On the Use of Suffix Arrays for Memory-Efficient Lempel-Ziv Data Compression

Much research has been devoted to optimizing algorithms of the Lempel-Ziv (LZ) 77 family, both in terms of speed and memory requirements. Binary search trees and suffix trees (ST) are data structures that have been often used for this purpose, as they allow fast searches at the expense of memory usage. In recent years, there has been interest on suffix arrays (SA), due to their simplicity and low memory requirements. One key issue is that an SA can solve the sub-string problem almost as efficiently as an ST, using less memory. This paper proposes two new SA-based algorithms for LZ encoding, which require no modifications on the decoder side. Experimental results on standard benchmarks show that our algorithms, though not faster, use 3 to 5 times less memory than the ST counterparts. Another important feature of our SA-based algorithms is that the amount of memory is independent of the text to search, thus the memory that has to be allocated can be defined a priori. These features of low and predictable memory requirements are of the utmost importance in several scenarios, such as embedded systems, where memory is at a premium and speed is not critical. Finally, we point out that the new algorithms are general, in the sense that they are adequate for applications other than LZ compression, such as text retrieval and forward/backward sub-string search.Comment: 10 pages, submited to IEEE - Data Compression Conference 200

Efficient Haplotype Inference with Pseudo-Boolean Optimization

Abstract. Haplotype inference from genotype data is a key computational problem in bioinformatics, since retrieving directly haplotype information from DNA samples is not feasible using existing technology. One of the methods for solving this problem uses the pure parsimony criterion, an approach known as Haplotype Inference by Pure Parsimony (HIPP). Initial work in this area was based on a number of different Integer Linear Programming (ILP) models and branch and bound algorithms. Recent work has shown that the utilization of a Boolean Satisfiability (SAT) formulation and state of the art SAT solvers represents the most efficient approach for solving the HIPP problem. Motivated by the promising results obtained using SAT techniques, this paper investigates the utilization of modern Pseudo-Boolean Optimization (PBO) algorithms for solving the HIPP problem. The paper starts by applying PBO to existing ILP models. The results are promising, and motivate the development of a new PBO model (RPoly) for the HIPP problem, which has a compact representation and eliminates key symmetries. Experimental results indicate that RPoly outperforms the SAT-based approach on most problem instances, being, in general, significantly more efficient

Pretraining the Vision Transformer using self-supervised methods for vision based Deep Reinforcement Learning

The Vision Transformer architecture has shown to be competitive in the computer vision (CV) space where it has dethroned convolution-based networks in several benchmarks. Nevertheless, Convolutional Neural Networks (CNN) remain the preferential architecture for the representation module in Reinforcement Learning. In this work, we study pretraining a Vision Transformer using several state-of-the-art self-supervised methods and assess data-efficiency gains from this training framework. We propose a new self-supervised learning method called TOV-VICReg that extends VICReg to better capture temporal relations between observations by adding a temporal order verification task. Furthermore, we evaluate the resultant encoders with Atari games in a sample-efficiency regime. Our results show that the vision transformer, when pretrained with TOV-VICReg, outperforms the other self-supervised methods but still struggles to overcome a CNN. Nevertheless, we were able to outperform a CNN in two of the ten games where we perform a 100k steps evaluation. Ultimately, we believe that such approaches in Deep Reinforcement Learning (DRL) might be the key to achieving new levels of performance as seen in natural language processing and computer vision. Source code will be available at: https://github.com/mgoulao/TOV-VICRe

LEMPEL-ZIV SLIDING WINDOW UPDATE WITH SUFFIX ARRAYS

The sliding window dictionary-based algorithms of the Lempel-Ziv (LZ) 77 family are widely used for universal lossless data compression. The encoding component of these algorithms performs repeated substring search. Data structures, such as hash tables, binary search trees, and suffix trees have been used to speedup these searches, at the expense of memory usage. Previous work has shown how suffix arrays (SA) can be used for dictionary representation and LZ77 decomposition. In this paper, we improve over that work by proposing a new efficient algorithm to update the sliding window each time a token is produced at the output. The proposed algorithm toggles between two SA on consecutive tokens. The resulting SA-based encoder requires less memory than the conventional tree-based encoders. In comparing our SA-based technique against tree-based encoders, on a large set of benchmark files, we find that, in some compression settings, our encoder is also faster than tree-based encoders

