Platforms for handling and development of audiovisual data

Estágio realizado na MOG Solutions e orientado por Vítor TeixeiraTese de mestrado integrado. Engenharia Informátca e Computação. Faculdade de Engenharia. Universidade do Porto. 200

Combined Industry, Space and Earth Science Data Compression Workshop

The sixth annual Space and Earth Science Data Compression Workshop and the third annual Data Compression Industry Workshop were held as a single combined workshop. The workshop was held April 4, 1996 in Snowbird, Utah in conjunction with the 1996 IEEE Data Compression Conference, which was held at the same location March 31 - April 3, 1996. The Space and Earth Science Data Compression sessions seek to explore opportunities for data compression to enhance the collection, analysis, and retrieval of space and earth science data. Of particular interest is data compression research that is integrated into, or has the potential to be integrated into, a particular space or earth science data information system. Preference is given to data compression research that takes into account the scien- tist's data requirements, and the constraints imposed by the data collection, transmission, distribution and archival systems

Compression of DNA sequencing data

With the release of the latest generations of sequencing machines, the cost of sequencing a whole human genome has dropped to less than US$1,000. The potential applications in several fields lead to the forecast that the amount of DNA sequencing data will soon surpass the volume of other types of data, such as video data. In this dissertation, we present novel data compression technologies with the aim of enhancing storage, transmission, and processing of DNA sequencing data. The first contribution in this dissertation is a method for the compression of aligned reads, i.e., read-out sequence fragments that have been aligned to a reference sequence. The method improves compression by implicitly assembling local parts of the underlying sequences. Compared to the state of the art, our method achieves the best trade-off between memory usage and compressed size. Our second contribution is a method for the quantization and compression of quality scores, i.e., values that quantify the error probability of each read-out base. Specifically, we propose two Bayesian models that are used to precisely control the quantization. With our method it is possible to compress the data down to 0.15 bit per quality score. Notably, we can recommend a particular parametrization for one of our models which—by removing noise from the data as a side effect—does not lead to any degradation in the distortion metric. This parametrization achieves an average rate of 0.45 bit per quality score. The third contribution is the first implementation of an entropy codec compliant to MPEG-G. We show that, compared to the state of the art, our method achieves the best compression ranks on average, and that adding our method to CRAM would be beneficial both in terms of achievable compression and speed. Finally, we provide an overview of the standardization landscape, and in particular of MPEG-G, in which our contributions have been integrated.Mit der Einführung der neuesten Generationen von Sequenziermaschinen sind die Kosten für die Sequenzierung eines menschlichen Genoms auf weniger als 1.000 US-Dollar gesunken. Es wird prognostiziert, dass die Menge der Sequenzierungsdaten bald diejenige anderer Datentypen, wie z.B. Videodaten, übersteigen wird. Daher werden in dieser Arbeit neue Datenkompressionsverfahren zur Verbesserung der Speicherung, Übertragung und Verarbeitung von Sequenzierungsdaten vorgestellt. Der erste Beitrag in dieser Arbeit ist eine Methode zur Komprimierung von alignierten Reads, d.h. ausgelesenen Sequenzfragmenten, die an eine Referenzsequenz angeglichen wurden. Die Methode verbessert die Komprimierung, indem sie die Reads nutzt, um implizit lokale Teile der zugrunde liegenden Sequenzen zu schätzen. Im Vergleich zum Stand der Technik erzielt die Methode das beste Ergebnis in einer gemeinsamen Betrachtung von Speichernutzung und erzielter Komprimierung. Der zweite Beitrag ist eine Methode zur Quantisierung und Komprimierung von Qualitätswerten, welche die Fehlerwahrscheinlichkeit jeder ausgelesenen Base quantifizieren. Konkret werden zwei Bayes’sche Modelle vorgeschlagen, mit denen die Quantisierung präzise gesteuert werden kann. Mit der vorgeschlagenen Methode können die Daten auf bis zu 0,15 Bit pro Qualitätswert komprimiert werden. Besonders hervorzuheben ist, dass eine bestimmte Parametrisierung für eines der Modelle empfohlen werden kann, die – durch die Entfernung von Rauschen aus den Daten als Nebeneffekt – zu keiner Verschlechterung der Verzerrungsmetrik führt. Mit dieser Parametrisierung wird eine durchschnittliche Rate von 0,45 Bit pro Qualitätswert erreicht. Der dritte Beitrag ist die erste Implementierung eines MPEG-G-konformen Entropie-Codecs. Es wird gezeigt, dass der vorgeschlagene Codec die durchschnittlich besten Kompressionswerte im Vergleich zum Stand der Technik erzielt und dass die Aufnahme des Codecs in CRAM sowohl hinsichtlich der erreichbaren Kompression als auch der Geschwindigkeit von Vorteil wäre. Abschließend wird ein Überblick über Standards zur Komprimierung von Sequenzierungsdaten gegeben. Insbesondere wird hier auf MPEG-G eingangen, da alle Beiträge dieser Arbeit in MPEG-G integriert wurden

