Automatically Evolving Rotation-invariant Texture Image Descriptors by Genetic Programming

In computer vision, training a model that performs classification effectively is highly dependent on the extracted features, and the number of training instances. Conventionally, feature detection and extraction are performed by a domain-expert who, in many cases, is expensive to employ and hard to find. Therefore, image descriptors have emerged to automate these tasks. However, designing an image descriptor still requires domain-expert intervention. Moreover, the majority of machine learning algorithms require a large number of training examples to perform well. However, labelled data is not always available or easy to acquire, and dealing with a large dataset can dramatically slow down the training process. In this paper, we propose a novel Genetic Programming based method that automatically synthesises a descriptor using only two training instances per class. The proposed method combines arithmetic operators to evolve a model that takes an image and generates a feature vector. The performance of the proposed method is assessed using six datasets for texture classification with different degrees of rotation, and is compared with seven domain-expert designed descriptors. The results show that the proposed method is robust to rotation, and has significantly outperformed, or achieved a comparable performance to, the baseline methods.

Développement et applications d’un outil bio-informatique pour la détection de similarités de champs d’interaction moléculaire

Résumé : Les méthodes de détection de similarités de sites de liaison servent entre autres à la prédiction de fonction et à la prédiction de cibles croisées. Ces méthodes peuvent aider à prévenir les effets secondaires, suggérer le repositionnement de médicament existants, identifier des cibles polypharmacologiques et des remplacements bio-isostériques. La plupart des méthodes utilisent des représentations basées sur les atomes, même si les champs d’interaction moléculaire (MIFs) représentent plus directement ce qui cherche à être identifié. Nous avons développé une méthode bio-informatique, IsoMif, qui détecte les similarités de MIF entre différents sites de liaisons et qui ne nécessite aucun alignement de séquence ou de structure. Sa performance a été comparée à d’autres méthodes avec des bancs d’essais, ce qui n’a jamais été fait pour une méthode basée sur les MIFs. IsoMif performe mieux en moyenne et est plus robuste. Nous avons noté des limites intrinsèques à la méthodologie et d’autres qui proviennent de la nature. L’impact de choix de conception sur la performance est discuté. Nous avons développé une interface en ligne qui permet la détection de similarités entre une protéine et différents ensembles de MIFs précalculés ou à des MIFs choisis par l’utilisateur. Des sessions PyMOL peuvent être téléchargées afin de visualiser les similarités identifiées pour différentes interactions intermoléculaires. Nous avons appliqué IsoMif pour identifier des cibles croisées potentielles de drogues lors d’une analyse à large échelle (5,6 millions de comparaisons). Des simulations d’arrimage moléculaire ont également été effectuées pour les prédictions significatives. L’objectif est de générer des hypothèses de repositionnement et de mécanismes d’effets secondaires observés. Plusieurs exemples sont présentés à cet égard.

Plane detection from monocular image sequences

AIRES, Kelson R. T. ; ARAÚJO, Hélder J. ; MEDEIROS, Adelardo A. D. . Plane Detection from Monocular Image Sequences. In: VISUALIZATION, IMAGING AND IMAGE PROCESSING, 2008, Palma de Mallorca, Spain. Proceedings..., Palma de Mallorca: VIIP, 2008

Coupled CFD Shape Optimization for aerodynamic profiles

The present document deals with the optimization of shape of aerodynamic profiles -- The objective is to reduce the drag coefficient on a given profile without penalising the lift coefficient -- A set of control points defining the geometry are passed and parameterized as a B-Spline curve -- These points are modified automatically by means of CFD analysis -- A given shape is defined by an user and a valid volumetric CFD domain is constructed from this planar data and a set of user-defined parameters -- The construction process involves the usage of 2D and 3D meshing algorithms that were coupled into own- code -- The volume of air surrounding the airfoil and mesh quality are also parametrically defined -- Some standard NACA profiles were used by obtaining first its control points in order to test the algorithm -- Navier-Stokes equations were solved for turbulent, steady-state ow of compressible uids using the k-epsilon model and SIMPLE algorithm -- In order to obtain data for the optimization process an utility to extract drag and lift data from the CFD simulation was added -- After a simulation is run drag and lift data are passed to the optimization process -- A gradient-based method using the steepest descent was implemented in order to define the magnitude and direction of the displacement of each control point -- The control points and other parameters defined as the design variables are iteratively modified in order to achieve an optimum -- Preliminary results on conceptual examples show a decrease in drag and a change in geometry that obeys to aerodynamic behavior principles

