Read alignment using deep neural networks

2019 Spring.Includes bibliographical references.Read alignment is the process of mapping short DNA sequences into the reference genome. With the advent of consecutively evolving "next generation" sequencing technologies, the need for sequence alignment tools appeared. Many scientific communities and the companies marketing the sequencing technologies developed a whole spectrum of read aligners/mappers for different error profiles and read length characteristics. Among the most recent successfully marketed sequencing technologies are Oxford Nanopore and PacBio SMRT sequencing, which are considered top players because of their extremely long reads and low cost. However, the reads may contain error up to 20% that are not generally uniformly distributed. To deal with that level of error rate and read length, proximity preserving hashing techniques, such as Minhash and Minimizers, were utilized to quickly map a read to the target region of the reference sequence. Subsequently, a variant of global or local alignment dynamic programming is then used to give the final alignment. In this research work, we train a Deep Neural Network (DNN) to yield a hashing scheme for the highly erroneous long reads, which is deemed superior to Minhash for mapping the reads. We implemented that idea to build a read alignment tool: DNNAligner. We evaluated the performance of our aligner against the popular read aligners in the bioinformatics community currently — minimap2, bwa-mem and graphmap. Our results show that the performance of DNNAligner is comparable to other tools without any code optimization or integration of other advanced features. Moreover, DNN exhibits superior performance in comparison with Minhashon neighborhood classification

A computational framework for unsupervised analysis of everyday human activities

In order to make computers proactive and assistive, we must enable them to perceive, learn, and predict what is happening in their surroundings. This presents us with the challenge of formalizing computational models of everyday human activities. For a majority of environments, the structure of the in situ activities is generally not known a priori. This thesis therefore investigates knowledge representations and manipulation techniques that can facilitate learning of such everyday human activities in a minimally supervised manner. A key step towards this end is finding appropriate representations for human activities. We posit that if we chose to describe activities as finite sequences of an appropriate set of events, then the global structure of these activities can be uniquely encoded using their local event sub-sequences. With this perspective at hand, we particularly investigate representations that characterize activities in terms of their fixed and variable length event subsequences. We comparatively analyze these representations in terms of their representational scope, feature cardinality and noise sensitivity. Exploiting such representations, we propose a computational framework to discover the various activity-classes taking place in an environment. We model these activity-classes as maximally similar activity-cliques in a completely connected graph of activities, and describe how to discover them efficiently. Moreover, we propose methods for finding concise characterizations of these discovered activity-classes, both from a holistic as well as a by-parts perspective. Using such characterizations, we present an incremental method to classify a new activity instance to one of the discovered activity-classes, and to automatically detect if it is anomalous with respect to the general characteristics of its membership class. Our results show the efficacy of our framework in a variety of everyday environments.Ph.D.Committee Chair: Aaron Bobick; Committee Member: Charles Isbell; Committee Member: David Hogg; Committee Member: Irfan Essa; Committee Member: James Reh

Music Synchronization, Audio Matching, Pattern Detection, and User Interfaces for a Digital Music Library System

