Dendritic Cells for Anomaly Detection

Artificial immune systems, more specifically the negative selection algorithm, have previously been applied to intrusion detection. The aim of this research is to develop an intrusion detection system based on a novel concept in immunology, the Danger Theory. Dendritic Cells (DCs) are antigen presenting cells and key to the activation of the human immune system. DCs perform the vital role of combining signals from the host tissue and correlate these signals with proteins known as antigens. In algorithmic terms, individual DCs perform multi-sensor data fusion based on time-windows. The whole population of DCs asynchronously correlates the fused signals with a secondary data stream. The behaviour of human DCs is abstracted to form the DC Algorithm (DCA), which is implemented using an immune inspired framework, libtissue. This system is used to detect context switching for a basic machine learning dataset and to detect outgoing portscans in real-time. Experimental results show a significant difference between an outgoing portscan and normal traffic.

A contribution to semantic description of images and videos: an application of soft biometrics

Humans have a high ability to extract visual data information acquired by sight. Trought a learning process, which starts at birth and continues throughout life, image interpretation becomes almost instinctively. At a glance, one can easily describe a scene with reasonable precision, naming its main components. Usually, this is done by extracting low-level features such as edges, shapes and textures, and associanting them to high level meanings. In this way, a semantic description of the scene is done. An example of this, is the human capacity to recognize and describe other people physical and behavioral characteristics, or biometrics. Soft-biometrics also represents inherent characteristics of human body and behaviour, but do not allow unique person identification. Computer vision area aims to develop methods capable of performing visual interpretation with performance similar to humans. This thesis aims to propose computer vison methods which allows high level information extraction from images in the form of soft biometrics. This problem is approached in two ways, unsupervised and supervised learning methods. The first seeks to group images via an automatic feature extraction learning , using both convolution techniques, evolutionary computing and clustering. In this approach employed images contains faces and people. Second approach employs convolutional neural networks, which have the ability to operate on raw images, learning both feature extraction and classification processes. Here, images are classified according to gender and clothes, divided into upper and lower parts of human body. First approach, when tested with different image datasets obtained an accuracy of approximately 80% for faces and non-faces and 70% for people and non-person. The second tested using images and videos, obtained an accuracy of about 70% for gender, 80% to the upper clothes and 90% to lower clothes. The results of these case studies, show that proposed methods are promising, allowing the realization of automatic high level information image annotation. This opens possibilities for development of applications in diverse areas such as content-based image and video search and automatica video survaillance, reducing human effort in the task of manual annotation and monitoring.

Implementación de un detector de coral utilizando filtros Gabor Wavelets y máquinas de aprendizaje

Este trabajo se enfoca en la implementación de un detector de arrecife de coral de desempeño rápido que se utiliza para un vehículo autónomo submarino (Autonomous Underwater Vehicle, AUV, por sus siglas en inglés). Una detección rápida de la presencia de coral asegura la estabilización del AUV frente al arrecife en el menor tiempo posible, evitando colisiones con el coral. La detección de coral se hace en una imagen que captura la escena que percibe la cámara del AUV. Se realiza una clasificación píxel por píxel entre dos clases: arrecife de coral y el plano de fondo que no es coral. A cada píxel de la imagen se le asigna un vector característico, el mismo que se genera mediante el uso de filtros Gabor Wavelets. Éstos son implementados en C++ y la librería OpenCV. Los vectores característicos son clasificados a través de nueve algoritmos de máquinas de aprendizaje. El desempeño de cada algoritmo se compara mediante la precisión y el tiempo de ejecución. El algoritmo de Árboles de Decisión resultó ser el más rápido y preciso de entre todos los algoritmos. Se creó una base de datos de 621 imágenes de corales de Belice (110 imágenes de entrenamiento y 511 imágenes de prueba).

