Implicit Feature Selection with the Value Difference Metric

Publisher PDF

Context-Aware Personalised Service Delivery

Postprint

A Molecular-scale Programmable Stochastic Process Based On Resonance Energy Transfer Networks: Modeling And Applications

While molecular and cellular processes are often modeled as stochastic processes, such as Brownian motion, chemical reaction networks and gene regulatory networks, there are few attempts to program a molecular-scale process to physically implement stochastic processes. DNA has been used as a substrate for programming molecular interactions, but its applications are restricted to deterministic functions and unfavorable properties such as slow processing, thermal annealing, aqueous solvents and difficult readout limit them to proof-of-concept purposes. To date, whether there exists a molecular process that can be programmed to implement stochastic processes for practical applications remains unknown.

In this dissertation, a fully specified Resonance Energy Transfer (RET) network between chromophores is accurately fabricated via DNA self-assembly, and the exciton dynamics in the RET network physically implement a stochastic process, specifically a continuous-time Markov chain (CTMC), which has a direct mapping to the physical geometry of the chromophore network. Excited by a light source, a RET network generates random samples in the temporal domain in the form of fluorescence photons which can be detected by a photon detector. The intrinsic sampling distribution of a RET network is derived as a phase-type distribution configured by its CTMC model. The conclusion is that the exciton dynamics in a RET network implement a general and important class of stochastic processes that can be directly and accurately programmed and used for practical applications of photonics and optoelectronics. Different approaches to using RET networks exist with vast potential applications. As an entropy source that can directly generate samples from virtually arbitrary distributions, RET networks can benefit applications that rely on generating random samples such as 1) fluorescent taggants and 2) stochastic computing.

By using RET networks between chromophores to implement fluorescent taggants with temporally coded signatures, the taggant design is not constrained by resolvable dyes and has a significantly larger coding capacity than spectrally or lifetime coded fluorescent taggants. Meanwhile, the taggant detection process becomes highly efficient, and the Maximum Likelihood Estimation (MLE) based taggant identification guarantees high accuracy even with only a few hundred detected photons.

Meanwhile, RET-based sampling units (RSU) can be constructed to accelerate probabilistic algorithms for wide applications in machine learning and data analytics. Because probabilistic algorithms often rely on iteratively sampling from parameterized distributions, they can be inefficient in practice on the deterministic hardware traditional computers use, especially for high-dimensional and complex problems. As an efficient universal sampling unit, the proposed RSU can be integrated into a processor / GPU as specialized functional units or organized as a discrete accelerator to bring substantial speedups and power savings.

Building autonomous sensitive artificial listeners (Extended abstract)

This paper describes a substantial effort to build a real-time interactive multimodal dialogue system with a focus on emotional and non-verbal interaction capabilities. The work is motivated by the aim to provide technology with competences in perceiving and producing the emotional and non-verbal behaviours required to sustain a conversational dialogue. We present the Sensitive Artificial Listener (SAL) scenario as a setting which seems particularly suited for the study of emotional and non-verbal behaviour, since it requires only very limited verbal understanding on the part of the machine. This scenario allows us to concentrate on non-verbal capabilities without having to address at the same time the challenges of spoken language understanding, task modeling etc. We first summarise three prototype versions of the SAL scenario, in which the behaviour of the Sensitive Artificial Listener characters was determined by a human operator. These prototypes served the purpose of verifying the effectiveness of the SAL scenario and allowed us to collect data required for building system components for analysing and synthesising the respective behaviours. We then describe the fully autonomous integrated real-time system we created, which combines incremental analysis of user behaviour, dialogue management, and synthesis of speaker and listener behaviour of a SAL character displayed as a virtual agent. We discuss principles that should underlie the evaluation of SAL-type systems. Since the system is designed for modularity and reuse, and since it is publicly available, the SAL system has potential as a joint research tool in the affective computing research community.

