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 prediction of disulphide bonding states of cysteine residues in proteins

The goal of this thesis work is to develop a computational method based on machine learning techniques for predicting disulfide-bonding states of cysteine residues in proteins, which is a sub-problem of a bigger and yet unsolved problem of protein structure prediction. Improvement in the prediction of disulfide bonding states of cysteine residues will help in putting a constraint in the three dimensional (3D) space of the respective protein structure, and thus will eventually help in the prediction of 3D structure of proteins. Results of this work will have direct implications in site-directed mutational studies of proteins, proteins engineering and the problem of protein folding. We have used a combination of Artificial Neural Network (ANN) and Hidden Markov Model (HMM), the so-called Hidden Neural Network (HNN) as a machine learning technique to develop our prediction method. By using different global and local features of proteins (specifically profiles, parity of cysteine residues, average cysteine conservation, correlated mutation, sub-cellular localization, and signal peptide) as inputs and considering Eukaryotes and Prokaryotes separately we have reached to a remarkable accuracy of 94% on cysteine basis for both Eukaryotic and Prokaryotic datasets, and an accuracy of 90% and 93% on protein basis for Eukaryotic dataset and Prokaryotic dataset respectively. These accuracies are best so far ever reached by any existing prediction methods, and thus our prediction method has outperformed all the previously developed approaches and therefore is more reliable. Most interesting part of this thesis work is the differences in the prediction performances of Eukaryotes and Prokaryotes at the basic level of input coding when ‘profile’ information was given as input to our prediction method. And one of the reasons for this we discover is the difference in the amino acid composition of the local environment of bonded and free cysteine residues in Eukaryotes and Prokaryotes. Eukaryotic bonded cysteine examples have a ‘symmetric-cysteine-rich’ environment, where as Prokaryotic bonded examples lack it.

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.

Innovative Man Machine Interfaces In Aeronautics

The research activity focused on the study, design and evaluation of innovative human-machine interfaces based on virtual three-dimensional environments. It is based on the brain electrical activities recorded in real time through the electrical impulses emitted by the brain waves of the user. The achieved target is to identify and sort in real time the different brain states and adapt the interface and/or stimuli to the corresponding emotional state of the user. The setup of an experimental facility based on an innovative experimental methodology for “man in the loop" simulation was established. It allowed involving during pilot training in virtually simulated flights, both pilot and flight examiner, in order to compare the subjective evaluations of this latter to the objective measurements of the brain activity of the pilot. This was done recording all the relevant information versus a time-line. Different combinations of emotional intensities obtained, led to an evaluation of the current situational awareness of the user. These results have a great implication in the current training methodology of the pilots, and its use could be extended as a tool that can improve the evaluation of a pilot/crew performance in interacting with the aircraft when performing tasks and procedures, especially in critical situations. This research also resulted in the design of an interface that adapts the control of the machine to the situation awareness of the user. The new concept worked on, aimed at improving the efficiency between a user and the interface, and gaining capacity by reducing the user’s workload and hence improving the system overall safety. This innovative research combining emotions measured through electroencephalography resulted in a human-machine interface that would have three aeronautical related applications: • An evaluation tool during the pilot training; • An input for cockpit environment; • An adaptation tool of the cockpit automation.

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.

Perceived difficulty and time effectiveness in translation: a comparison of machine translation post-editing and translation memory use

Con il presente studio si è inteso analizzare l’impatto dell’utilizzo di una memoria di traduzione (TM) e del post-editing (PE) di un output grezzo sul livello di difficoltà percepita e sul tempo necessario per ottenere un testo finale di alta qualità. L’esperimento ha coinvolto sei studenti, di madrelingua italiana, del corso di Laurea Magistrale in Traduzione Specializzata dell’Università di Bologna (Vicepresidenza di Forlì). I partecipanti sono stati divisi in tre coppie, a ognuna delle quali è stato assegnato un estratto di comunicato stampa in inglese. Per ogni coppia, ad un partecipante è stato chiesto di tradurre il testo in italiano usando la TM all’interno di SDL Trados Studio 2011. All’altro partecipante è stato chiesto di fare il PE completo in italiano dell’output grezzo ottenuto da Google Translate. Nei casi in cui la TM o l’output non contenevano traduzioni (corrette), i partecipanti avrebbero potuto consultare Internet. Ricorrendo ai Think-aloud Protocols (TAPs), è stato chiesto loro di riflettere a voce alta durante lo svolgimento dei compiti. È stato quindi possibile individuare i problemi traduttivi incontrati e i casi in cui la TM e l’output grezzo hanno fornito soluzioni corrette; inoltre, è stato possibile osservare le strategie traduttive impiegate, per poi chiedere ai partecipanti di indicarne la difficoltà attraverso interviste a posteriori. È stato anche misurato il tempo impiegato da ogni partecipante. I dati sulla difficoltà percepita e quelli sul tempo impiegato sono stati messi in relazione con il numero di soluzioni corrette rispettivamente fornito da TM e output grezzo. È stato osservato che usare la TM ha comportato un maggior risparmio di tempo e che, al contrario del PE, ha portato a una riduzione della difficoltà percepita. Il presente studio si propone di aiutare i futuri traduttori professionisti a scegliere strumenti tecnologici che gli permettano di risparmiare tempo e risorse.

Translating food on the Internet: from American TV series dubbed for the Italian audience to subtitles on YouTube.

The aim of this dissertation is to analyze the adaptation of food realia and food-related terms from English into Italian in the world of screen translation. Food has always been at the heart of every human being’s life and is an essential lens of analysis when trying to understand culture. With the awareness of what has been done in the past in American TV series dubbed into Italian and looking at how translations have been changing in the last decade, my thesis demonstrates how strategies are more inclined to an overt approach, which leaves the audiovisual text deeply tied to its source language and culture. The work will also include a practical subtitling exercise of three episodes of the currently most famous YouTube cooking show: Nerdy Nummies by Rosanna Pansino. The fact that the show is published weekly on a YouTube channel gives me the opportunity to comment on the evolution of media in the third millennium and how this implies an improvement as far as the knowledge, the skills and the possibilities for audiovisual translators are concerned.

Applicazione smartphone Social Time Machine

La prima parte del documento contiene una breve introduzione al mondo mobile, cloud computing e social network. La seconda parte si concentra sulla progettazione di un'applicazione per i dispositivi mobili usando le tecnologie Facebook e Parse. Infine, viene implementata un'applicazione Android usando le techiche descritte in precedenza.

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.

Fully Automatic Segmentation of Brain Tumor Images using Support Vector Machine Classiffication in Combination with Hierarchical Conditional Random Field Regularization

Delineating brain tumor boundaries from magnetic resonance images is an essential task for the analysis of brain cancer. We propose a fully automatic method for brain tissue segmentation, which combines Support Vector Machine classification using multispectral intensities and textures with subsequent hierarchical regularization based on Conditional Random Fields. The CRF regularization introduces spatial constraints to the powerful SVM classification, which assumes voxels to be independent from their neighbors. The approach first separates healthy and tumor tissue before both regions are subclassified into cerebrospinal fluid, white matter, gray matter and necrotic, active, edema region respectively in a novel hierarchical way. The hierarchical approach adds robustness and speed by allowing to apply different levels of regularization at different stages. The method is fast and tailored to standard clinical acquisition protocols. It was assessed on 10 multispectral patient datasets with results outperforming previous methods in terms of segmentation detail and computation times.