SEQUENTIAL DECISIONS AND PREDICTIONS IN NATURAL LANGUAGE PROCESSING

Natural language processing has achieved great success in a wide range of ap- plications, producing both commercial language services and open-source language tools. However, most methods take a static or batch approach, assuming that the model has all information it needs and makes a one-time prediction. In this disser- tation, we study dynamic problems where the input comes in a sequence instead of all at once, and the output must be produced while the input is arriving. In these problems, predictions are often made based only on partial information. We see this dynamic setting in many real-time, interactive applications. These problems usually involve a trade-off between the amount of input received (cost) and the quality of the output prediction (accuracy). Therefore, the evaluation considers both objectives (e.g., plotting a Pareto curve). Our goal is to develop a formal understanding of sequential prediction and decision-making problems in natural language processing and to propose efficient solutions. Toward this end, we present meta-algorithms that take an existent batch model and produce a dynamic model to handle sequential inputs and outputs. Webuild our framework upon theories of Markov Decision Process (MDP), which allows learning to trade off competing objectives in a principled way. The main machine learning techniques we use are from imitation learning and reinforcement learning, and we advance current techniques to tackle problems arising in our settings. We evaluate our algorithm on a variety of applications, including dependency parsing, machine translation, and question answering. We show that our approach achieves a better cost-accuracy trade-off than the batch approach and heuristic-based decision- making approaches. We first propose a general framework for cost-sensitive prediction, where dif- ferent parts of the input come at different costs. We formulate a decision-making process that selects pieces of the input sequentially, and the selection is adaptive to each instance. Our approach is evaluated on both standard classification tasks and a structured prediction task (dependency parsing). We show that it achieves similar prediction quality to methods that use all input, while inducing a much smaller cost. Next, we extend the framework to problems where the input is revealed incremen- tally in a fixed order. We study two applications: simultaneous machine translation and quiz bowl (incremental text classification). We discuss challenges in this set- ting and show that adding domain knowledge eases the decision-making problem. A central theme throughout the chapters is an MDP formulation of a challenging problem with sequential input/output and trade-off decisions, accompanied by a learning algorithm that solves the MDP.

A Visual Analytics Approach to Comparing Cohorts of Event Sequences

Sequences of timestamped events are currently being generated across nearly every domain of data analytics, from e-commerce web logging to electronic health records used by doctors and medical researchers. Every day, this data type is reviewed by humans who apply statistical tests, hoping to learn everything they can about how these processes work, why they break, and how they can be improved upon. To further uncover how these processes work the way they do, researchers often compare two groups, or cohorts, of event sequences to find the differences and similarities between outcomes and processes. With temporal event sequence data, this task is complex because of the variety of ways single events and sequences of events can differ between the two cohorts of records: the structure of the event sequences (e.g., event order, co-occurring events, or frequencies of events), the attributes about the events and records (e.g., gender of a patient), or metrics about the timestamps themselves (e.g., duration of an event). Running statistical tests to cover all these cases and determining which results are significant becomes cumbersome. Current visual analytics tools for comparing groups of event sequences emphasize a purely statistical or purely visual approach for comparison. Visual analytics tools leverage humans' ability to easily see patterns and anomalies that they were not expecting, but is limited by uncertainty in findings. Statistical tools emphasize finding significant differences in the data, but often requires researchers have a concrete question and doesn't facilitate more general exploration of the data. Combining visual analytics tools with statistical methods leverages the benefits of both approaches for quicker and easier insight discovery. Integrating statistics into a visualization tool presents many challenges on the frontend (e.g., displaying the results of many different metrics concisely) and in the backend (e.g., scalability challenges with running various metrics on multi-dimensional data at once). I begin by exploring the problem of comparing cohorts of event sequences and understanding the questions that analysts commonly ask in this task. From there, I demonstrate that combining automated statistics with an interactive user interface amplifies the benefits of both types of tools, thereby enabling analysts to conduct quicker and easier data exploration, hypothesis generation, and insight discovery. The direct contributions of this dissertation are: (1) a taxonomy of metrics for comparing cohorts of temporal event sequences, (2) a statistical framework for exploratory data analysis with a method I refer to as high-volume hypothesis testing (HVHT), (3) a family of visualizations and guidelines for interaction techniques that are useful for understanding and parsing the results, and (4) a user study, five long-term case studies, and five short-term case studies which demonstrate the utility and impact of these methods in various domains: four in the medical domain, one in web log analysis, two in education, and one each in social networks, sports analytics, and security. My dissertation contributes an understanding of how cohorts of temporal event sequences are commonly compared and the difficulties associated with applying and parsing the results of these metrics. It also contributes a set of visualizations, algorithms, and design guidelines for balancing automated statistics with user-driven analysis to guide users to significant, distinguishing features between cohorts. This work opens avenues for future research in comparing two or more groups of temporal event sequences, opening traditional machine learning and data mining techniques to user interaction, and extending the principles found in this dissertation to data types beyond temporal event sequences.

