António J. R. Neves

A survey on palette reordering methods for improving the compression of color-indexed images

Palette reordering is a well-known and very effective approach for improving the compression of color-indexed images. In this paper, we provide a survey of palette reordering methods, and we give experimental results comparing the ability of seven of them in improving the compression efficiency of JPEG-LS and lossless JPEG 2000. We concluded that the pairwise merging heuristic proposed by Memon et al. is the most effective, but also the most computationally demanding. Moreover, we found that the second most effective method is a modified version of Zengs reordering technique, which was 3%-5% worse than pairwise merging, but much faster.

On the representability of complete genomes by multiple competing finite-context (Markov) models.

A finite-context (Markov) model of order yields the probability distribution of the next symbol in a sequence of symbols, given the recent past up to depth . Markov modeling has long been applied to DNA sequences, for example to find gene-coding regions. With the first studies came the discovery that DNA sequences are non-stationary: distinct regions require distinct model orders. Since then, Markov and hidden Markov models have been extensively used to describe the gene structure of prokaryotes and eukaryotes. However, to our knowledge, a comprehensive study about the potential of Markov models to describe complete genomes is still lacking. We address this gap in this paper. Our approach relies on (i) multiple competing Markov models of different orders (ii) careful programming techniques that allow orders as large as sixteen (iii) adequate inverted repeat handling (iv) probability estimates suited to the wide range of context depths used. To measure how well a model fits the data at a particular position in the sequence we use the negative logarithm of the probability estimate at that position. The measure yields information profiles of the sequence, which are of independent interest. The average over the entire sequence, which amounts to the average number of bits per base needed to describe the sequence, is used as a global performance measure. Our main conclusion is that, from the probabilistic or information theoretic point of view and according to this performance measure, multiple competing Markov models explain entire genomes almost as well or even better than state-of-the-art DNA compression methods, such as XM, which rely on very different statistical models. This is surprising, because Markov models are local (short-range), contrasting with the statistical models underlying other methods, where the extensive data repetitions in DNA sequences is explored, and therefore have a non-local character.

A note on Zeng's technique for color reindexing of palette-based images

Palette reindexing is a well-known and very effective approach for improving the compression of color-indexed images. In this letter, we address the reindexing technique proposed by Zeng et al. and we show how its performance can be improved through a theoretically motivated choice of parameters. Experimental results show the practical appropriateness of the proposed modification.

An omnidirectional vision system for soccer robots

This paper describes a complete and efficient vision system developed for the robotic soccer team of the University of Aveiro, CAMBADA (Cooperative Autonomous Mobile roBots with Advanced Distributed Architecture). The system consists on a firewire camera mounted vertically on the top of the robots. A hyperbolic mirror placed above the camera reflects the 360 degrees of the field around the robot. The omnidirectional system is used to find the ball, the goals, detect the presence of obstacles and the white lines, used by our localization algorithm. In this paper we present a set of algorithms to extract efficiently the color information of the acquired images and, in a second phase, extract the information of all objects of interest. Our vision system architecture uses a distributed paradigm where the main tasks, namely image acquisition, color extraction, object detection and image visualization, are separated in several processes that can run at the same time. We developed an efficient color extraction algorithm based on lookup tables and a radial model for object detection. Our participation in the last national robotic contest, ROBOTICA 2007, where we have obtained the first place in the Medium Size League of robotic soccer, shows the effectiveness of our algorithms. Moreover, our experiments show that the system is fast and accurate having a maximum processing time independently of the robot position and the number of objects found in the field.

Lossless Compression of Microarray Images Using Image-Dependent Finite-Context Models

The use of microarray expression data in state-of-the-art biology has been well established. The widespread adoption of this technology, coupled with the significant volume of data generated per experiment, in the form of images, has led to significant challenges in storage and query retrieval. In this paper, we present a lossless bitplane-based method for efficient compression of microarray images. This method is based on arithmetic coding driven by image-dependent multibitplane finite-context models. It produces an embedded bitstream that allows progressive, lossy-to-lossless decoding. We compare the compression efficiency of the proposed method with three image compression standards (JPEG2000, JPEG-LS, and JBIG) and also with the two most recent specialized methods for microarray image coding. The proposed method gives better results for all images of the test sets and confirms the effectiveness of bitplane-based methods and finite-context modeling for the lossless compression of microarray images.