Treino não supervisionado de modelos acústicos para reconhecimento de fala

Tese de doutoramento em Engenharia Electrotécnica e de Computadores, apresentada ao Departamento de Engenharia Electrotécnica e de Computadores da Faculdade de Ciências e Tecnologia da Universidade de CoimbraEsta tese resume os trabalhos desenvolvidos na área de processamento automático de fala com o objetivo de incrementar a quantidade de recursos linguísticos disponíveis para o português europeu. O estágio de desenvolvimento e a aplicação das tecnologias de fala para uma língua estão relacionados com a quantidade e a qualidade de recursos disponíveis por esta língua. Poucas línguas apresentam, no domínio público e livre, todos os recursos necessários para desenvolver as tecnologias de fala. A língua portuguesa, como muitas outras, tem escassez de recursos públicos e livres, o que pode dificultar o desenvolvimento e a aplicação de tecnologias de fala que incorporam esta língua. Os trabalhos descritos nesta tese apresentam uma abordagem para criar bases de dados de fala, recorrendo apenas aos recursos do domínio público e livres, partindo de sinais multimédia sem transcrições ortográficas ou fonéticas. É apresentada uma solução para aproveitar a grande disponibilidade de material multimédia existente no domínio público (podcasts por exemplo) e selecionar segmentos de fala adequados para treinar modelos acústicos. Para isso, foram desenvolvidos vários sistemas para segmentar e classificar automaticamente os noticiários. Estes sistemas podem ser combinados para criar bases de dados de fala com transcrição fonética sem a intervenção humana. Foi desenvolvido um sistema de conversão automático de grafemas para fonemas que apoia em regras fonológicas e modelos estatísticos. Esta abordagem híbrida é justificada pelos desenvolvimentos de algoritmos de aprendizagem automática aplicados a conversão de grafemas para fonemas e pelo fato do português apresentar uma razoável regularidade fonética e fonológica bem como uma ortografia de base fonológica. Com auxílio deste sistema, foi criado um dicionário de pronunciação com cerca de 40 mil entradas que foram verificadas manualmente. Foram implementados sistemas de segmentação e de diarização de locutor para segmentar sinais de áudio. Estes sistemas utilizam várias técnicas como a impressão digital acústica, modelos com misturas de gaussianas e critério de informação bayesiana que normalmente são aplicadas noutras tarefas de processamento de fala. Para selecionar os segmentos adequados ou descartar os segmentos com fala não preparada que podem prejudicar o treino de modelos acústicos, foi desenvolvido um sistema de deteção de estilos de fala. A deteção de estilos de fala baseia-se na combinação de parâmetros acústicos e parâmetros prosódicos, na segmentação automática e em classificadores de máquinas de vetores de suporte. Ainda neste âmbito, fez-se um estudo com o intuito de caracterizar os eventos de hesitações presentes nos noticiários em português. A transcrição fonética da base de dados de fala é indispensável no processo de treino de modelos acústicos. É frequente recorrer a sistema de reconhecimento de fala de grande vocabulário para fazer transcrição automática quando a base de dados não apresenta nenhuma transcrição. Nesta tese, é proposto um sistema de word-spotting para fazer a transcrição fonética dos segmentos de fala. Fez-se uma implementação preliminar de um sistema de word-spotting baseado em modelos de fonemas. Foi proposta uma estratégia para diminuir o tempo de resposta do sistema, criando, a priori, uma espécie de “assinatura acústica” para cada sinal de áudio com os valores de todos os cálculos que não dependem da palavra a pesquisar, como a verosimilhanças de todos os estados dos modelos de fonemas. A deteção de uma palavra utiliza medidas de similaridades entre as verosimilhanças do modelo da palavra e do modelo de enchimento, um detetor de picos e um limiar definido por forma a minimizar os erros de deteção. Foram publicados vários recursos para a língua portuguesa que resultaram da aplicação dos vários sistemas desenvolvidos ao longo da execução desta tese com especial destaque para o sistema de conversão de grafemas para fonemas a partir do qual publicou-se vários dicionários de pronunciação, dicionários com as palavras homógrafas heterofónicas, dicionário com estrangeirismos, modelos estatísticos para a conversão de grafemas para fonemas, código fonte de todo sistema de treino e conversão e um demonstrador online.This thesis summarizes the works done in the automatic speech processing field aiming to increase the amount of the linguistic resources available for European Portuguese language. The development stage and the application of speech technologies into a language are related to the quantity and quality of resources available for that given language. Few languages have all the required resources to implement speech technologies within free-access and public domain. Like many other language, the Portuguese language lacks public and free resources which may hinder the development and the application of speech technologies that incorporate the Portuguese language. The works described in this thesis present an approach to create speech databases, using only the public and free-access resources, starting from multimedia signals without orthographic or phonetic transcriptions. It this sense, a solution is presented to take advantage of the wide availability in the public domain of multimedia material (e.g. podcasts) and select appropriate speech segments to train acoustic models. To this end, several systems have been developed to automatically segment and classify broadcast news. These systems can be combined to build speech databases with phonetic transcription without human intervention. A system was developed to automatically convert graphemes to phonemes based on phonological rules and statistical models. This hybrid approach is justified by the developments in machine learning algorithms applied to the conversion of graphemes into phonemes and by the fact that the Portuguese language presents a reasonable phonetic/phonologic regularity and an orthography that is roughly phonologically based. Using this system, a pronunciation dictionary was created including about 40 thousands entries that where manually confirmed. They were implemented a system for segmentation into five predetermined acoustic classes (speech, music, noise, speech with music and speech with noise) and a system for speaker diarization. These systems use various techniques such as acoustic fingerprint, Gaussian mixture model and Bayesian information criterion that normally are used in other speech processing tasks. In order to select appropriate audio segments or discard non-prepared speech segments that may impair acoustic models training, it was developed a system to detect speaking styles. The detection of speaking styles is based on the combination of acoustic and prosodic parameters, on automatic segmentation and on support vector machine classifiers. Also in this scope, a study was made in order to characterize the hesitation events present in the Portuguese broadcast news. The transcription of the audio databases is essential in the process of acoustic models training. The large-vocabulary continuous speech recognition system is usually used to do automatic transcription wen the database do not have any transcripts. In this thesis, it is proposed to use word-spotting system to provide phonetic transcriptions of speech segments. A preliminary implementation of a word-spotting system based on phoneme models was conducted. A strategy was proposed to decrease the system response time, creating, a priori, a sort of “acoustic signature” for each audio signal with the values of all calculations which do not depend on the searching word as for example the likelihood of all states of phoneme models. The detection of a word uses similarity measures based on likelihood of word model and likelihood of filler model, a peak detector and a threshold value defined as to minimize detection errors. Several resources for the Portuguese language were published that resulted from the application of the various systems developed throughout the development of this thesis with particular emphasis on the graphemes to phonemes system from which it was published several dictionaries of pronunciation, dictionary with heterophonic homographs words, dictionary of foreign words, statistical models for converting graphemes to phonemes, the source code of the whole system of training as well as conversion and an online demo

BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data

<p>Abstract</p> <p>Background</p> <p>The ability to monitor changes in expression patterns over time, and to observe the emergence of coherent temporal responses using expression time series, is critical to advance our understanding of complex biological processes. Biclustering has been recognized as an effective method for discovering local temporal expression patterns and unraveling potential regulatory mechanisms. The general biclustering problem is NP-hard. In the case of time series this problem is tractable, and efficient algorithms can be used. However, there is still a need for specialized applications able to take advantage of the temporal properties inherent to expression time series, both from a computational and a biological perspective.</p> <p>Findings</p> <p>BiGGEsTS makes available state-of-the-art biclustering algorithms for analyzing expression time series. Gene Ontology (GO) annotations are used to assess the biological relevance of the biclusters. Methods for preprocessing expression time series and post-processing results are also included. The analysis is additionally supported by a visualization module capable of displaying informative representations of the data, including heatmaps, dendrograms, expression charts and graphs of enriched GO terms.</p> <p>Conclusion</p> <p>BiGGEsTS is a free open source graphical software tool for revealing local coexpression of genes in specific intervals of time, while integrating meaningful information on gene annotations. It is freely available at: <url>http://kdbio.inesc-id.pt/software/biggests</url>. We present a case study on the discovery of transcriptional regulatory modules in the response of <it>Saccharomyces cerevisiae </it>to heat stress.</p