VLSI Design

This book provides some recent advances in design nanometer VLSI chips. The selected topics try to present some open problems and challenges with important topics ranging from design tools, new post-silicon devices, GPU-based parallel computing, emerging 3D integration, and antenna design. The book consists of two parts, with chapters such as: VLSI design for multi-sensor smart systems on a chip, Three-dimensional integrated circuits design for thousand-core processors, Parallel symbolic analysis of large analog circuits on GPU platforms, Algorithms for CAD tools VLSI design, A multilevel memetic algorithm for large SAT-encoded problems, etc

Algorithmic and Technical Improvements for Next Generation Drug Design Software Tools

[eng] The pharmaceutical industry is actively looking for new ways of boosting the efficiency and effectiveness of their R&D programmes. The extensive use of computational modeling tools in the drug discovery pipeline (DDP) is having a positive impact on research performance, since in silico experiments are usually faster and cheaper that their real counterparts. The lead identification step is a very sensitive point in the DDP. In this context, Virtual high-throughput screening techniques (VHTS) work as a filtering mecha-nism that benefits the following stages by reducing the number of compounds to be tested experimentally. Unfortunately the simplifications applied in the VHTS docking software make them prone generate false positives and negatives. These errors spread across the rest of the DDP stages, and have a negative impact in terms of financial and time costs. In the Electronic and Atomic Protein Modelling group (Barcelona Supercomputing Center, Life Sciences department), we have developed the Protein Energy Landscape Exploration (PELE) software. PELE has demonstrated to be a good alternative to explore the conformational space of proteins and perform ligand-protein docking simulations. In this thesis we discuss how to turn PELE into a faster and more efficient tool by improving its technical and algorithmic features, so that it can be eventually used in VHTS protocols. Besides, we have addressed the difficulties of analyzing extensive data associated with massive simulation production. First, we have rewritten the software using C++ and modern software engineering techniques. As a consequence, our code base is now well organized and tested. PELE has become a piece of software which is easier to modify, understand, and extend. It is also more robust and reliable. The rewriting the code has helped us to overcome some of its previous technical limitations, such as the restrictions on the size of the systems. Also, it has allowed us to extend PELE with new solvent models, force fields, and types of biomolecules. Moreover, the rewriting has make it possible to adapt the code in order to take advantage of new parallel architectures and accelerators obtaining promising speedup results. Second, we have improved the way PELE handles protein flexibility by im-plemented and internal coordinate Normal Mode Analysis (icNMA) method. This method is able to produce more energy favorable perturbations than the current Anisotropic Network Model (ANM) based strategy. This has allowed us to eliminate the unneeded relaxation phase of PELE. As a consequence, the overall computational performance of the sampling is significantly improved (-5-7x). The new internal coordinates-based methodology is able to capture the flexibility of the backbone better than the old method and is in closer agreement to molecular dynamics than the ANM-based method

Projection-Based Clustering through Self-Organization and Swarm Intelligence

It covers aspects of unsupervised machine learning used for knowledge discovery in data science and introduces a data-driven approach to cluster analysis, the Databionic swarm (DBS). DBS consists of the 3D landscape visualization and clustering of data. The 3D landscape enables 3D printing of high-dimensional data structures. The clustering and number of clusters or an absence of cluster structure are verified by the 3D landscape at a glance. DBS is the first swarm-based technique that shows emergent properties while exploiting concepts of swarm intelligence, self-organization and the Nash equilibrium concept from game theory. It results in the elimination of a global objective function and the setting of parameters. By downloading the R package DBS can be applied to data drawn from diverse research fields and used even by non-professionals in the field of data mining

Projection-Based Clustering through Self-Organization and Swarm Intelligence: Combining Cluster Analysis with the Visualization of High-Dimensional Data

Cluster Analysis; Dimensionality Reduction; Swarm Intelligence; Visualization; Unsupervised Machine Learning; Data Science; Knowledge Discovery; 3D Printing; Self-Organization; Emergence; Game Theory; Advanced Analytics; High-Dimensional Data; Multivariate Data; Analysis of Structured Dat

Compression of dynamic polygonal meshes with constant and variable connectivity

This work was supported by the projects 20-02154S and 17-07690S of the Czech Science Foundation and SGS-2019-016 of the Czech Ministry of Education.Polygonal mesh sequences with variable connectivity are incredibly versatile dynamic surface representations as they allow a surface to change topology or details to suddenly appear or disappear. This, however, comes at the cost of large storage size. Current compression methods inefficiently exploit the temporal coherence of general data because the correspondences between two subsequent frames might not be bijective. We study the current state of the art including the special class of mesh sequences for which connectivity is static. We also focus on the state of the art of a related field of dynamic point cloud sequences. Further, we point out parts of the compression pipeline with the possibility of improvement. We present the progress we have already made in designing a temporal model capturing the temporal coherence of the sequence, and point out to directions for a future research