Deep Corals, Deep Learning: Moving the Deep Net Towards Real-Time Image Annotation

The mismatch between human capacity and the acquisition of Big Data such as Earth imagery undermines commitments to Convention on Biological Diversity (CBD) and Aichi targets. Artificial intelligence (AI) solutions to Big Data issues are urgently needed as these could prove to be faster, more accurate, and cheaper. Reducing costs of managing protected areas in remote deep waters and in the High Seas is of great importance, and this is a realm where autonomous technology will be transformative.

Clustering-based Query Routing in Cooperative Semi-structured Peer to Peer Networks

We consider the problem of resource selection in clustered Peer-to-Peer Information Retrieval (P2P IR) networks with cooperative peers. The clustered P2P IR framework presents a significant departure from general P2P IR architectures by employing clustering to ensure content coherence between resources at the resource selection layer, without disturbing document allocation. We propose that such a property could be leveraged in resource selection by adapting well-studied and popular inverted lists for centralized document retrieval. Accordingly, we propose the Inverted PeerCluster Index (IPI), an approach that adapts the inverted lists, in a straightforward manner, for resource selection in clustered P2P IR. IPI also encompasses a strikingly simple peer-specific scoring mechanism that exploits the said index for resource selection. Through an extensive empirical analysis on P2P IR testbeds, we establish that IPI competes well with the sophisticated state-of-the-art methods in virtually every parameter of interest for the resource selection task, in the context of clustered P2P IR.

Predictive Analytics and Decision Support for Heart Failure patients

Thesis (Master's)--University of Washington, 2016-08

Learning to Interpret and Generate Instructional Recipes

Thesis (Ph.D.)--University of Washington, 2016-08

Music Learning Networks: Supporting the Music Learning of Adolescents

Thesis (Ph.D.)--University of Washington, 2016-08

Optimization and Applications of Large-Scale Biomedical Event Networks

The overwhelming amount and unprecedented speed of publication in the biomedical domain make it difficult for life science researchers to acquire and maintain a broad view of the field and gather all information that would be relevant for their research. As a response to this problem, the BioNLP (Biomedical Natural Language Processing) community of researches has emerged and strives to assist life science researchers by developing modern natural language processing (NLP), information extraction (IE) and information retrieval (IR) methods that can be applied at large-scale, to scan the whole publicly available biomedical literature and extract and aggregate the information found within, while automatically normalizing the variability of natural language statements. Among different tasks, biomedical event extraction has received much attention within BioNLP community recently. Biomedical event extraction constitutes the identification of biological processes and interactions described in biomedical literature, and their representation as a set of recursive event structures. The 2009–2013 series of BioNLP Shared Tasks on Event Extraction have given raise to a number of event extraction systems, several of which have been applied at a large scale (the full set of PubMed abstracts and PubMed Central Open Access full text articles), leading to creation of massive biomedical event databases, each of which containing millions of events. Sinece top-ranking event extraction systems are based on machine-learning approach and are trained on the narrow-domain, carefully selected Shared Task training data, their performance drops when being faced with the topically highly varied PubMed and PubMed Central documents. Specifically, false-positive predictions by these systems lead to generation of incorrect biomolecular events which are spotted by the end-users. This thesis proposes a novel post-processing approach, utilizing a combination of supervised and unsupervised learning techniques, that can automatically identify and filter out a considerable proportion of incorrect events from large-scale event databases, thus increasing the general credibility of those databases. The second part of this thesis is dedicated to a system we developed for hypothesis generation from large-scale event databases, which is able to discover novel biomolecular interactions among genes/gene-products. We cast the hypothesis generation problem as a supervised network topology prediction, i.e predicting new edges in the network, as well as types and directions for these edges, utilizing a set of features that can be extracted from large biomedical event networks. Routine machine learning evaluation results, as well as manual evaluation results suggest that the problem is indeed learnable. This work won the Best Paper Award in The 5th International Symposium on Languages in Biology and Medicine (LBM 2013).

