In the past decade, fast advancements have been made in the sequencing, digitalization and collection of the biological data. However the bottleneck remains at the point of analysis and extraction of patterns from the data. We have developed a method that is aimed at widening this bottleneck by automating the knowledge extraction from the biological data. Our approach is aimed at discovering patterns in a set of DNA sequences based on the location of transcription factor binding sites or any other biological markers with the emphasis of discovering relationships. A variety of statistical and computational methods exists to analyze such data. However, they either require an initial hypothesis, which is later tested, or classify the data based on its attributes. Our approach does not require an initial hypothesis and the classification it produces is based on the relationships between attributes. The value of such approach is that is is able to uncover new knowledge about the data by inducing a general theory based on basic known rules. The core of our approach lies in an inductive logic programming engine, which, based on positive and negative examples as well as background knowledge, is able to induce a descriptive, human-readable theory, describing the data. An application provides an end-to-end analysis of DNA sequences. A simple to use Web interface accepts a set of related sequences to be analyzed, set of negative example sequences to contrast the main set (optional), and a set of possible genetic markers as position-specific scoring matrices. A Java-based backend formats the sequences, determines the location of the genetic markers inside them and passes the information to the ILP engine, which induces the theory. The model, assumed in our background knowledge, is a set of basic interactions between biological markers in any DNA sequence. This makes our approach applicable to analyze a wide variety of biological problems, including detection of cis-regulatory modules and analysis of ChIP-Sequencing experiments. We have evaluated our method in the context of such applications on two real world datasets as well as a number of specially designed synthetic datasets. The approach has shown to have merit even in situations when no significant classification could be determined.

No description available.

Some upstream open reading frames (uORFs) regulate gene expression (i.e. they are functional) and can play key roles in keeping organisms healthy. However, how uORFs are involved in gene regulation is not het fully understood. In order to get a complete view of how uORFs are involved in gene regulation, it is expected that a large number of functional uORFs are needed. Unfortunately , lab experiments to verify that uORFs are functional are expensive. In this thesis, for the first time, the use of inductive logic programming (ILP) is explored for the task of learning which uORFs regulate gene expression in the yeast Saccharomyces cerevisiae. This work is directed to help select sets of candidate functional uORFs for experimental studies. With limited background knowledge, ILP can generate hypotheses which make the search for novel functional uORFs 17 times more efficient than random sampling. Adding mRNA secondary structure to the background knowledge results in hypotheses with significantly increased performance. This work is the first machine learning work to study both uORFs and mRNA secondary structures in the context of gene regulation. Using a novel combination of knowledge about biological conservation, gene ontology annotations and genes' response to different conditions results in hypotheses that are simple, informative, have an estimated sensitivity of 81% and provide provisional insights into biological characteristics of functional uORFs. The hypotheses predict 299 further genes to have 450 novel functional uORFs. A comparison with a related study suggests that 8 of these predicted functional uORFs (from 8 genes) are strong candidates for experimental studies.

Inductive logic programming is a discipline investigating invention of clausal theories from observed examples such that for given evidence and background knowledge we are finding a hypothesis covering all positive examples and excluding all negative ones. In this thesis we extend an existing work on template consistency to general consistency. We present a three-phase algorithm DeMeR decomposing the original problem into smaller subtasks, merging all subsolutions together yielding a complete solution and finally refining the result in order to get a compact final hypothesis. Furthermore, we focus on a method how each individual subtask is solved and we introduce a generate-and-test method based on the probabilistic history-driven approach for this purpose. We analyze each stage of the proposed algorithms and demonstrate its impact on a runtime and a hypothesis structure. In particular, we show that the first phase of the algorithm concentrates on solving the problem quickly at the cost of longer solutions whereas the other phases refine these solutions into an admissible form. Finally, we prove that our technique outperforms other algorithms by comparing its results for identifying common structures in random graphs to existing systems.