Machine learning methods for pattern analysis and clustering

Ph.DDOCTOR OF PHILOSOPH

Cognitive Task Planning for Smart Industrial Robots

This research work presents a novel Cognitive Task Planning framework for Smart Industrial Robots. The framework makes an industrial mobile manipulator robot Cognitive by applying Semantic Web Technologies. It also introduces a novel Navigation Among Movable Obstacles algorithm for robots navigating and manipulating inside a firm. The objective of Industrie 4.0 is the creation of Smart Factories: modular firms provided with cyber-physical systems able to strong customize products under the condition of highly flexible mass-production. Such systems should real-time communicate and cooperate with each other and with humans via the Internet of Things. They should intelligently adapt to the changing surroundings and autonomously navigate inside a firm while moving obstacles that occlude free paths, even if seen for the first time. At the end, in order to accomplish all these tasks while being efficient, they should learn from their actions and from that of other agents. Most of existing industrial mobile robots navigate along pre-generated trajectories. They follow ectrified wires embedded in the ground or lines painted on th efloor. When there is no expectation of environment changes and cycle times are critical, this planning is functional. When workspaces and tasks change frequently, it is better to plan dynamically: robots should autonomously navigate without relying on modifications of their environments. Consider the human behavior: humans reason about the environment and consider the possibility of moving obstacles if a certain goal cannot be reached or if moving objects may significantly shorten the path to it. This problem is named Navigation Among Movable Obstacles and is mostly known in rescue robotics. This work transposes the problem on an industrial scenario and tries to deal with its two challenges: the high dimensionality of the state space and the treatment of uncertainty. The proposed NAMO algorithm aims to focus exploration on less explored areas. For this reason it extends the Kinodynamic Motion Planning by Interior-Exterior Cell Exploration algorithm. The extension does not impose obstacles avoidance: it assigns an importance to each cell by combining the efforts necessary to reach it and that needed to free it from obstacles. The obtained algorithm is scalable because of its independence from the size of the map and from the number, shape, and pose of obstacles. It does not impose restrictions on actions to be performed: the robot can both push and grasp every object. Currently, the algorithm assumes full world knowledge but the environment is reconfigurable and the algorithm can be easily extended in order to solve NAMO problems in unknown environments. The algorithm handles sensor feedbacks and corrects uncertainties. Usually Robotics separates Motion Planning and Manipulation problems. NAMO forces their combined processing by introducing the need of manipulating multiple objects, often unknown, while navigating. Adopting standard precomputed grasps is not sufficient to deal with the big amount of existing different objects. A Semantic Knowledge Framework is proposed in support of the proposed algorithm by giving robots the ability to learn to manipulate objects and disseminate the information gained during the fulfillment of tasks. The Framework is composed by an Ontology and an Engine. The Ontology extends the IEEE Standard Ontologies for Robotics and Automation and contains descriptions of learned manipulation tasks and detected objects. It is accessible from any robot connected to the Cloud. It can be considered a data store for the efficient and reliable execution of repetitive tasks; and a Web-based repository for the exchange of information between robots and for the speed up of the learning phase. No other manipulation ontology exists respecting the IEEE Standard and, regardless the standard, the proposed ontology differs from the existing ones because of the type of features saved and the efficient way in which they can be accessed: through a super fast Cascade Hashing algorithm. The Engine lets compute and store the manipulation actions when not present in the Ontology. It is based on Reinforcement Learning techniques that avoid massive trainings on large-scale databases and favors human-robot interactions. The overall system is flexible and easily adaptable to different robots operating in different industrial environments. It is characterized by a modular structure where each software block is completely reusable. Every block is based on the open-source Robot Operating System. Not all industrial robot controllers are designed to be ROS-compliant. This thesis presents the method adopted during this research in order to Open Industrial Robot Controllers and create a ROS-Industrial interface for them