A survey of intrusion detection system technologies

This paper provides an overview of IDS types and how they work as well as configuration considerations and issues that affect them. Advanced methods of increasing the performance of an IDS are explored such as specification based IDS for protecting Supervisory Control And Data Acquisition (SCADA) and Cloud networks. Also by providing a review of varied studies ranging from issues in configuration and specific problems to custom techniques and cutting edge studies a reference can be provided to others interested in learning about and developing IDS solutions. Intrusion Detection is an area of much required study to provide solutions to satisfy evolving services and networks and systems that support them. This paper aims to be a reference for IDS technologies other researchers and developers interested in the field of intrusion detection.

Structure learning of context-specific graphical models

Abstract The ultimate problem considered in this thesis is modeling a high-dimensional joint distribution over a set of discrete variables. For this purpose, we consider classes of context-specific graphical models and the main emphasis is on learning the structure of such models from data. Traditional graphical models compactly represent a joint distribution through a factorization justi ed by statements of conditional independence which are encoded by a graph structure. Context-speci c independence is a natural generalization of conditional independence that only holds in a certain context, speci ed by the conditioning variables. We introduce context-speci c generalizations of both Bayesian networks and Markov networks by including statements of context-specific independence which can be encoded as a part of the model structures. For the purpose of learning context-speci c model structures from data, we derive score functions, based on results from Bayesian statistics, by which the plausibility of a structure is assessed. To identify high-scoring structures, we construct stochastic and deterministic search algorithms designed to exploit the structural decomposition of our score functions. Numerical experiments on synthetic and real-world data show that the increased exibility of context-specific structures can more accurately emulate the dependence structure among the variables and thereby improve the predictive accuracy of the models.

Modelagem de emoções utilizando redes bayesianas

As emoções são consideradas a regra central de nossas vidas, tendo grande impacto na tomada de decisões, ações, memória, atenção, etc. Sendo assim, existe grande interesse em simulá-las em ambientes computacionais, possibilitando que situações do cotidiano humano possam ser estudadas em ambientes controlados. Embora existam modelos teóricos para o funcionamento de emoções, estes por si só são insuficientes para uma simulação precisa em meios computacionais. Tendo como base um destes modelos, o modelo OCC, essa dissertação propõe a simulação de emoções em ambientes mutiagentes através da criação de uma rede Bayesiana capaz de traduzir estímulos gerados neste ambiente em emoções. A utilização de redes Bayesianas combinadas à estrutura do modelo OCC busca a adição de imprevisibilidade ao modelo, além de fornecê-lo uma estrutura computacional. A aplicação do modelo proposto a um sistema multiagentes proporciona o estudo da influência das emoções sobre as ações e comportamento dos agentes, possibilitando um estudo de comparação entre os resultados obtidos ao se realizar uma simulação multiagentes clássica e uma simulação multiagentes contendo emoções. De forma a validar e avaliar seu funcionamento, é apresentado o estudo da aplicação da rede Bayesiana de emoções sobre um modelo multiagentes exemplo, observando as variações que as emoções provocam sobre o comportamento dos agentes.

Navegação de um robô móvel baseado em um modelo de consciência artificial

This work presents a study about a the Baars-Franklin architecture, which defines a model of computational consciousness, and use it in a mobile robot navigation task. The insertion of mobile robots in dynamic environments carries a high complexity in navigation tasks, in order to deal with the constant environment changes, it is essential that the robot can adapt to this dynamism. The approach utilized in this work is to make the execution of these tasks closer to how human beings react to the same conditions by means of a model of computational consci-ousness. The LIDA architecture (Learning Intelligent Distribution Agent) is a cognitive system that seeks tomodel some of the human cognitive aspects, from low-level perceptions to decision making, as well as attention mechanism and episodic memory. In the present work, a computa-tional implementation of the LIDA architecture was evaluated by means of a case study, aiming to evaluate the capabilities of a cognitive approach to navigation of a mobile robot in dynamic and unknown environments, using experiments both with virtual environments (simulation) and a real robot in a realistic environment. This study concluded that it is possible to obtain benefits by using conscious cognitive models in mobile robot navigation tasks, presenting the positive and negative aspects of this approach.