O Aprendizado de Máquina trata da questão de como desenvolver programas de computador capazes de aprender um conceito ou hipótese a partir de um conjunto de exemplos ou casos observados. Baseado no conjunto de treinamento o algoritmo de aprendizado induz a classificação de uma hipótese capaz de determinar corretamente a classe de novos exemplos ainda não rotulados. Linguagens de descrição são necessárias para escrever exemplos, conhecimento do domínio bem como as hipóteses aprendidas a partir dos exemplos. Em geral, essas linguagens podem ser divididas em dois tipos: linguagem baseada em atributo-valor ou proposicional e linguagem relacional. Algoritmos de aprendizado são classificados como proposicional ou relacional dependendo da liguagem de descrição que eles utilizam. Além disso, no aprendizado simbólico o objetivo é gerar a classificação de hipóteses que possam ser facilmente interpretadas pelos humanos. Algoritmos de aprendizado proposicional utilizam a representação atributo-valor, a qual é inadequada para representar objetos estruturados e relações entre esses objetos. Por outro lado, a Programação lógica Indutiva (PLI) é realizada com o desenvolvimento de técnicas e ferramentas para o aprendizado relacional. Sistemas de PLI são capazes de aprender levando em consideração conhecimento do domínio na forma de um programa lógico e também usar a linguagem de programas lógicos para descrever o conhecimento induzido. Neste trabalho foi implementado um módulo chamado Kaeru para converter dados no formato atributo-valor para o formato relacional utilizado pelo sistema de PLI Aleph. Uma série de experimentos foram realizados com quatro conjuntos de dados naturais e um conjunto de dados real no formato atributo valor. Utilizando o módulo conversor Kaeru esses dados foram convertidos para o formato relacional utilizado pelo Aleph e hipóteses de classificação foram induzidas utilizando aprendizado proposicional bem como aprendizado relacional. É mostrado também, que o aprendizado proposicional pode ser utilizado para incrementar o conhecimento do domínio utilizado pelos sistemas de aprendizado relacional para melhorar a qualidade das hipóteses induzidas. / Machine Learning addresses the question of how to build computer programs that learn a concept or hypotheses from a set of examples, objects or cases. Descriptive languages are necessary in machine learning to describe the set of examples, domain knowledge as well as the hypothesis learned from these examples. In general, these languages can be divided into two types: languages based on attribute values, or em propositional languages, and relational languages. Learning algorithms are often classified as propositional or relational taking into consideration the descriptive language they use. Typical propositional learning algorithms employ the attribute value representation, which is inadequate for problem-domains that require reasoning about the structure of objects in the domain and relations among such objects. On the other hand, Inductive Logig Programming (ILP) is concerned with the development of techniques and tools for relational learning. ILP systems are able to take into account domain knowledge in the form of a logic program and also use the language of logic programs for describing the induced knowledge or hypothesis. In this work we propose and implement a module, named kaeru, to convert data in the attribute-value format to the relational format used by the ILP system Aleph. We describe a series of experiments performed on four natural data sets and one real data set in the attribute value format. Using the kaeru module these data sets were converted to the relational format used by Aleph and classifying hipoteses were induced using propositional as well as relational learning. We also show that propositional knowledge can be used to increment the background knowledge used by relational learners in order to improve the induded hypotheses quality.

Este trabalho investiga Aprendizado Indutivo de Máquina como função das linguagens de descrição, utilizadas para expressar instancias, conceitos e teoria do domínio. A ampliação do poder de representação do aprendizado proporcional e abordada no contexto de indução construtiva, no domínio de funções booleanas, com a proposta de uma estratégia de composição de atributos denominada root-fringe. Avaliações experimentais dessa e de outras estratégias de construção de novos atributos foram conduzidas e os resultados analisados. Dois métodos de poda, para tratamento de ruídos, em aprendizado de arvores de decisão, foram avaliados num ambiente de indução construtiva e os resultados discutidos. Devido a limitação do aprendizado proposicional, foram investigadas formas de ampliação dos limites do aprendizado, através da ampliação do poder representacional das linguagens de descrição. Foi escolhida Programação Lógica Indutiva - PLI - que e um paradigma de aprendizado indutivo que usa restrições de Lógica de Primeira Ordem como linguagens de descrição. O aprendizado em PLI só é factível quando as linguagens utilizadas estão restritas e é fortemente controlado, caso contrário, o aprendizado em PLI se torna indecidível. A pesquisa em PLI se direcionou a formas de restrição das linguagens de descrição da teoria do domínio e de hipóteses. Três algoritmos que \"traduzem\" a teoria do domínio de sua forma intencional, para extensional, são apresentados. As implementações de dois deles são discutidas. As implementações realizadas deram origem a dois ambientes experimentais de aprendizado: o ambiente proposicional experimental, do qual fazem parte o ambiente experimental construtivo, e o ambiente experimental relacional. / This work investigates Inductive Machine Learning as a function of the description languages employed to express instances, concepts and domain theory. The enlargement of the representational power of propositional learning methods is approached via constructive induction, in the domain of boolean functions, through the proposal of a bias for composing attributes, namely, the bias root-fringe. Experimental evaluation of root-fringe, as well as other biases for constructing new attributes was conducted and the results analyzed. Two pruning methods for decision trees were evaluated in an environment of constructive induction and the results discussed. Due to the limitations of propositional learning, ways of enlarging the limits of the learning process were investigated through enlarging the representational power of the description languages. It was chosen Inductive Logic Programming - ILP - that is an inductive learning paradigm that uses restrictions of First Order Logic as description languages. Learning using ILP is only feasible when the languages are restricted and are strongly controlled; otherwise, learning in ILP becomes undecidible. Research work in ILP was directed towards restricting domain theory and hypotheses description languages. Three algorithms that \"translate\" the intentional expression of a domain theory into its extensional expression are presented. The implementations of two of them are discussed. The implementations gave rise to two experimental learning environments: the propositional environment, which includes the constructive environment, and the relational environment.