Nonlinear Dimensionality Reduction by Manifold Unfolding

Every second, an enormous volume of data is being gathered from various sources and stored in huge data banks. Most of the time, monitoring a data source requires several parallel measurements, which form a high-dimensional sample vector. Due to the curse of dimensionality, applying machine learning methods, that is, studying and analyzing high-dimensional data, could be difficult. The essential task of dimensionality reduction is to faithfully represent a given set of high-dimensional data samples with a few variables. The goal of this thesis is to develop and propose new techniques for handling high-dimensional data, in order to address contemporary demand in machine learning applications. Most prominent nonlinear dimensionality reduction methods do not explicitly provide a way to handle out-of-samples. The starting point of this thesis is a nonlinear technique, called Embedding by Affine Transformations (EAT), which reduces the dimensionality of out-of-sample data as well. In this method, a convex optimization is solved for estimating a transformation between the high-dimensional input space and the low-dimensional embedding space. To the best of our knowledge, EAT is the only distance-preserving method for nonlinear dimensionality reduction capable of handling out-of-samples. The second method that we propose is TesseraMap. This method is a scalable extension of EAT. Conceptually, TesseraMap partitions the underlying manifold of data into a set of tesserae and then unfolds it by constructing a tessellation in a low-dimensional subspace of the embedding space. Crucially, the desired tessellation is obtained through solving a small semidefinite program; therefore, this method can efficiently handle tens of thousands of data points in a short time. The final outcome of this thesis is a novel method in dimensionality reduction called Isometric Patch Alignment (IPA). Intuitively speaking, IPA first considers a number of overlapping flat patches, which cover the underlying manifold of the high-dimensional input data. Then, IPA rearranges the patches and stitches the neighbors together on their overlapping parts. We prove that stitching two neighboring patches aligns them together; thereby, IPA unfolds the underlying manifold of data. Although this method and TesseraMap have similar approaches, IPA is more scalable; it embeds one million data points in only a few minutes. More importantly, unlike EAT and TesseraMap, which unfold the underlying manifold by stretching it, IPA constructs the unfolded manifold through patch alignment. We show this novel approach is advantageous in many cases. In addition, compared to the other well-known dimensionality reduction methods, IPA has several important characteristics; for example, it is noise tolerant, it handles non-uniform samples, and it can embed non-convex manifolds properly. In addition to these three dimensionality reduction methods, we propose a method for subspace clustering called Low-dimensional Localized Clustering (LDLC). In subspace clustering, data is partitioned into clusters, such that the points of each cluster lie close to a low-dimensional subspace. The unique property of LDLC is that it produces localized clusters on the underlying manifold of data. By conducting several experiments, we show this property is an asset in many machine learning tasks. This method can also be used for local dimensionality reduction. Moreover, LDLC is a suitable tool for forming the tesserae in TesseraMap, and also for creating the patches in IPA.1 yea

Development of statistical methodologies applied to anthropometric data oriented towards the ergonomic design of products