Search for Higgs Boson Production Beyond the Standard Model Using the Razor Kinematic Variables in pp Collisions at √s=8 TeV and Optimization of Higgs Boson Identification Using a Quantum Annealer

In the first part of this thesis we search for beyond the Standard Model physics through the search for anomalous production of the Higgs boson using the razor kinematic variables. We search for anomalous Higgs boson production using proton-proton collisions at center of mass energy √s=8 TeV collected by the Compact Muon Solenoid experiment at the Large Hadron Collider corresponding to an integrated luminosity of 19.8 fb^-1.

In the second part we present a novel method for using a quantum annealer to train a classifier to recognize events containing a Higgs boson decaying to two photons. We train that classifier using simulated proton-proton collisions at √s=8 TeV producing either a Standard Model Higgs boson decaying to two photons or a non-resonant Standard Model process that produces a two photon final state.

The production mechanisms of the Higgs boson are precisely predicted by the Standard Model based on its association with the mechanism of electroweak symmetry breaking. We measure the yield of Higgs bosons decaying to two photons in kinematic regions predicted to have very little contribution from a Standard Model Higgs boson and search for an excess of events, which would be evidence of either non-standard production or non-standard properties of the Higgs boson. We divide the events into disjoint categories based on kinematic properties and the presence of additional b-quarks produced in the collisions. In each of these disjoint categories, we use the razor kinematic variables to characterize events with topological configurations incompatible with typical configurations found from standard model production of the Higgs boson.

We observe an excess of events with di-photon invariant mass compatible with the Higgs boson mass and localized in a small region of the razor plane. We observe 5 events with a predicted background of 0.54 ± 0.28, which observation has a p-value of 10^-3 and a local significance of 3.35σ. This background prediction comes from 0.48 predicted non-resonant background events and 0.07 predicted SM higgs boson events. We proceed to investigate the properties of this excess, finding that it provides a very compelling peak in the di-photon invariant mass distribution and is physically separated in the razor plane from predicted background. Using another method of measuring the background and significance of the excess, we find a 2.5σ deviation from the Standard Model hypothesis over a broader range of the razor plane.

In the second part of the thesis we transform the problem of training a classifier to distinguish events with a Higgs boson decaying to two photons from events with other sources of photon pairs into the Hamiltonian of a spin system, the ground state of which is the best classifier. We then use a quantum annealer to find the ground state of this Hamiltonian and train the classifier. We find that we are able to do this successfully in less than 400 annealing runs for a problem of median difficulty at the largest problem size considered. The networks trained in this manner exhibit good classification performance, competitive with the more complicated machine learning techniques, and are highly resistant to overtraining. We also find that the nature of the training gives access to additional solutions that can be used to improve the classification performance by up to 1.2% in some regions.

