Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Genetic Programming for Smart Phone Personalisation

Personalisation in smart phones requires adaptability to dynamic context based on user mobility, application usage and sensor inputs. Current personalisation approaches, which rely on static logic that is developed a priori, do not provide sufficient adaptability to dynamic and unexpected context. This paper proposes genetic programming (GP), which can evolve program logic in realtime, as an online learning method to deal with the highly dynamic context in smart phone personalisation. We introduce the concept of collaborative smart phone personalisation through the GP Island Model, in order to exploit shared context among co-located phone users and reduce convergence time. We implement these concepts on real smartphones to demonstrate the capability of personalisation through GP and to explore the benefits of the Island Model. Our empirical evaluations on two example applications confirm that the Island Model can reduce convergence time by up to two-thirds over standalone GP personalisation.Comment: 43 pages, 11 figure

Multi-PBil: an estimation distribution algorithm applied to multimodal optimization problems

The Estimation Distribution Algorithms (EDAs) compose an evolutionary metaheuristic whose main characteristic is the construction of solutions in randomly form, using a distribution of probabilities that evolves during the execution. The Population-Based Incremental Learning Algorithm (PBIL) is a type of EDA where the variables are independent, that is, they do not have significant interactions between themselves. The PBIL considers that the solutions can be represented as vectors of discrete variables, what makes it more adequate for combinatorial optimization problems. This paper presents a method called Multi-PBil that is an extension of PBIL with applications in multimodal problems. The Multi-PBil was developed with the goal to have an efficient and non expensive algorithm of search in multimodal spaces. From PBIL, it was implemented a routine that allows the Multi-PBil to create a probability model to act in the search space. A formula that allows initiating the probability models in regions of the search space next to the searched global points was applied in the process of the probability model initialization rule. The Multi-PBil method was tested and analyzed, presenting some experimental results that highlight its viability and characteristics. It is also shown a comparison of the performance between the Multi-PBil and a traditional Genetic Algorithm using the sharing method.VII Workshop de Agentes y Sistemas Inteligentes (WASI)Red de Universidades con Carreras en Informática (RedUNCI

Optimización del diseño estructural de pavimentos asfálticos para calles y carreteras

gráficos, tablasThe construction of asphalt pavements in streets and highways is an activity that requires optimizing the consumption of significant economic and natural resources. Pavement design optimization meets contradictory objectives according to the availability of resources and users’ needs. This dissertation explores the application of metaheuristics to optimize the design of asphalt pavements using an incremental design based on the prediction of damage and vehicle operating costs (VOC). The costs are proportional to energy and resource consumption and polluting emissions. The evolution of asphalt pavement design and metaheuristic optimization techniques on this topic were reviewed. Four computer programs were developed: (1) UNLEA, a program for the structural analysis of multilayer systems. (2) PSO-UNLEA, a program that uses particle swarm optimization metaheuristic (PSO) for the backcalculation of pavement moduli. (3) UNPAVE, an incremental pavement design program based on the equations of the North American MEPDG and includes the computation of vehicle operating costs based on IRI. (4) PSO-PAVE, a PSO program to search for thicknesses that optimize the design considering construction and vehicle operating costs. The case studies show that the backcalculation and structural design of pavements can be optimized by PSO considering restrictions in the thickness and the selection of materials. Future developments should reduce the computational cost and calibrate the pavement performance and VOC models. (Texto tomado de la fuente)La construcción de pavimentos asfálticos en calles y carreteras es una actividad que requiere la optimización del consumo de cuantiosos recursos económicos y naturales. La optimización del diseño de pavimentos atiende objetivos contradictorios de acuerdo con la disponibilidad de recursos y las necesidades de los usuarios. Este trabajo explora el empleo de metaheurísticas para optimizar el diseño de pavimentos asfálticos empleando el diseño incremental basado en la predicción del deterioro y los costos de operación vehicular (COV). Los costos son proporcionales al consumo energético y de recursos y las emisiones contaminantes. Se revisó la evolución del diseño de pavimentos asfálticos y el desarrollo de técnicas metaheurísticas de optimización en este tema. Se desarrollaron cuatro programas de computador: (1) UNLEA, programa para el análisis estructural de sistemas multicapa. (2) PSO-UNLEA, programa que emplea la metaheurística de optimización con enjambre de partículas (PSO) para el cálculo inverso de módulos de pavimentos. (3) UNPAVE, programa de diseño incremental de pavimentos basado en las ecuaciones de la MEPDG norteamericana, y el cálculo de costos de construcción y operación vehicular basados en el IRI. (4) PSO-PAVE, programa que emplea la PSO en la búsqueda de espesores que permitan optimizar el diseño considerando los costos de construcción y de operación vehicular. Los estudios de caso muestran que el cálculo inverso y el diseño estructural de pavimentos pueden optimizarse mediante PSO considerando restricciones en los espesores y la selección de materiales. Los desarrollos futuros deben enfocarse en reducir el costo computacional y calibrar los modelos de deterioro y COV.DoctoradoDoctor en Ingeniería - Ingeniería AutomáticaDiseño incremental de pavimentosEléctrica, Electrónica, Automatización Y Telecomunicacione