Over the last two decades, growing efforts to digitize our cultural heritage could be observed. Most of these digitization initiatives pursuit either one or both of the following goals: to conserve the documents - especially those threatened by decay - and to provide remote access on a grand scale. For music documents these trends are observable as well, and by now several digital music libraries are in existence. An important characteristic of these music libraries is an inherent multimodality resulting from the large variety of available digital music representations, such as scanned score, symbolic score, audio recordings, and videos. In addition, for each piece of music there exists not only one document of each type, but many. Considering and exploiting this multimodality and multiplicity, the DFG-funded digital library initiative PROBADO MUSIC aimed at developing a novel user-friendly interface for content-based retrieval, document access, navigation, and browsing in large music collections. The implementation of such a front end requires the multimodal linking and indexing of the music documents during preprocessing. As the considered music collections can be very large, the automated or at least semi-automated calculation of these structures would be recommendable. The field of music information retrieval (MIR) is particularly concerned with the development of suitable procedures, and it was the goal of PROBADO MUSIC to include existing and newly developed MIR techniques to realize the envisioned digital music library system. In this context, the present thesis discusses the following three MIR tasks: music synchronization, audio matching, and pattern detection. We are going to identify particular issues in these fields and provide algorithmic solutions as well as prototypical implementations. In Music synchronization, for each position in one representation of a piece of music the corresponding position in another representation is calculated. This thesis focuses on the task of aligning scanned score pages of orchestral music with audio recordings. Here, a previously unconsidered piece of information is the textual specification of transposing instruments provided in the score. Our evaluations show that the neglect of such information can result in a measurable loss of synchronization accuracy. Therefore, we propose an OCR-based approach for detecting and interpreting the transposition information in orchestral scores. For a given audio snippet, audio matching methods automatically calculate all musically similar excerpts within a collection of audio recordings. In this context, subsequence dynamic time warping (SSDTW) is a well-established approach as it allows for local and global tempo variations between the query and the retrieved matches. Moving to real-life digital music libraries with larger audio collections, however, the quadratic runtime of SSDTW results in untenable response times. To improve on the response time, this thesis introduces a novel index-based approach to SSDTW-based audio matching. We combine the idea of inverted file lists introduced by Kurth and Müller (Efficient index-based audio matching, 2008) with the shingling techniques often used in the audio identification scenario. In pattern detection, all repeating patterns within one piece of music are determined. Usually, pattern detection operates on symbolic score documents and is often used in the context of computer-aided motivic analysis. Envisioned as a new feature of the PROBADO MUSIC system, this thesis proposes a string-based approach to pattern detection and a novel interactive front end for result visualization and analysis

Leveraging process data to assess adults' problem-solving skills: Using sequence mining to identify behavioral patterns across digital tasks

This paper illustrates how process data can be used to identify behavioral patterns in a computer-based problem-solving assessment. Using sequence-mining techniques, we identify patterns of behavior across multiple digital tasks from the sequences of actions undertaken by respondents. We then examine how respondents’ action sequences (which we label “strategies”) differ from optimal strategies. In our application, optimality is defined ex-ante as the sequence of actions that content experts involved in the development of the assessment tasks identified as most efficient to solve the task given the range of possible actions available to test-takers. Data on 7462 respondents from five countries (the United Kingdom, Ireland, Japan, the Netherlands, and the United States) participating in the Problem Solving in Technology-Rich Environment (PSTRE) assessment, administered as part of the OECD Programme for the International Assessment of Adult Competencies (PIAAC), indicate that valuable insights can be derived from the analysis of process data. Adults who follow optimal strategies are more likely to obtain high scores in the PSTRE assessment, while low performers consistently adopt strategies that are very distant from optimal ones. Very few high performers are able to solve the items in an efficient way, i.e. by minimizing the number of actions and by avoiding undertaking unnecessary or redundant actions. Women and adults above the age of 40 are more likely to adopt sub-optimal problem-solving strategies

Randomized shortest paths and their applications

In graph analysis, the Shortest Path problem identifies the optimal, most cost effective, path between two nodes. This problem has been the object of many studies and extensions in heterogeneous domains such as: speech recognition, social network analysis, biological sequence alignment, path planning, or zero-sum games among others. Although the shortest path focuses on the optimal cost of reaching a destination node, it does not take into account other useful information contained on the graph, such as the degree of connectivity of two nodes. On the other hand, measures taking connectivity information into account have their own drawbacks, specially when graphs become large. A new family of distances which interpolates between both extremes is introduced by the Randomized Shortest Path (RSP) framework. By spreading randomization through a graph, the RSP leads to applications where some degree of randomness would be desired. Through this work, we try to investigate whether the RSP framework can be applied to different domains in which randomization is useful, and either solve an existing problem with a new approach, or prove to outperform existing methods.(FSA - Sciences de l'ingénieur) -- UCL, 201

Developing 3-in-1 Index Structures on Complex Structure Similarity Search

Ph.DDOCTOR OF PHILOSOPH