Functional, clustered, feedforward, and mesoscale brain networks

The brain is a network spanning multiple scales from subcellular to macroscopic. In this thesis I present four projects studying brain networks at different levels of abstraction. The first involves determining a functional connectivity network based on neural spike trains and using a graph theoretical method to cluster groups of neurons into putative cell assemblies. In the second project I model neural networks at a microscopic level. Using diferent clustered wiring schemes, I show that almost identical spatiotemporal activity patterns can be observed, demonstrating that there is a broad neuro-architectural basis to attain structured spatiotemporal dynamics. Remarkably, irrespective of the precise topological mechanism, this behavior can be predicted by examining the spectral properties of the synaptic weight matrix. The third project introduces, via two circuit architectures, a new paradigm for feedforward processing in which inhibitory neurons have the complex and pivotal role in governing information flow in cortical network models. Finally, I analyze axonal projections in sleep deprived mice using data collected as part of the Allen Institute's Mesoscopic Connectivity Atlas. After normalizing for experimental variability, the results indicate there is no single explanatory difference in the mesoscale network between control and sleep deprived mice. Using machine learning techniques, however, animal classification could be done at levels significantly above chance. This reveals that intricate changes in connectivity do occur due to chronic sleep deprivation.

Towards person-centered neuroimaging markers for resilience and vulnerability in Bipolar Disorder

Improved clinical care for Bipolar Disorder (BD) relies on the identification of diagnostic markers that can reliably detect disease-related signals in clinically heterogeneous populations. At the very least, diagnostic markers should be able to differentiate patients with BD from healthy individuals and from individuals at familial risk for BD who either remain well or develop other psychopathology, most commonly Major Depressive Disorder (MDD). These issues are particularly pertinent to the development of translational applications of neuroimaging as they represent challenges for which clinical observation alone is insufficient. We therefore applied pattern classification to task-based functional magnetic resonance imaging (fMRI) data of the n-back working memory task, to test their predictive value in differentiating patients with BD (n=30) from healthy individuals (n=30) and from patients' relatives who were either diagnosed with MDD (n=30) or were free of any personal lifetime history of psychopathology (n=30). Diagnostic stability in these groups was confirmed with 4-year prospective follow-up. Task-based activation patterns from the fMRI data were analyzed with Gaussian Process Classifiers (GPC), a machine learning approach to detecting multivariate patterns in neuroimaging datasets. Consistent significant classification results were only obtained using data from the 3-back versus 0-back contrast. Using contrast, patients with BD were correctly classified compared to unrelated healthy individuals with an accuracy of 83.5%, sensitivity of 84.6% and specificity of 92.3%. Classification accuracy, sensitivity and specificity when comparing patients with BD to their relatives with MDD, were respectively 73.1%, 53.9% and 94.5%. Classification accuracy, sensitivity and specificity when comparing patients with BD to their healthy relatives were respectively 81.8%, 72.7% and 90.9%. We show that significant individual classification can be achieved using whole brain pattern analysis of task-based working memory fMRI data. The high accuracy and specificity achieved by all three classifiers suggest that multivariate pattern recognition analyses can aid clinicians in the clinical care of BD in situations of true clinical uncertainty regarding the diagnosis and prognosis.

Classifying And Predicting Software Security Vulnerabilities based on Reproducibility

Security defects are common in large software systems because of their size and complexity. Although efficient development processes, testing, and maintenance policies are applied to software systems, there are still a large number of vulnerabilities that can remain, despite these measures. Some vulnerabilities stay in a system from one release to the next one because they cannot be easily reproduced through testing. These vulnerabilities endanger the security of the systems. We propose vulnerability classification and prediction frameworks based on vulnerability reproducibility. The frameworks are effective to identify the types and locations of vulnerabilities in the earlier stage, and improve the security of software in the next versions (referred to as releases). We expand an existing concept of software bug classification to vulnerability classification (easily reproducible and hard to reproduce) to develop a classification framework for differentiating between these vulnerabilities based on code fixes and textual reports. We then investigate the potential correlations between the vulnerability categories and the classical software metrics and some other runtime environmental factors of reproducibility to develop a vulnerability prediction framework. The classification and prediction frameworks help developers adopt corresponding mitigation or elimination actions and develop appropriate test cases. Also, the vulnerability prediction framework is of great help for security experts focus their effort on the top-ranked vulnerability-prone files. As a result, the frameworks decrease the number of attacks that exploit security vulnerabilities in the next versions of the software. To build the classification and prediction frameworks, different machine learning techniques (C4.5 Decision Tree, Random Forest, Logistic Regression, and Naive Bayes) are employed. The effectiveness of the proposed frameworks is assessed based on collected software security defects of Mozilla Firefox.

