect changes in the dynamic heterogeneous networks.The evidence is presented in this research shows that the proposed framework and methods work very efficiently on the benchmark big dynamic heterogeneous datasets. The empirical results can contribute to a better understanding of the rich semantics of DHIN and how to mine them using the proposed hybrid approach. The proposed framework has been evaluated with the previous six dynamic change detection algorithms or frameworks and it performs very well to detect microscopic as well as macroscopic human-understandable changes. The number of change patterns extracted in this approach was higher than the previous approaches which help to reduce the information loss

The European Lake Microbiome: A Study in Complexity

While it is known that microbes play many indispensable roles in ecosystems, the relationship between microbiomes and their environment is far from being well-understood. In part, this is the case because the methods necessary for studying environmental microbiomes, such as Next- Generation Sequencing and high-dimensional Machine Learning, have been developed relatively recently. However, the complex nature of ecosystems and environmental microbiomes acts as a further barrier to progress in this field of research. This thesis develops methods and concepts used to gain insight into the ecology of micro- biomes in lakes. It is based around two metabarcoding datasets sampled from lakes in Austria and the whole of Europe, respectively, and attempts to elucidate the microbiome’s relationship to environmental parameters. To this end, a tool for GPS-based dataset enhancement and a ma- chine learning framework for measuring microbiome covariation is developed. Building on this, the latent structure of the microbiome is estimated. In the discussion, a novel theory of informa- tion transmission in complex environments is described. Taken together, the work included herein presents a thorough analysis of the European lake microbiome that takes the complexity of the study object into account. The results point to- wards parameters that act as drivers of lake microbiome structure as well as microorganisms that might act as keystone species for ecosystem functioning. Furthermore, this work might provide the basis for considerable future progress in the study of environmental microbiomes