Concept discovery is the problem of finding definitions of target relation in terms or other relation given as a background knowledge. Inductive Logic Programming (ILP)-based and graph-based approaches are two competitors in concept discovery problem. Although ILP-based systems have long dominated the area, graph-based systems have recently gained popularity as they overcome certain shortcomings of ILP-based systems. While having applications in numerous domains, ILP-based concept discovery systems still sustain scalability and efficiency issues. These issues generally arose due to the large search spaces such systems build. In this work we propose memoization-based and parallelization-based methods that modify the search space construction step and the evaluation step of ILP-based concept discovery systems to overcome these problem. In this work we propose three memoization-based methods, called Tabular CRIS, Tabular CRIS-wEF, and Selective Tabular CRIS. In these methods, basically, evaluation queries are stored in look-up tables for later uses. While preserving some core functions in common, each proposed method improves e_ciency and scalability of its predecessor by introducing constraints on what kind of evaluation queries to store in look-up tables and for how long. The proposed parallelization method, called pCRIS, parallelizes the search space construction and evaluation steps of ILP-based concept discovery systems in a data-parallel manner. The proposed method introduces policies to minimize the redundant work and waiting time among the workers at synchronization points. Graph-based approaches were first introduced to the concept discovery domain to handle the so called local plateau problem. Graph-based approaches have recently gained more popularity in concept discovery system as they provide convenient environment to represent relational data and are able to overcome certain shortcomings of ILP-based concept discovery systems. Graph-based approaches can be classified as structure-based approaches and path-finding approaches. The first class of approaches need to employ expensive algorithms such as graph isomorphism to find frequently appearing substructures. The methods that fall into the second class need to employ sophisticated indexing mechanisms to find out the frequently appearing paths that connect some nodes in interest. In this work, we also propose a hybrid method for graph-based concept discovery which does not require costly substructure matching algorithms and path indexing mechanism. The proposed method builds the graph in such a way that similar facts are grouped together and paths that eventually turn to be concept descriptors are build while the graph is constructed.

Real-world learning tasks present a range of issues for learning systems. Learning tasks can be complex and the training data noisy. When operating as part of a larger system, there may be limitations on available memory and computational resources. Learners may also be required to provide results from a stream. This thesis investigates the problem of incremental, relational learning from imperfect data with constrained time and memory resources. The learning process involves incremental update of a theory when an example is presented that contradicts the theory. Contradictions occur if there is an incorrect theory or noisy data. The learner cannot discriminate between the two possibilities, so both are considered and the better possibility used. Additionally, all changes to the theory must have support from multiple examples. These two principles allow learning from imperfect data. The Minimum Description Length principle is used for selection between possible worlds and determining appropriate levels of additional justification. A new encoding scheme allows the use of MDL within the framework of Inductive Logic Programming. Examples must be stored to provide additional justification for revisions without violating resource requirements. A new algorithm determines when to discard examples, minimising total usage while ensuring sufficient storage for justifications. Searching for revisions is the most computationally expensive part of the process, yet not all searches are successful. Another new algorithm uses a notion of theory stability as a guide to occasionally disallow entire searches to reduce overall time. The approach has been implemented as a learner called NILE. Empirical tests include two challenging domains where this type of learner acts as one component of a larger task. The first of these involves recognition of behavior activation conditions in another agent as part of an opponent modeling task. The second, more challenging task is learning to identify objects in visual images by recognising relationships between image features. These experiments highlight NILE'S strengths and limitations as well as providing new n domains for future work in ILP.

