Balancing Exploration and Exploitation: A New Algorithm for Active Machine Learning

Active machine learning algorithms are used when large numbers of unlabeled examples are available and getting labels for them is costly (e.g. requiring consulting a human expert). Many conventional active learning algorithms focus on refining the decision boundary, at the expense of exploring new regions that the current hypothesis misclassifies. We propose a new active learning algorithm that balances such exploration with refining of the decision boundary by dynamically adjusting the probability to explore at each step. Our experimental results demonstrate improved performance on data sets that require extensive exploration while remaining competitive on data sets that do not. Our algorithm also shows significant tolerance of noise.

Using Machine Learning Classifiers to Assist Healthcare-Related Decisions: Classification of Electronic Patient Records

Surveillance Levels (SLs) are categories for medical patients (used in Brazil) that represent different types of medical recommendations. SLs are defined according to risk factors and the medical and developmental history of patients. Each SL is associated with specific educational and clinical measures. The objective of the present paper was to verify computer-aided, automatic assignment of SLs. The present paper proposes a computer-aided approach for automatic recommendation of SLs. The approach is based on the classification of information from patient electronic records. For this purpose, a software architecture composed of three layers was developed. The architecture is formed by a classification layer that includes a linguistic module and machine learning classification modules. The classification layer allows for the use of different classification methods, including the use of preprocessed, normalized language data drawn from the linguistic module. We report the verification and validation of the software architecture in a Brazilian pediatric healthcare institution. The results indicate that selection of attributes can have a great effect on the performance of the system. Nonetheless, our automatic recommendation of surveillance level can still benefit from improvements in processing procedures when the linguistic module is applied prior to classification. Results from our efforts can be applied to different types of medical systems. The results of systems supported by the framework presented in this paper may be used by healthcare and governmental institutions to improve healthcare services in terms of establishing preventive measures and alerting authorities about the possibility of an epidemic.

Can neuroimaging be used as a support to diagnosis of borderline personality disorder? An approach based on computational neuroanatomy and machine learning

Several recent studies in literature have identified brain morphological alterations associated to Borderline Personality Disorder (BPD) patients. These findings are reported by studies based on voxel-based-morphometry analysis of structural MRI data, comparing mean gray-matter concentration between groups of BPD patients and healthy controls. On the other hand, mean differences between groups are not informative about the discriminative value of neuroimaging data to predict the group of individual subjects. In this paper, we go beyond mean differences analyses, and explore to what extent individual BPD patients can be differentiated from controls (25 subjects in each group), using a combination of automated-morphometric tools for regional cortical thickness/volumetric estimation and Support Vector Machine classifier. The approach included a feature selection step in order to identify the regions containing most discriminative information. The accuracy of this classifier was evaluated using the leave-one-subject-out procedure. The brain regions indicated as containing relevant information to discriminate groups were the orbitofrontal, rostral anterior cingulate, posterior cingulate, middle temporal cortices, among others. These areas, which are distinctively involved in emotional and affect regulation of BPD patients, were the most informative regions to achieve both sensitivity and specificity values of 80% in SVM classification. The findings suggest that this new methodology can add clinical and potential diagnostic value to neuroimaging of psychiatric disorders. (C) 2012 Elsevier Ltd. All rights reserved.

Estimación de la potencia eólica en una zona mediante el apoyo de estaciones meteorológicas de referencia y el empleo de técnicas estadísticas no paramétricas, funcionales y de machine learning: aplicación a las islas Canarias

Programa de doctorado: Tecnología industrial

Predizione dell'effetto delle mutazioni sulla variazione della stabilita' proteica con metodi di "machine-learning".

La tesi consiste nell’implementare un software in grado a predire la variazione della stabilità di una proteina sottoposta ad una mutazione. Il predittore implementato fa utilizzo di tecniche di Machine-Learning ed, in particolare, di SVM. In particolare, riguarda l’analisi delle prestazioni di un predittore, precedentemente implementato, sotto opportune variazioni dei parametri di input e relativamente all’utilizzo di nuova informazione rispetto a quella utilizzata dal predittore basilare.

