Bit-parallel and SIMD alignment algorithms for biological sequence analysis

High-throughput next-generation sequencing techniques have hugely decreased the cost and increased the speed of sequencing, resulting in an explosion of sequencing data. This motivates the development of high-efficiency sequence alignment algorithms. In this thesis, I present multiple bit-parallel and Single Instruction Multiple Data (SIMD) algorithms that greatly accelerate the processing of biological sequences. The first chapter describes the BitPAl bit-parallel algorithms for global alignment with general integer scoring, which assigns integer weights for match, mismatch, and insertion/deletion. The bit-parallel approach represents individual cells in an alignment scoring matrix as bits in computer words and emulates the calculation of scores by a series of logic operations. Bit-parallelism has previously been applied to other pattern matching problems, producing fast algorithms. In timed tests, we show that BitPAl runs 7 - 25 times faster than a standard iterative algorithm. The second part involves two approaches to alignment with substitution scoring, which assigns a potentially different substitution weight to every pair of alphabet characters, better representing the relative rates of different mutations. The first approach extends the existing BitPAl method. The second approach is a new SIMD algorithm that uses partial sums of adjacent score differences. I present a simple partial sum method as well as one that uses parallel scan for additional acceleration. Results demonstrate that these algorithms are significantly faster than existing SIMD dynamic programming algorithms. Finally, I describe two extensions to the partial sums algorithm. The first adds support for affine gap penalty scoring. Affine gap scoring represents the biological likelihood that it is more likely for gaps to be continuous than to be distributed throughout a region by introducing a gap opening penalty and a gap extension penalty. The second extension is an algorithm that uses the partial sums method to calculate the tandem alignment of a pattern against a text sequence using a single pattern copy. Next generation sequencing data provides a wealth of information to researchers. Extracting that information in a timely manner increases the utility and practicality of sequence analysis algorithms. This thesis presents a family of algorithms which provide alignment scores in less time than previous algorithms

Quantum-Inspired Machine Learning: a Survey

Quantum-inspired Machine Learning (QiML) is a burgeoning field, receiving global attention from researchers for its potential to leverage principles of quantum mechanics within classical computational frameworks. However, current review literature often presents a superficial exploration of QiML, focusing instead on the broader Quantum Machine Learning (QML) field. In response to this gap, this survey provides an integrated and comprehensive examination of QiML, exploring QiML's diverse research domains including tensor network simulations, dequantized algorithms, and others, showcasing recent advancements, practical applications, and illuminating potential future research avenues. Further, a concrete definition of QiML is established by analyzing various prior interpretations of the term and their inherent ambiguities. As QiML continues to evolve, we anticipate a wealth of future developments drawing from quantum mechanics, quantum computing, and classical machine learning, enriching the field further. This survey serves as a guide for researchers and practitioners alike, providing a holistic understanding of QiML's current landscape and future directions.Comment: 56 pages, 13 figures, 8 table

Tensor Networks for Dimensionality Reduction and Large-Scale Optimizations. Part 2 Applications and Future Perspectives

Part 2 of this monograph builds on the introduction to tensor networks and their operations presented in Part 1. It focuses on tensor network models for super-compressed higher-order representation of data/parameters and related cost functions, while providing an outline of their applications in machine learning and data analytics. A particular emphasis is on the tensor train (TT) and Hierarchical Tucker (HT) decompositions, and their physically meaningful interpretations which reflect the scalability of the tensor network approach. Through a graphical approach, we also elucidate how, by virtue of the underlying low-rank tensor approximations and sophisticated contractions of core tensors, tensor networks have the ability to perform distributed computations on otherwise prohibitively large volumes of data/parameters, thereby alleviating or even eliminating the curse of dimensionality. The usefulness of this concept is illustrated over a number of applied areas, including generalized regression and classification (support tensor machines, canonical correlation analysis, higher order partial least squares), generalized eigenvalue decomposition, Riemannian optimization, and in the optimization of deep neural networks. Part 1 and Part 2 of this work can be used either as stand-alone separate texts, or indeed as a conjoint comprehensive review of the exciting field of low-rank tensor networks and tensor decompositions.Comment: 232 page

Tensor Networks for Dimensionality Reduction and Large-Scale Optimizations. Part 2 Applications and Future Perspectives

Part 2 of this monograph builds on the introduction to tensor networks and their operations presented in Part 1. It focuses on tensor network models for super-compressed higher-order representation of data/parameters and related cost functions, while providing an outline of their applications in machine learning and data analytics. A particular emphasis is on the tensor train (TT) and Hierarchical Tucker (HT) decompositions, and their physically meaningful interpretations which reflect the scalability of the tensor network approach. Through a graphical approach, we also elucidate how, by virtue of the underlying low-rank tensor approximations and sophisticated contractions of core tensors, tensor networks have the ability to perform distributed computations on otherwise prohibitively large volumes of data/parameters, thereby alleviating or even eliminating the curse of dimensionality. The usefulness of this concept is illustrated over a number of applied areas, including generalized regression and classification (support tensor machines, canonical correlation analysis, higher order partial least squares), generalized eigenvalue decomposition, Riemannian optimization, and in the optimization of deep neural networks. Part 1 and Part 2 of this work can be used either as stand-alone separate texts, or indeed as a conjoint comprehensive review of the exciting field of low-rank tensor networks and tensor decompositions.Comment: 232 page

Scaling Attributed Network Embedding to Massive Graphs

Given a graph G where each node is associated with a set of attributes, attributed network embedding (ANE) maps each node vin G to a compact vector Xv, which can be used in downstream machine learning tasks. Ideally, Xv should capture node v's affinity to each attribute, which considers not only v's own attribute associations, but also those of its connected nodes along edges in G. It is challenging to obtain high-utility embeddings that enable accurate predictions; scaling effective ANE computation to massive graphs with millions of nodes pushes the difficulty of the problem to a whole new level. Existing solutions largely fail on such graphs, leading to prohibitive costs, low-quality embeddings, or both. This paper proposes PANE, an effective and scalable approach to ANE computation for massive graphs that achieves state-of-the-art result quality on multiple benchmark datasets, measured by the accuracy of three common prediction tasks: attribute inference, link prediction, and node classification. PANE obtains high scalability and effectiveness through three main algorithmic designs. First, it formulates the learning objective based on a novel random walk model for attributed networks. The resulting optimization task is still challenging on large graphs. Second, PANE includes a highly efficient solver for the above optimization problem, whose key module is a carefully designed initialization of the embeddings, which drastically reduces the number of iterations required to converge. Finally, PANE utilizes multi-core CPUs through non-trivial parallelization of the above solver, which achieves scalability while retaining the high quality of the resulting embeddings. Extensive experiments, comparing 10 existing approaches on 8 real datasets, demonstrate that PANE consistently outperforms all existing methods in terms of result quality, while being orders of magnitude faster.Comment: 16 pages. PVLDB 2021. Volume 14, Issue

Study of the Quantum Advantage in Quantum Machine Learning Applications for drug discovery

Εθνικό Μετσόβιο Πολυτεχνείο--Μεταπτυχιακή Εργασία. Διεπιστημονικό-Διατμηματικό Πρόγραμμα Μεταπτυχιακών Σπουδών (Δ.Π.Μ.Σ.) “Μαθηματική Προτυποποίηση σε Σύγχρονες Τεχνολογίες και στα Χρηματοοικονομικά