Made available in DSpace on 2014-12-17T15:12:16Z (GMT). No. of bitstreams: 1 RicardoGAP_DISSERT.pdf: 757603 bytes, checksum: bfeae294ee68b7c0f314886fbbd624fb (MD5) Previous issue date: 2012-10-02 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / The following work is to interpret and analyze the problem of induction under a vision founded on set theory and probability theory as a basis for solution of its negative philosophical implications related to the systems of inductive logic in general. Due to the importance of the problem and the relatively recent developments in these fields of knowledge (early 20th century), as well as the visible relations between them and the process of inductive inference, it has been opened a field of relatively unexplored and promising possibilities. The key point of the study consists in modeling the information acquisition process using concepts of set theory, followed by a treatment using probability theory. Throughout the study it was identified as a major obstacle to the probabilistic justification, both: the problem of defining the concept of probability and that of rationality, as well as the subtle connection between the two. This finding called for a greater care in choosing the criterion of rationality to be considered in order to facilitate the treatment of the problem through such specific situations, but without losing their original characteristics so that the conclusions can be extended to classic cases such as the question about the continuity of the sunrise / O seguinte trabalho consiste na interpreta??o e an?lise do problema da indu??o sob uma vis?o fundamentada em teoria de conjuntos e teoria de probabilidades como base para a solu??o de suas implica??es filos?ficas negativas relativas aos sistemas de l?gica indutiva de maneira geral. Devido ? import?ncia do problema e aos desenvolvimentos recentes nos referidos campos de conhecimento (in?cio do s?culo 20), bem como ?s rela??es vis?veis entre eles e o processo de infer?ncia indutivo, tem-se aberto um campo de possibilidades relativamente inexplorado e promissor. O ponto-chave para o estudo consiste na modelagem do processo de aquisi??o de informa??o usando conceitos de teoria de conjuntos, seguido por um tratamento usando teoria de probabilidades. Ao longo do estudo foi poss?vel identificar, como obst?culos principais ? justifica??o probabil?stica, tanto o problema da defini??o do conceito de probabilidade quanto do de racionalidade, al?m da sutil conex?o entre ambos. Essa constata??o permitiu um maior cuidado na escolha do crit?rio de racionalidade a ser considerado no intuito de viabilizar o tratamento do problema por meio de situa??es-exemplo espec?ficas, mas sem a perda de suas caracter?sticas originais, de modo que as conclus?es obtidas possam ser estendidas a casos cl?ssicos como o relativo ? d?vida sobre a continuidade do nascer do sol

Este trabalho investiga Aprendizado Indutivo de Máquina como função das linguagens de descrição, utilizadas para expressar instancias, conceitos e teoria do domínio. A ampliação do poder de representação do aprendizado proporcional e abordada no contexto de indução construtiva, no domínio de funções booleanas, com a proposta de uma estratégia de composição de atributos denominada root-fringe. Avaliações experimentais dessa e de outras estratégias de construção de novos atributos foram conduzidas e os resultados analisados. Dois métodos de poda, para tratamento de ruídos, em aprendizado de arvores de decisão, foram avaliados num ambiente de indução construtiva e os resultados discutidos. Devido a limitação do aprendizado proposicional, foram investigadas formas de ampliação dos limites do aprendizado, através da ampliação do poder representacional das linguagens de descrição. Foi escolhida Programação Lógica Indutiva - PLI - que e um paradigma de aprendizado indutivo que usa restrições de Lógica de Primeira Ordem como linguagens de descrição. O aprendizado em PLI só é factível quando as linguagens utilizadas estão restritas e é fortemente controlado, caso contrário, o aprendizado em PLI se torna indecidível. A pesquisa em PLI se direcionou a formas de restrição das linguagens de descrição da teoria do domínio e de hipóteses. Três algoritmos que \"traduzem\" a teoria do domínio de sua forma intencional, para extensional, são apresentados. As implementações de dois deles são discutidas. As implementações realizadas deram origem a dois ambientes experimentais de aprendizado: o ambiente proposicional experimental, do qual fazem parte o ambiente experimental construtivo, e o ambiente experimental relacional. / This work investigates Inductive Machine Learning as a function of the description languages employed to express instances, concepts and domain theory. The enlargement of the representational power of propositional learning methods is approached via constructive induction, in the domain of boolean functions, through the proposal of a bias for composing attributes, namely, the bias root-fringe. Experimental evaluation of root-fringe, as well as other biases for constructing new attributes was conducted and the results analyzed. Two pruning methods for decision trees were evaluated in an environment of constructive induction and the results discussed. Due to the limitations of propositional learning, ways of enlarging the limits of the learning process were investigated through enlarging the representational power of the description languages. It was chosen Inductive Logic Programming - ILP - that is an inductive learning paradigm that uses restrictions of First Order Logic as description languages. Learning using ILP is only feasible when the languages are restricted and are strongly controlled; otherwise, learning in ILP becomes undecidible. Research work in ILP was directed towards restricting domain theory and hypotheses description languages. Three algorithms that \"translate\" the intentional expression of a domain theory into its extensional expression are presented. The implementations of two of them are discussed. The implementations gave rise to two experimental learning environments: the propositional environment, which includes the constructive environment, and the relational environment.