Machine-learning methods for structure prediction of β-barrel membrane proteins

Different types of proteins exist with diverse functions that are essential for living organisms. An important class of proteins is represented by transmembrane proteins which are specifically designed to be inserted into biological membranes and devised to perform very important functions in the cell such as cell communication and active transport across the membrane. Transmembrane β-barrels (TMBBs) are a sub-class of membrane proteins largely under-represented in structure databases because of the extreme difficulty in experimental structure determination. For this reason, computational tools that are able to predict the structure of TMBBs are needed. In this thesis, two computational problems related to TMBBs were addressed: the detection of TMBBs in large datasets of proteins and the prediction of the topology of TMBB proteins. Firstly, a method for TMBB detection was presented based on a novel neural network framework for variable-length sequence classification. The proposed approach was validated on a non-redundant dataset of proteins. Furthermore, we carried-out genome-wide detection using the entire Escherichia coli proteome. In both experiments, the method significantly outperformed other existing state-of-the-art approaches, reaching very high PPV (92%) and MCC (0.82). Secondly, a method was also introduced for TMBB topology prediction. The proposed approach is based on grammatical modelling and probabilistic discriminative models for sequence data labeling. The method was evaluated using a newly generated dataset of 38 TMBB proteins obtained from high-resolution data in the PDB. Results have shown that the model is able to correctly predict topologies of 25 out of 38 protein chains in the dataset. When tested on previously released datasets, the performances of the proposed approach were measured as comparable or superior to the current state-of-the-art of TMBB topology prediction.

Learning with Kernels on Graphs: DAG-based kernels, data streams and RNA function prediction.

In many application domains data can be naturally represented as graphs. When the application of analytical solutions for a given problem is unfeasible, machine learning techniques could be a viable way to solve the problem. Classical machine learning techniques are defined for data represented in a vectorial form. Recently some of them have been extended to deal directly with structured data. Among those techniques, kernel methods have shown promising results both from the computational complexity and the predictive performance point of view. Kernel methods allow to avoid an explicit mapping in a vectorial form relying on kernel functions, which informally are functions calculating a similarity measure between two entities. However, the definition of good kernels for graphs is a challenging problem because of the difficulty to find a good tradeoff between computational complexity and expressiveness. Another problem we face is learning on data streams, where a potentially unbounded sequence of data is generated by some sources. There are three main contributions in this thesis. The first contribution is the definition of a new family of kernels for graphs based on Directed Acyclic Graphs (DAGs). We analyzed two kernels from this family, achieving state-of-the-art results from both the computational and the classification point of view on real-world datasets. The second contribution consists in making the application of learning algorithms for streams of graphs feasible. Moreover,we defined a principled way for the memory management. The third contribution is the application of machine learning techniques for structured data to non-coding RNA function prediction. In this setting, the secondary structure is thought to carry relevant information. However, existing methods considering the secondary structure have prohibitively high computational complexity. We propose to apply kernel methods on this domain, obtaining state-of-the-art results.

Le tecniche di machine learning per il trattamento della sindrome dell'arto fantasma

Questo elaborato ha come scopo quello di analizzare ed esaminare una patologia oggetto di attiva ricerca scientifica, la sindrome dell’arto fantasma o phantom limb pain: tracciando la storia delle terapie più utilizzate per la sua attenuazione, si è giunti ad analizzarne lo stato dell’arte. Consapevoli che la sindrome dell’arto fantasma costituisce, oltre che un disturbo per chi la prova, uno strumento assai utile per l’analisi delle attività nervose del segmento corporeo superstite (moncone), si è svolta un’attività al centro Inail di Vigorso di Budrio finalizzata a rilevare segnali elettrici provenienti dai monconi superiori dei pazienti che hanno subito un’amputazione. Avendo preliminarmente trattato l’argomento “Machine learning” per raggiungere una maggiore consapevolezza delle potenzialità dell’apprendimento automatico, si sono analizzate la attività neuronali dei pazienti mentre questi muovevano il loro arto fantasma per riuscire a settare nuove tipologie di protesi mobili in base ai segnali ricevuti dal moncone.