Assessment of exposure to the Penicillium glabrum complex in cork industry using complementing methods

Cork oak is the second most dominant forest species in Portugal and makes this country the world leader in cork export. Occupational exposure to Chrysonilia sitophila and the Penicillium glabrum complex in cork industry is common, and the latter fungus is associated with suberosis. However, as conventional methods seem to underestimate its presence in occupational environments, the aim of our study was to see whether information obtained by polymerase chain reaction (PCR), a molecular-based method, can complement conventional findings and give a better insight into occupational exposure of cork industry workers. We assessed fungal contamination with the P. glabrum complex in three cork manufacturing plants in the outskirts of Lisbon using both conventional and molecular methods. Conventional culturing failed to detect the fungus at six sampling sites in which PCR did detect it. This confirms our assumption that the use of complementing methods can provide information for a more accurate assessment of occupational exposure to the P. glabrum complex in cork industry.

Automated Discovery of Social Networks in Online Learning Communities

As a way to gain greater insights into the operation of online communities, this dissertation applies automated text mining techniques to text-based communication to identify, describe and evaluate underlying social networks among online community members. The main thrust of the study is to automate the discovery of social ties that form between community members, using only the digital footprints left behind in their online forum postings. Currently, one of the most common but time consuming methods for discovering social ties between people is to ask questions about their perceived social ties. However, such a survey is difficult to collect due to the high investment in time associated with data collection and the sensitive nature of the types of questions that may be asked. To overcome these limitations, the dissertation presents a new, content-based method for automated discovery of social networks from threaded discussions, referred to as ‘name network’. As a case study, the proposed automated method is evaluated in the context of online learning communities. The results suggest that the proposed ‘name network’ method for collecting social network data is a viable alternative to costly and time-consuming collection of users’ data using surveys. The study also demonstrates how social networks produced by the ‘name network’ method can be used to study online classes and to look for evidence of collaborative learning in online learning communities. For example, educators can use name networks as a real time diagnostic tool to identify students who might need additional help or students who may provide such help to others. Future research will evaluate the usefulness of the ‘name network’ method in other types of online communities.

Plane Detection Using Affine Homography

AIRES, Kelson R. T.; ARAÚJO, Hélder J.; MEDEIROS, Adelardo A. D. Plane Detection Using Affine Homography. In: CONGRESSO BRASILEIRO DE AUTOMÁTICA, 2008, Juiz de Fora, MG: Anais... do CBA 2008.

Leveraging Multiple Features for Image Retrieval and Matching

The goal of image retrieval and matching is to find and locate object instances in images from a large-scale image database. While visual features are abundant, how to combine them to improve performance by individual features remains a challenging task. In this work, we focus on leveraging multiple features for accurate and efficient image retrieval and matching. We first propose two graph-based approaches to rerank initially retrieved images for generic image retrieval. In the graph, vertices are images while edges are similarities between image pairs. Our first approach employs a mixture Markov model based on a random walk model on multiple graphs to fuse graphs. We introduce a probabilistic model to compute the importance of each feature for graph fusion under a naive Bayesian formulation, which requires statistics of similarities from a manually labeled dataset containing irrelevant images. To reduce human labeling, we further propose a fully unsupervised reranking algorithm based on a submodular objective function that can be efficiently optimized by greedy algorithm. By maximizing an information gain term over the graph, our submodular function favors a subset of database images that are similar to query images and resemble each other. The function also exploits the rank relationships of images from multiple ranked lists obtained by different features. We then study a more well-defined application, person re-identification, where the database contains labeled images of human bodies captured by multiple cameras. Re-identifications from multiple cameras are regarded as related tasks to exploit shared information. We apply a novel multi-task learning algorithm using both low level features and attributes. A low rank attribute embedding is joint learned within the multi-task learning formulation to embed original binary attributes to a continuous attribute space, where incorrect and incomplete attributes are rectified and recovered. To locate objects in images, we design an object detector based on object proposals and deep convolutional neural networks (CNN) in view of the emergence of deep networks. We improve a Fast RCNN framework and investigate two new strategies to detect objects accurately and efficiently: scale-dependent pooling (SDP) and cascaded rejection classifiers (CRC). The SDP improves detection accuracy by exploiting appropriate convolutional features depending on the scale of input object proposals. The CRC effectively utilizes convolutional features and greatly eliminates negative proposals in a cascaded manner, while maintaining a high recall for true objects. The two strategies together improve the detection accuracy and reduce the computational cost.