DNA coding using finite-context models and arithmetic coding

The interest in DNA coding has been growing with the availability of extensive genomic databases. Although only two bits are sufficient to encode the four DNA bases, efficient lossless compression methods are still needed due to the size of DNA sequences and because standard compression algorithms do not perform well on DNA sequences. As a result, several specific coding methods have been proposed. Most of these methods are based on searching procedures for finding exact or approximate repeats. Low order finite-context models have only been used as secondary, fall back mechanisms. In this paper, we show that finite-context models can also be used as main DNA encoding methods. We propose a coding method based on two finite-context models that compete for the encoding of data, on a block by block basis. The experimental results confirm the effectiveness of the proposed method.

On the use of standards for microarray lossless image compression

The interest in methods that are able to efficiently compress microarray images is relatively new. This is not surprising, since the appearance and fast growth of the technology responsible for producing these images is also quite recent. In this paper, we present a set of compression results obtained with 49 publicly available images, using three image coding standards: lossless JPEG2000, JBIG, and JPEG-LS. We concluded that the compression technology behind JBIG seems to be the one that offers the best combination of compression efficiency and flexibility for microarray image compression.

A Three-State Model for DNA Protein-Coding Regions

It is known that the protein-coding regions of DNA are usually characterized by a three-base periodicity. In this paper, we exploit this property, studying a DNA model based on three deterministic states, where each state implements a finite-context model. The experimental results obtained confirm the appropriateness of the proposed approach, showing compression gains in relation to the single finite-context model counterpart. Additionally, and potentially more interesting than the compression gain on its own, is the observation that the entropy associated to each of the three base positions of a codon differs and that this variation is not the same among the organisms analyzed

Humanoid behaviors: from simulation to a real robot

This paper presents the modifications needed to adapt a humanoid agent architecture and behaviors from simulation to a real robot. The experiments were conducted using the Aldebaran Nao robot model. The agent architecture was adapted from the RoboCup 3D Simulation League to the Standard Platform League with as few changes as possible. The reasons for the modifications include small differences in the dimensions and dynamics of the simulated and the real robot and the fact that the simulator does not create an exact copy of a real environment. In addition, the real robot API is different from the simulated robot API and there are a few more restrictions on the allowed joint configurations. The general approach for using behaviors developed for simulation in the real robot was to: first, (if necessary) make the simulated behavior compliant with the real robot restrictions, second, apply the simulated behavior to the real robot reducing its velocity, and finally, increase the velocity, while adapting the behavior parameters, until the behavior gets unstable or inefficient. This paper also presents an algorithm to calculate the three angles of the hip that produce the desired vertical hip rotation, since the Nao robot does not have a vertical hip joint. All simulation behaviors described in this paper were successfully adapted to the real robot.

CAMBADA Soccer Team: from Robot Architecture to Multiagent Coordination

Robotic soccer is nowadays a popular research domain in the area of multi-robot systems. RoboCup is an international joint project to promote research in artificial intelligence, robotics and related fields. RoboCup chose soccer as the main problem aiming at innovations to be applied for socially relevant problems. It includes several competition leagues, each one with a specific emphasis, some only at software level, others at both hardware and software, with single or multiple agents, cooperative and competitive. In the context of RoboCup, the Middle Size League (MSL) is one of the most challenging. In this league, each team is composed of up to 5 robots with a maximum size of 50cm× 50cm, 80cm height and a maximumweight of 40Kg, playing in a field of 18m× 12m. The rules of the game are similar to the official FIFA rules, with minor changes required to adapt them for the playing robots CAMBADA, Cooperative Autonomous Mobile roBots with Advanced Distributed Architecture, is the MSL Soccer team from the University of Aveiro. The project started in 2003, coordinated by the Transverse Activity on Intelligent Robotics group of the Institute of Electronic and Telematic Engineering of Aveiro (IEETA). This project involves people working on several areas for building the mechanical structure of the robot, its hardware architecture and controllers (Almeida et al., 2002; Azevedo et al., 2007) and the software development in areas such as image analysis and processing (Caleiro et al., 2007; Cunha et al., 2007; Martins et al., 2008; Neves et al., 2007; 2008), sensor and information fusion (Silva et al., 2008; 2009), reasoning and control (Lau et al., 2008), cooperative sensing approach based on a Real-Time Database (Almeida et al., 2004), communications among robots (Santos et al., 2009; 2007) and the development of an efficient basestation. The main contribution of this chapter is to present the new advances in the areas described above involving the development of an MSL team of soccer robots, taking the example of the CAMBADA team that won the RoboCup 2008 and attained the third place in the last edition of the MSL tournament at RoboCup 2009. CAMBADA also won the last three editions