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.

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.

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.

Reduction of Transient Particulate Matter Spikes with Decision Tree Based Control

Decision trees have been proposed as a basis for modifying table based injection to reduce transient particulate spikes during the turbocharger lag period. It has been shown that decision trees can detect particulate spikes in real time. In well calibrated electronically controlled diesel engines these spikes are narrow and are encompassed by a wider NOx spike. Decision trees have been shown to pinpoint the exact location of measured opacity spikes in real time thus enabling targeted PM reduction with near zero NOx penalty. A calibrated dimensional model has been used to demonstrate the possible reduction of particulate matter with targeted injection pressure pulses. Post injection strategy optimized for near stoichiometric combustion has been shown to provide additional benefits. Empirical models have been used to calculate emission tradeoffs over the entire FTP cycle. An empirical model based transient calibration has been used to demonstrate that such targeted transient modifiers are more beneficial at lower engine-out NOx levels.

A Decision-Tree-Based Approach to Smoke Spike Detection in a Heavy-Duty Diesel Engine

Smoke spikes occurring during transient engine operation have detrimental health effects and increase fuel consumption by requiring more frequent regeneration of the diesel particulate filter. This paper proposes a decision tree approach to real-time detection of smoke spikes for control and on-board diagnostics purposes. A contemporary, electronically controlled heavy-duty diesel engine was used to investigate the deficiencies of smoke control based on the fuel-to-oxygen-ratio limit. With the aid of transient and steady state data analysis and empirical as well as dimensional modeling, it was shown that the fuel-to-oxygen ratio was not estimated correctly during the turbocharger lag period. This inaccuracy was attributed to the large manifold pressure ratios and low exhaust gas recirculation flows recorded during the turbocharger lag period, which meant that engine control module correlations for the exhaust gas recirculation flow and the volumetric efficiency had to be extrapolated. The engine control module correlations were based on steady state data and it was shown that, unless the turbocharger efficiency is artificially reduced, the large manifold pressure ratios observed during the turbocharger lag period cannot be achieved at steady state. Additionally, the cylinder-to-cylinder variation during this period were shown to be sufficiently significant to make the average fuel-to-oxygen ratio a poor predictor of the transient smoke emissions. The steady state data also showed higher smoke emissions with higher exhaust gas recirculation fractions at constant fuel-to-oxygen-ratio levels. This suggests that, even if the fuel-to-oxygen ratios were to be estimated accurately for each cylinder, they would still be ineffective as smoke limiters. A decision tree trained on snap throttle data and pruned with engineering knowledge was able to use the inaccurate engine control module estimates of the fuel-to-oxygen ratio together with information on the engine control module estimate of the exhaust gas recirculation fraction, the engine speed, and the manifold pressure ratio to predict 94% of all spikes occurring over the Federal Test Procedure cycle. The advantages of this non-parametric approach over other commonly used parametric empirical methods such as regression were described. An application of accurate smoke spike detection in which the injection pressure is increased at points with a high opacity to reduce the cumulative particulate matter emissions substantially with a minimum increase in the cumulative nitrogrn oxide emissions was illustrated with dimensional and empirical modeling.

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.

Combining Wireless Sensor Networks and Machine Learning for Flash Flood Nowcasting

This paper addresses an investigation with machine learning (ML) classification techniques to assist in the problem of flash flood now casting. We have been attempting to build a Wireless Sensor Network (WSN) to collect measurements from a river located in an urban area. The machine learning classification methods were investigated with the aim of allowing flash flood now casting, which in turn allows the WSN to give alerts to the local population. We have evaluated several types of ML taking account of the different now casting stages (i.e. Number of future time steps to forecast). We have also evaluated different data representation to be used as input of the ML techniques. The results show that different data representation can lead to results significantly better for different stages of now casting.