A Survey of Parallel Data Mining

With the fast, continuous increase in the number and size of databases, parallel data mining is a natural and cost-effective approach to tackle the problem of scalability in data mining. Recently there has been a considerable research on parallel data mining. However, most projects focus on the parallelization of a single kind of data mining algorithm/paradigm. This paper surveys parallel data mining with a broader perspective. More precisely, we discuss the parallelization of data mining algorithms of four knowledge discovery paradigms, namely rule induction, instance-based learning, genetic algorithms and neural networks. Using the lessons learned from this discussion, we also derive a set of heuristic principles for designing efficient parallel data mining algorithms

Hysteresis Modeling in Iron-Dominated Magnets Based on a Multi-Layered Narx Neural Network Approach

A full-fledged neural network modeling, based on a Multi-layered Nonlinear Autoregressive Exogenous Neural Network (NARX) architecture, is proposed for quasi-static and dynamic hysteresis loops, one of the most challenging topics for computational magnetism. This modeling approach overcomes drawbacks in attaining better than percent-level accuracy of classical and recent approaches for accelerator magnets, that combine hybridization of standard hysteretic models and neural network architectures. By means of an incremental procedure, different Deep Neural Network Architectures are selected, fine-tuned and tested in order to predict magnetic hysteresis in the context of electromagnets. Tests and results show that the proposed NARX architecture best fits the measured magnetic field behavior of a reference quadrupole at CERN. In particular, the proposed modeling framework leads to a percent error below 0.02% for the magnetic field prediction, thus outperforming state of the art approaches and paving a very promising way for future real time applications

Discovering gated recurrent neural network architectures

Reinforcement Learning agent networks with memory are a key component in solving POMDP tasks. Gated recurrent networks such as those composed of Long Short-Term Memory (LSTM) nodes have recently been used to improve state of the art in many supervised sequential processing tasks such as speech recognition and machine translation. However, scaling them to deep memory tasks in reinforcement learning domain is challenging because of sparse and deceptive reward function. To address this challenge first, a new secondary optimization objective is introduced that maximizes the information (Info-max) stored in the LSTM network. Results indicate that when combined with neuroevolution, Info-max can discover powerful LSTM-based memory solutions that outperform traditional RNNs. Next, for the supervised learning tasks, neuroevolution techniques are employed to design new LSTM architectures. Such architectural variations include discovering new pathways between the recurrent layers as well as designing new gated recurrent nodes. This dissertation proposes evolution of a tree-based encoding of the gated memory nodes, and shows that it makes it possible to explore new variations more effectively than other methods. The method discovers nodes with multiple recurrent paths and multiple memory cells, which lead to significant improvement in the standard language modeling benchmark task. The dissertation also shows how the search process can be speeded up by training an LSTM network to estimate performance of candidate structures, and by encouraging exploration of novel solutions. Thus, evolutionary design of complex neural network structures promises to improve performance of deep learning architectures beyond human ability to do so.Computer Science

Symbol Emergence in Robotics: A Survey

Humans can learn the use of language through physical interaction with their environment and semiotic communication with other people. It is very important to obtain a computational understanding of how humans can form a symbol system and obtain semiotic skills through their autonomous mental development. Recently, many studies have been conducted on the construction of robotic systems and machine-learning methods that can learn the use of language through embodied multimodal interaction with their environment and other systems. Understanding human social interactions and developing a robot that can smoothly communicate with human users in the long term, requires an understanding of the dynamics of symbol systems and is crucially important. The embodied cognition and social interaction of participants gradually change a symbol system in a constructive manner. In this paper, we introduce a field of research called symbol emergence in robotics (SER). SER is a constructive approach towards an emergent symbol system. The emergent symbol system is socially self-organized through both semiotic communications and physical interactions with autonomous cognitive developmental agents, i.e., humans and developmental robots. Specifically, we describe some state-of-art research topics concerning SER, e.g., multimodal categorization, word discovery, and a double articulation analysis, that enable a robot to obtain words and their embodied meanings from raw sensory--motor information, including visual information, haptic information, auditory information, and acoustic speech signals, in a totally unsupervised manner. Finally, we suggest future directions of research in SER.Comment: submitted to Advanced Robotic