Characterization of Non-linear Polymer Properties to Predict Process Induced Warpage and Residual Stress of Electronic Packages

Nonlinear thermo-mechanical properties of advanced polymers are crucial to accurate prediction of the process induced warpage and residual stress of electronics packages. The Fiber Bragg grating (FBG) sensor based method is advanced and implemented to determine temperature and time dependent nonlinear properties. The FBG sensor is embedded in the center of the cylindrical specimen, which deforms together with the specimen. The strains of the specimen at different loading conditions are monitored by the FBG sensor. Two main sources of the warpage are considered: curing induced warpage and coefficient of thermal expansion (CTE) mismatch induced warpage. The effective chemical shrinkage and the equilibrium modulus are needed for the curing induced warpage prediction. Considering various polymeric materials used in microelectronic packages, unique curing setups and procedures are developed for elastomers (extremely low modulus, medium viscosity, room temperature curing), underfill materials (medium modulus, low viscosity, high temperature curing), and epoxy molding compound (EMC: high modulus, high viscosity, high temperature pressure curing), most notably, (1) zero-constraint mold for elastomers; (2) a two-stage curing procedure for underfill materials and (3) an air-cylinder based novel setup for EMC. For the CTE mismatch induced warpage, the temperature dependent CTE and the comprehensive viscoelastic properties are measured. The cured cylindrical specimen with a FBG sensor embedded in the center is further used for viscoelastic property measurements. A uni-axial compressive loading is applied to the specimen to measure the time dependent Young’s modulus. The test is repeated from room temperature to the reflow temperature to capture the time-temperature dependent Young’s modulus. A separate high pressure system is developed for the bulk modulus measurement. The time temperature dependent bulk modulus is measured at the same temperatures as the Young’s modulus. The master curve of the Young’s modulus and bulk modulus of the EMC is created and a single set of the shift factors is determined from the time temperature superposition. The supplementary experiments are conducted to verify the validity of the assumptions associated with the linear viscoelasticity. The measured time-temperature dependent properties are further verified by a shadow moiré and Twyman/Green test.

Neuronal Assembly Detection and Cell Membership Specification by Principal Component Analysis

LOPES-DOS-SANTOS, V. , CONDE-OCAZIONEZ, S. ; NICOLELIS, M. A. L. , RIBEIRO, S. T. , TORT, A. B. L. . Neuronal assembly detection and cell membership specification by principal component analysis. Plos One, v. 6, p. e20996, 2011.

Bioanalytical applications of microfluidic devices

The first part of the thesis describes a new patterning technique--microfluidic contact printing--that combines several of the desirable aspects of microcontact printing and microfluidic patterning and addresses some of their important limitations through the integration of a track-etched polycarbonate (PCTE) membrane. Using this technique, biomolecules (e.g., peptides, polysaccharides, and proteins) were printed in high fidelity on a receptor modified polyacrylamide hydrogel substrate. The patterns obtained can be controlled through modifications of channel design and secondary programming via selective membrane wetting. The protocols support the printing of multiple reagents without registration steps and fast recycle times. The second part describes a non-enzymatic, isothermal method to discriminate single nucleotide polymorphisms (SNPs). SNP discrimination using alkaline dehybridization has long been neglected because the pH range in which thermodynamic discrimination can be done is quite narrow. We found, however, that SNPs can be discriminated by the kinetic differences exhibited in the dehybridization of PM and MM DNA duplexes in an alkaline solution using fluorescence microscopy. We combined this method with multifunctional encoded hydrogel particle array (fabricated by stop-flow lithography) to achieve fast kinetics and high versatility. This approach may serve as an effective alternative to temperature-based method for analyzing unamplified genomic DNA in point-of-care diagnostic.