Techniques for distributed theory synthesis in multiagent systems

Data sources are often dispersed geographically in real life applications. Finding a knowledge model may require to join all the data sources and to run a machine learning algorithm on the joint set. We present an alternative based on a Multi Agent System (MAS): an agent mines one data source in order to extract a local theory (knowledge model) and then merges it with the previous MAS theory using a knowledge fusion technique. This way, we obtain a global theory that summarizes the distributed knowledge without spending resources and time in joining data sources. New experiments have been executed including statistical significance analysis. The results show that, as a result of knowledge fusion, the accuracy of initial theories is significantly improved as well as the accuracy of the monolithic solution.

Aplicaciones de los modelos de predicción bio-inspirados en la administración

Las organizaciones y sus entornos son sistemas complejos. Tales sistemas son difíciles de comprender y predecir. Pese a ello, la predicción es una tarea fundamental para la gestión empresarial y para la toma de decisiones que implica siempre un riesgo. Los métodos clásicos de predicción (entre los cuales están: la regresión lineal, la Autoregresive Moving Average y el exponential smoothing) establecen supuestos como la linealidad, la estabilidad para ser matemática y computacionalmente tratables. Por diferentes medios, sin embargo, se han demostrado las limitaciones de tales métodos. Pues bien, en las últimas décadas nuevos métodos de predicción han surgido con el fin de abarcar la complejidad de los sistemas organizacionales y sus entornos, antes que evitarla. Entre ellos, los más promisorios son los métodos de predicción bio-inspirados (ej. redes neuronales, algoritmos genéticos /evolutivos y sistemas inmunes artificiales). Este artículo pretende establecer un estado situacional de las aplicaciones actuales y potenciales de los métodos bio-inspirados de predicción en la administración.

Processamento de imagem digital para o controlo de qualidade do queijo regional de Évora

A utilização generalizada do computador para a automatização das mais diversas tarefas, tem conduzido ao desenvolvimento de aplicações que possibilitam a realização de actividades que até então poderiam não só ser demoradas, como estar sujeitas a erros inerentes à actividade humana. A investigação desenvolvida no âmbito desta tese, tem como objectivo o desenvolvimento de um software e algoritmos que permitam a avaliação e classificação de queijos produzidos na região de Évora, através do processamento de imagens digitais. No decurso desta investigação, foram desenvolvidos algoritmos e metodologias que permitem a identificação dos olhos e dimensões do queijo, a presença de textura na parte exterior do queijo, assim como características relativas à cor do mesmo, permitindo que com base nestes parâmetros possa ser efectuada uma classificação e avaliação do queijo. A aplicação de software, resultou num produto de simples utilização. As fotografias devem respeitar algumas regras simples, sobre as quais se efectuará o processamento e classificação do queijo. ABSTRACT: The widespread use of computers for the automation of repetitive tasks, has resulted in developing applications that allow a range of activities, that until now could not only be time consuming and also subject to errors inherent to human activity, to be performed without or with little human intervention. The research carried out within this thesis, aims to develop a software application and algorithms that enable the assessment and classification of cheeses produced in the region of Évora, by digital images processing. Throughout this research, algorithms and methodologies have been developed that allow the identification of the cheese eyes, the dimensions of the cheese, the presence of texture on the outside of cheese, as well as an analysis of the color, so that, based on these parameters, a classification and evaluation of the cheese can be conducted. The developed software application, is product simple to use, requiring no special computer knowledge. Requires only the acquisition of the photographs following a simple set of rules, based on which it will do the processing and classification of cheese.