Ergonomics is the scientific discipline that studies the interactions between human beings and the elements of a system and presents multiple applications in areas such as clothing and footwear design or both working and household environments. In each of these sectors, knowing the anthropometric dimensions of the current target population is fundamental to ensure that products suit as well as possible most of the users who make up the population. Anthropometry refers to the study of the measurements and dimensions of the human body and it is considered a very important branch of Ergonomics because its considerable influence on the ergonomic design of products. Human body measurements have usually been taken using rules, calipers or measuring tapes. These procedures are simple and cheap to carry out. However, they have one major drawback: the body measurements obtained and consequently, the human shape information, is imprecise and inaccurate. Furthermore, they always require interaction with real subjects, which increases the measure time and data collecting. The development of new three-dimensional (3D) scanning techniques has represented a huge step forward in the way of obtaining anthropometric data. This technology allows 3D images of human shape to be captured and at the same time, generates highly detailed and reproducible anthropometric measurements. The great potential of these new scanning systems for the digitalization of human body has contributed to promoting new anthropometric studies in several countries, such as United Kingdom, Australia, Germany, France or USA, in order to acquire accurate anthropometric data of their current population. In this context, in 2006 the Spanish Ministry of Health commissioned a 3D anthropometric survey of the Spanish female population, following the agreement signed by the Ministry itself with the Spanish associations and companies of manufacturing, distribution, fashion design and knitted sectors. A sample of 10415 Spanish females from 12 to 70 years old, randomly selected from the official Postcode Address File, was measured. The two main objectives of this study, which was conducted by the Biomechanics Institute of Valencia, were the following: on the one hand, to characterize the shape and body dimensions of the current Spanish women population to develop a standard sizing system that could be used by all clothing designers. On the other hand, to promote a healthy image of beauty through the representation of suited mannequins. In order to tackle both objectives, Statistics plays an essential role. Thus, the statistical methodologies presented in this PhD work have been applied to the database obtained from the Spanish anthropometric study. Clothing sizing systems classify the population into homogeneous groups (size groups) based on some key anthropometric dimensions. All members of the same group are similar in body shape and size, so they can wear the same garment. In addition, members of different groups are very different with respect to their body dimensions. An efficient and optimal sizing system aims at accommodating as large a percentage of the population as possible, in the optimum number of size groups that better describes the shape variability of the population. Besides, the garment fit for the accommodated individuals must be as good as possible. A very valuable reference related to sizing systems is the book Sizing in clothing: Developing effective sizing systems for ready-to-wear clothing, by Susan Ashdown. Each clothing size is defined from a person whose body measurements are located toward the central value for each of the dimensions considered in the analysis. The central person, which is considered as the size representative (the size prototype), becomes the basic pattern from which the clothing line in the same size is designed. Clustering is the statistical tool that divides a set of individuals in groups (clusters), in such a way that subjects of the same cluster are more similar to each other than to those in other groups. In addition, clustering defines each group by means of a representative individual. Therefore, it arises in a natural way the idea of using clustering to try to define an efficient sizing system. Specifically, four of the methodologies presented in this PhD thesis aimed at segmenting the population into optimal sizes, use different clustering methods. The first one, called trimowa, has been published in Expert Systems with Applications. It is based on using an especially defined distance to examine differences between women regarding their body measurements. The second and third ones (called biclustAnthropom and TDDclust, respectively) will soon be submitted in the same paper. BiclustAnthropom adapts to the field of Anthropometry a clustering method addressed in the specific case of gene expression data. Moreover, TDDclust uses the concept of statistical depth for grouping according to the most central (deep) observation in each size. As mentioned, current sizing systems are based on using an appropriate set of anthropometric dimensions, so clustering is carried out in the Euclidean space. In the three previous proposals, we have always worked in this way. Instead, in the fourth and last approach, called kmeansProcrustes, a clustering procedure is proposed for grouping taking into account the women shape, which is represented by a set of anatomical markers (landmarks). For this purpose, the statistical shape analysis will be fundamental. This contribution has been submitted for publication. A sizing system is intended to cover the so-called standard population, discarding the individuals with extreme sizes (both large and small). In mathematical language, these individuals can be considered outliers. An outlier is an observation point that is distant from other observations. In our case, a person with extreme anthopometric measurements would be considered as a statistical outlier. Clothing companies usually design garments for the standard sizes so that their market share is optimal. Nevertheless, with their foreign expansion, a lot of brands are spreading their collection and they already have a special sizes section. In last years, Internet shopping has been an alternative for consumers with extreme sizes looking for clothes that follow trends. The custom-made fabrication is other possibility with the advantage of making garments according to the customers' preferences. The four aforementioned methodologies (trimowa, biclustAnthropom, TDDclust and kmeansProcrustes) have been adapted to only accommodate the standard population. Once a particular garment has been designed, the assessing and analysis of fit is performed using one or more fit models. The fit model represents the body dimensions selected by each company to define the proportional relationships needed to achieve the fit the company has determined. The definition of an efficient sizing system relies heavily on the accuracy and representativeness of the fit models regarding the population to which it is addressed. In this PhD work, a statistical approach is proposed to identify representative fit models. It is based on another clustering method originally developed for grouping gene expression data. This method, called hipamAnthropom, has been published in Decision Support Systems. From well-defined fit models and prototypes, representative and accurate mannequins of the population can be made. Unlike clothing design, where representative cases correspond with central individuals, in the design of working and household environments, the variability of human shape is described by extreme individuals, which are those that have the largest or smallest values (or extreme combinations) in the dimensions involved in the study. This is often referred to as the accommodation problem. A very interesting reference in this area is the book entitled Guidelines for Using Anthropometric Data in Product Design, published by The Human Factors and Ergonomics Society. The idea behind this way of proceeding is that if a product fits extreme observations, it will also fit the others (less extreme). To that end, in this PhD thesis we propose two methodological contributions based on the statistical archetypal analysis. An archetype in Statistics is an extreme individual that is obtained as a convex combination of other subjects of the sample. The first of these methodologies has been published in Computers and Industrial Engineering, whereas the second one has been submitted for publication. The outline of this PhD report is as follows: Chapter 1 reviews the state of the art of Ergonomics and Anthropometry and introduces the anthropometric survey of the Spanish female population. Chapter 2 presents the trimowa, biclustAnthropom and hipamAnthropom methodologies. In Chapter 3 the kmeansProcrustes proposal is detailed. The TDDclust methodology is explained in Chapter 4. Chapter 5 presents the two methodologies related to the archetypal analysis. Since all these contributions have been programmed in the statistical software R, Chapter 6 presents the Anthropometry R package, that brings together all the algorithms associated with each approach. In this way, from Chapter 2 to Chapter 6 all the methodologies and results included in this PhD thesis are presented. At last, Chapter 7 provides the most important conclusions