Hybrid Variable Neighborhood HyperHeuristics for Exam Timetabling Problems

This paper presents our work on analysing the high level search within a graph based hyperheuristic. The graph based hyperheuristic solves the problem at a higher level by searching through permutations of graph heuristics rather than the actual solutions. The heuristic permutations are then used to construct the solutions. Variable Neighborhood Search, Steepest Descent, Iterated Local Search and Tabu Search are compared. An analysis of their performance within the high level search space of heuristics is also carried out. Experimental results on benchmark exam timetabling problems demonstrate the simplicity and efficiency of this hyperheuristic approach. They also indicate that the choice of the high level search methodology is not crucial and the high level search should explore the heuristic search space as widely as possible within a limited searching time. This simple and general graph based hyperheuristic may be applied to a range of timetabling and optimisation problems.

Hybrid Variable Neighborhood HyperHeuristics for Exam Timetabling Problems

This paper presents our work on analysing the high level search within a graph based hyperheuristic. The graph based hyperheuristic solves the problem at a higher level by searching through permutations of graph heuristics rather than the actual solutions. The heuristic permutations are then used to construct the solutions. Variable Neighborhood Search, Steepest Descent, Iterated Local Search and Tabu Search are compared. An analysis of their performance within the high level search space of heuristics is also carried out. Experimental results on benchmark exam timetabling problems demonstrate the simplicity and efficiency of this hyperheuristic approach. They also indicate that the choice of the high level search methodology is not crucial and the high level search should explore the heuristic search space as widely as possible within a limited searching time. This simple and general graph based hyperheuristic may be applied to a range of timetabling and optimisation problems.

Múltiplas antenas como alternativa para aumentar a taxa de extração de chaves secretas em redes veiculares com desvanecimento lento

The communication in vehicular ad hoc networks (VANETs) is commonly divided in two scenarios, namely vehicle-to-vehicle (V2V) and vehicle-to-infrastructure (V2I). Aiming at establishing secure communication against eavesdroppers, recent works have proposed the exchange of secret keys based on the variation in received signal strength (RSS). However, the performance of such scheme depends on the channel variation rate, being more appropriate for scenarios where the channel varies rapidly, as is usually the case with V2V communication. In the communication V2I, the channel commonly undergoes slow fading. In this work we propose the use of multiple antennas in order to artificially generate a fast fading channel so that the extraction of secret keys out of the RSS becomes feasible in a V2I scenario. Numerical analysis shows that the proposed model can outperform, in terms of secret bit extraction rate, a frequency hopping-based method proposed in the literature.

Motion Planning and Controls with Safety and Temporal Constraints

Motion planning, or trajectory planning, commonly refers to a process of converting high-level task specifications into low-level control commands that can be executed on the system of interest. For different applications, the system will be different. It can be an autonomous vehicle, an Unmanned Aerial Vehicle(UAV), a humanoid robot, or an industrial robotic arm. As human machine interaction is essential in many of these systems, safety is fundamental and crucial. Many of the applications also involve performing a task in an optimal manner within a given time constraint. Therefore, in this thesis, we focus on two aspects of the motion planning problem. One is the verification and synthesis of the safe controls for autonomous ground and air vehicles in collision avoidance scenarios. The other part focuses on the high-level planning for the autonomous vehicles with the timed temporal constraints. In the first aspect of our work, we first propose a verification method to prove the safety and robustness of a path planner and the path following controls based on reachable sets. We demonstrate the method on quadrotor and automobile applications. Secondly, we propose a reachable set based collision avoidance algorithm for UAVs. Instead of the traditional approaches of collision avoidance between trajectories, we propose a collision avoidance scheme based on reachable sets and tubes. We then formulate the problem as a convex optimization problem seeking control set design for the aircraft to avoid collision. We apply our approach to collision avoidance scenarios of quadrotors and fixed-wing aircraft. In the second aspect of our work, we address the high level planning problems with timed temporal logic constraints. Firstly, we present an optimization based method for path planning of a mobile robot subject to timed temporal constraints, in a dynamic environment. Temporal logic (TL) can address very complex task specifications such as safety, coverage, motion sequencing etc. We use metric temporal logic (MTL) to encode the task specifications with timing constraints. We then translate the MTL formulae into mixed integer linear constraints and solve the associated optimization problem using a mixed integer linear program solver. We have applied our approach on several case studies in complex dynamical environments subjected to timed temporal specifications. Secondly, we also present a timed automaton based method for planning under the given timed temporal logic specifications. We use metric interval temporal logic (MITL), a member of the MTL family, to represent the task specification, and provide a constructive way to generate a timed automaton and methods to look for accepting runs on the automaton to find an optimal motion (or path) sequence for the robot to complete the task.