Machine Learning applicato al Web Semantico: Statistical Relational Learning vs Tensor Factorization

Obiettivo della tesi è analizzare e testare i principali approcci di Machine Learning applicabili in contesti semantici, partendo da algoritmi di Statistical Relational Learning, quali Relational Probability Trees, Relational Bayesian Classifiers e Relational Dependency Networks, per poi passare ad approcci basati su fattorizzazione tensori, in particolare CANDECOMP/PARAFAC, Tucker e RESCAL.

Predicting CMS datasets popularity with machine learning

In CMS è stato lanciato un progetto di Data Analytics e, all’interno di esso, un’attività specifica pilota che mira a sfruttare tecniche di Machine Learning per predire la popolarità dei dataset di CMS. Si tratta di un’osservabile molto delicata, la cui eventuale predizione premetterebbe a CMS di costruire modelli di data placement più intelligenti, ampie ottimizzazioni nell’uso dello storage a tutti i livelli Tiers, e formerebbe la base per l’introduzione di un solito sistema di data management dinamico e adattivo. Questa tesi descrive il lavoro fatto sfruttando un nuovo prototipo pilota chiamato DCAFPilot, interamente scritto in python, per affrontare questa sfida.

Big data, nosql e machine learning: un'applicazione di prediction e recommendation basata sulle api di Amazon

In questa tesi sono stati introdotti e studiati i Big Data, dando particolare importanza al mondo NoSQL, approfondendo MongoDB, e al mondo del Machine Learning, approfondendo PredictionIO. Successivamente è stata sviluppata un'applicazione attraverso l'utilizzo di tecnologie web, nodejs, node-webkit e le tecnologie approfondite prima. L'applicazione utilizza l'interpolazione polinomiale per predirre il prezzo di un bene salvato nello storico presente su MongoDB. Attraverso PredictionIO, essa analizza il comportamento degli altri utenti consigliando dei prodotti per l'acquisto. Infine è stata effetuata un'analisi dei risultati dell'errore prodotto dall'interpolazione.

Radiation metabolomics. 3. Biomarker discovery in the urine of gamma-irradiated rats using a simplified metabolomics protocol of gas chromatography-mass spectrometry combined with random forests machine learning algorithm

Abstract Radiation metabolomics employing mass spectral technologies represents a plausible means of high-throughput minimally invasive radiation biodosimetry. A simplified metabolomics protocol is described that employs ubiquitous gas chromatography-mass spectrometry and open source software including random forests machine learning algorithm to uncover latent biomarkers of 3 Gy gamma radiation in rats. Urine was collected from six male Wistar rats and six sham-irradiated controls for 7 days, 4 prior to irradiation and 3 after irradiation. Water and food consumption, urine volume, body weight, and sodium, potassium, calcium, chloride, phosphate and urea excretion showed major effects from exposure to gamma radiation. The metabolomics protocol uncovered several urinary metabolites that were significantly up-regulated (glyoxylate, threonate, thymine, uracil, p-cresol) and down-regulated (citrate, 2-oxoglutarate, adipate, pimelate, suberate, azelaate) as a result of radiation exposure. Thymine and uracil were shown to derive largely from thymidine and 2'-deoxyuridine, which are known radiation biomarkers in the mouse. The radiation metabolomic phenotype in rats appeared to derive from oxidative stress and effects on kidney function. Gas chromatography-mass spectrometry is a promising platform on which to develop the field of radiation metabolomics further and to assist in the design of instrumentation for use in detecting biological consequences of environmental radiation release.