Improving understandability in consumer health information search: Uevora @ 2016 fire chis

This paper presents our work at 2016 FIRE CHIS. Given a CHIS query and a document associated with that query, the task is to classify the sentences in the document as relevant to the query or not; and further classify the relevant sentences to be supporting, neutral or opposing to the claim made in the query. In this paper, we present two different approaches to do the classification. With the first approach, we implement two models to satisfy the task. We first implement an information retrieval model to retrieve the sentences that are relevant to the query; and then we use supervised learning method to train a classification model to classify the relevant sentences into support, oppose or neutral. With the second approach, we only use machine learning techniques to learn a model and classify the sentences into four classes (relevant & support, relevant & neutral, relevant & oppose, irrelevant & neutral). Our submission for CHIS uses the first approach.

Experiments on identification of argumentative sentences

The main purpose of this study is to evaluate the best set of features that automatically enables the identification of argumentative sentences from unstructured text. As corpus, we use case laws from the European Court of Human Rights (ECHR). Three kinds of experiments are conducted: Basic Experiments, Multi Feature Experiments and Tree Kernel Experiments. These experiments are basically categorized according to the type of features available in the corpus. The features are extracted from the corpus and Support Vector Machine (SVM) and Random Forest are the used as Machine learning algorithms. We achieved F1 score of 0.705 for identifying the argumentative sentences which is quite promising result and can be used as the basis for a general argument-mining framework.

Normalização automática de descrições de hotéis

As descrições de produtos turísticos na área da hotelaria, aviação, rent-a-car e pacotes de férias baseiam-se sobretudo em descrições textuais em língua natural muito heterogénea com estilos, apresentações e conteúdos muito diferentes entre si. Uma vez que o sector do turismo é bastante dinâmico e que os seus produtos e ofertas estão constantemente em alteração, o tratamento manual de normalização de toda essa informação não é possível. Neste trabalho construiu-se um protótipo que permite a classificação e extracção automática de informação a partir de descrições de produtos de turismo. Inicialmente a informação é classificada quanto ao tipo. Seguidamente são extraídos os elementos relevantes de cada tipo e gerados objectos facilmente computáveis. Sobre os objectos extraídos, o protótipo com recurso a modelos de textos e imagens gera automaticamente descrições normalizadas e orientadas a um determinado mercado. Esta versatilidade permite um novo conjunto de serviços na promoção e venda dos produtos que seria impossível implementar com a informação original. Este protótipo, embora possa ser aplicado a outros domínios, foi avaliado na normalização da descrição de hotéis. As frases descritivas do hotel são classificadas consoante o seu tipo (Local, Serviços e/ou Equipamento) através de um algoritmo de aprendizagem automática que obtém valores médios de cobertura de 96% e precisão de 72%. A cobertura foi considerada a medida mais importante uma vez que a sua maximização permite que não se percam frases para processamentos posteriores. Este trabalho permitiu também a construção e população de uma base de dados de hotéis que possibilita a pesquisa de hotéis pelas suas características. Esta funcionalidade não seria possível utilizando os conteúdos originais. ABSTRACT: The description of tourism products, like hotel, aviation, rent-a-car and holiday packages, is strongly supported on natural language expressions. Due to the extent of tourism offers and considering the high dynamics in the tourism sector, manual data management is not a reliable or scalable solution. Offer descriptions - in the order of thousands - are structured in different ways, possibly comprising different languages, complementing and/or overlap one another. This work aims at creating a prototype for the automatic classification and extraction of relevant knowledge from tourism-related text expressions. Captured knowledge is represented in a normalized/standard format to enable new services based on this information in order to promote and sale tourism products that would be impossible to implement with the raw information. Although it could be applied to other areas, this prototype was evaluated in the normalization of hotel descriptions. Hotels descriptive sentences are classified according their type (Location, Services and/or Equipment) using a machine learning algorithm. The built setting obtained an average recall of 96% and precision of 72%. Recall considered the most important measure of performance since its maximization allows that sentences were not lost in further processes. As a side product a database of hotels was built and populated with search facilities on its characteristics. This ability would not be possible using the original contents.