Coding for the Optical Channel: the Ghost-Pulse Constraint

We consider a number of constrained coding techniques that can be used to mitigate a nonlinear effect in the optical fiber channel that causes the formation of spurious pulses, called ``ghost pulses.'' Specifically, if $b_1 b_2 ... b_{n}$ is a sequence of bits sent across an optical channel, such that $b_k=b_l=b_m=1$ for some $k,l,m$ (not necessarily all distinct) but $b_{k+l-m} = 0$, then the ghost-pulse effect causes $b_{k+l-m}$ to change to 1, thereby creating an error. We design and analyze several coding schemes using binary and ternary sequences constrained so as to avoid patterns that give rise to ghost pulses. We also discuss the design of encoders and decoders for these coding schemes.Comment: 13 pages, 6 figures; accepted for publication in IEEE Transactions on Information Theor

The Fifth NASA Symposium on VLSI Design

The fifth annual NASA Symposium on VLSI Design had 13 sessions including Radiation Effects, Architectures, Mixed Signal, Design Techniques, Fault Testing, Synthesis, Signal Processing, and other Featured Presentations. The symposium provides insights into developments in VLSI and digital systems which can be used to increase data systems performance. The presentations share insights into next generation advances that will serve as a basis for future VLSI design

A Survey of Paraphrasing and Textual Entailment Methods

Paraphrasing methods recognize, generate, or extract phrases, sentences, or longer natural language expressions that convey almost the same information. Textual entailment methods, on the other hand, recognize, generate, or extract pairs of natural language expressions, such that a human who reads (and trusts) the first element of a pair would most likely infer that the other element is also true. Paraphrasing can be seen as bidirectional textual entailment and methods from the two areas are often similar. Both kinds of methods are useful, at least in principle, in a wide range of natural language processing applications, including question answering, summarization, text generation, and machine translation. We summarize key ideas from the two areas by considering in turn recognition, generation, and extraction methods, also pointing to prominent articles and resources.Comment: Technical Report, Natural Language Processing Group, Department of Informatics, Athens University of Economics and Business, Greece, 201

Decoding error-correcting codes via linear programming

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2003.Includes bibliographical references (p. 147-151).Error-correcting codes are fundamental tools used to transmit digital information over unreliable channels. Their study goes back to the work of Hamming [Ham50] and Shannon [Sha48], who used them as the basis for the field of information theory. The problem of decoding the original information up to the full error-correcting potential of the system is often very complex, especially for modern codes that approach the theoretical limits of the communication channel. In this thesis we investigate the application of linear programming (LP) relaxation to the problem of decoding an error-correcting code. Linear programming relaxation is a standard technique in approximation algorithms and operations research, and is central to the study of efficient algorithms to find good (albeit suboptimal) solutions to very difficult optimization problems. Our new "LP decoders" have tight combinatorial characterizations of decoding success that can be used to analyze error-correcting performance. Furthermore, LP decoders have the desirable (and rare) property that whenever they output a result, it is guaranteed to be the optimal result: the most likely (ML) information sent over the channel. We refer to this property as the ML certificate property. We provide specific LP decoders for two major families of codes: turbo codes and low-density parity-check (LDPC) codes. These codes have received a great deal of attention recently due to their unprecedented error-correcting performance.(cont.) Our decoder is particularly attractive for analysis of these codes because the standard message-passing algorithms used for decoding are often difficult to analyze. For turbo codes, we give a relaxation very close to min-cost flow, and show that the success of the decoder depends on the costs in a certain residual graph. For the case of rate-1/2 repeat-accumulate codes (a certain type of turbo code), we give an inverse polynomial upper bound on the probability of decoding failure. For LDPC codes (or any binary linear code), we give a relaxation based on the factor graph representation of the code. We introduce the concept of fractional distance, which is a function of the relaxation, and show that LP decoding always corrects a number of errors up to half the fractional distance. We show that the fractional distance is exponential in the girth of the factor graph. Furthermore, we give an efficient algorithm to compute this fractional distance. We provide experiments showing that the performance of our decoders are comparable to the standard message-passing decoders. We also give new provably convergent message-passing decoders based on linear programming duality that have the ML certificate property.by Jon Feldman.Ph.D