THE ALCOHOL TREATMENT PROFILE SYSTEM: ITS DEVELOPMENT AND AN EVALUATION OF ITS CAPABILITIES

The development of the Alcohol Treatment Profile System (ATPS) was described and an evaluation of its perceived value by various States was undertaken, The ATPS is a treatment needs assessment tool based on the unification of several large national epidemiologic and treatment data sets. It was developed by the National Institute on Alcohol Abuse and Alcoholism (NIAAA) and responsibility for its creation was given to the NIAAA's Alcohol Epidemiologic Data System (AEDS). The ATPS merges county-level measures of alcohol problem prevalence (the specially constructed AEDS Alcohol Problem Indicators), indicating "need" for treatment, and treatment utilization measures (the National Drug and Alcohol Treatment Utilization Survey), indicating treatment "demand." The capabilities of the ATPS in the unique planning and policy-making settings of several States were evaluated.^

Detection and Tracking of Traffic Signs Using a Recursive Bayesian Decision Framework

In this paper we propose a new method for the automatic detection and tracking of road traffic signs using an on-board single camera. This method aims to increase the reliability of the detections such that it can boost the performance of any traffic sign recognition scheme. The proposed approach exploits a combination of different features, such as color, appearance, and tracking information. This information is introduced into a recursive Bayesian decision framework, in which prior probabilities are dynamically adapted to tracking results. This decision scheme obtains a number of candidate regions in the image, according to their HS (Hue-Saturation). Finally, a Kalman filter with an adaptive noise tuning provides the required time and spatial coherence to the estimates. Results have shown that the proposed method achieves high detection rates in challenging scenarios, including illumination changes, rapid motion and significant perspective distortion

Hybrid Approach Combining Machine Learning and a Rule-Based Expert System for Text Categorization

This paper discusses a novel hybrid approach for text categorization that combines a machine learning algorithm, which provides a base model trained with a labeled corpus, with a rule-based expert system, which is used to improve the results provided by the previous classifier, by filtering false positives and dealing with false negatives. The main advantage is that the system can be easily fine-tuned by adding specific rules for those noisy or conflicting categories that have not been successfully trained. We also describe an implementation based on k-Nearest Neighbor and a simple rule language to express lists of positive, negative and relevant (multiword) terms appearing in the input text. The system is evaluated in several scenarios, including the popular Reuters-21578 news corpus for comparison to other approaches, and categorization using IPTC metadata, EUROVOC thesaurus and others. Results show that this approach achieves a precision that is comparable to top ranked methods, with the added value that it does not require a demanding human expert workload to train

Microarray analysis of autoimmune diseases by machine learning procedures

—Microarray-based global gene expression profiling, with the use of sophisticated statistical algorithms is providing new insights into the pathogenesis of autoimmune diseases. We have applied a novel statistical technique for gene selection based on machine learning approaches to analyze microarray expression data gathered from patients with systemic lupus erythematosus (SLE) and primary antiphospholipid syndrome (PAPS), two autoimmune diseases of unknown genetic origin that share many common features. The methodology included a combination of three data discretization policies, a consensus gene selection method, and a multivariate correlation measurement. A set of 150 genes was found to discriminate SLE and PAPS patients from healthy individuals. Statistical validations demonstrate the relevance of this gene set from an univariate and multivariate perspective. Moreover, functional characterization of these genes identified an interferon-regulated gene signature, consistent with previous reports. It also revealed the existence of other regulatory pathways, including those regulated by PTEN, TNF, and BCL-2, which are altered in SLE and PAPS. Remarkably, a significant number of these genes carry E2F binding motifs in their promoters, projecting a role for E2F in the regulation of autoimmunity.

Statistical Machine Learning for Automatic Assessment of Physical Activity Intensity Using Multi-axial Accelerometry and Heart Rate

This work explores the automatic recognition of physical activity intensity patterns from multi-axial accelerometry and heart rate signals. Data collection was carried out in free-living conditions and in three controlled gymnasium circuits, for a total amount of 179.80 h of data divided into: sedentary situations (65.5%), light-to-moderate activity (17.6%) and vigorous exercise (16.9%). The proposed machine learning algorithms comprise the following steps: time-domain feature definition, standardization and PCA projection, unsupervised clustering (by k-means and GMM) and a HMM to account for long-term temporal trends. Performance was evaluated by 30 runs of a 10-fold cross-validation. Both k-means and GMM-based approaches yielded high overall accuracy (86.97% and 85.03%, respectively) and, given the imbalance of the dataset, meritorious F-measures (up to 77.88%) for non-sedentary cases. Classification errors tended to be concentrated around transients, what constrains their practical impact. Hence, we consider our proposal to be suitable for 24 h-based monitoring of physical activity in ambulatory scenarios and a first step towards intensity-specific energy expenditure estimators