Automatic learning of pre-miRNAs from different species.

Discovery of microRNAs (miRNAs) relies on predictive models for characteristic features from miRNA precursors (pre-miRNAs). The short length of miRNA genes and the lack of pronounced sequence features complicate this task. To accommodate the peculiarities of plant and animal miRNAs systems, tools for both systems have evolved differently. However, these tools are biased towards the species for which they were primarily developed and, consequently, their predictive performance on data sets from other species of the same kingdom might be lower. While these biases are intrinsic to the species, their characterization can lead to computational approaches capable of diminishing their negative effect on the accuracy of pre-miRNAs predictive models. We investigate in this study how 45 predictive models induced for data sets from 45 species, distributed in eight subphyla/classes, perform when applied to a species different from the species used in its induction. Results: Our computational experiments show that the separability of pre-miRNAs and pseudo pre-miRNAs instances is species-dependent and no feature set performs well for all species, even within the same subphylum/class. Mitigating this species dependency, we show that an ensemble of classifiers reduced the classification errors for all 45 species. As the ensemble members were obtained using meaningful, and yet computationally viable feature sets, the ensembles also have a lower computational cost than individual classifiers that rely on energy stability parameters, which are of prohibitive computational cost in large scale applications. Conclusion: In this study, the combination of multiple pre-miRNAs feature sets and multiple learning biases enhanced the predictive accuracy of pre-miRNAs classifiers of 45 species. This is certainly a promising approach to be incorporated in miRNA discovery tools towards more accurate and less species-dependent tools.

A PHENOMENOLOGY OF MIMETIC LEARNING AND MULTIMODAL COGNITION: INTEGRATING EXPERIENTIAL KNOWLEDGE INTO PROGRAMS IN RHETORIC, COMPOSITION, AND TECHNICAL COMMUNICATION

My dissertation emphasizes a cognitive account of multimodality that explicitly integrates experiential knowledge work into the rhetorical pedagogy that informs so many composition and technical communication programs. In these disciplines, multimodality is widely conceived in terms of what Gunther Kress calls “socialsemiotic” modes of communication shaped primarily by culture. In the cognitive and neurolinguistic theories of Vittorio Gallese and George Lakoff, however, multimodality is described as a key characteristic of our bodies’ sensory-motor systems which link perception to action and action to meaning, grounding all communicative acts in knowledge shaped through body-engaged experience. I argue that this “situated” account of cognition – which closely approximates Maurice Merleau-Ponty’s phenomenology of perception, a major framework for my study – has pedagogical precedence in the mimetic pedagogy that informed ancient Sophistic rhetorical training, and I reveal that training’s multimodal dimensions through a phenomenological exegesis of the concept mimesis. Plato’s denigration of the mimetic tradition and his elevation of conceptual contemplation through reason, out of which developed the classic Cartesian separation of mind from body, resulted in a general degradation of experiential knowledge in Western education. But with the recent introduction into college classrooms of digital technologies and multimedia communication tools, renewed emphasis is being placed on the “hands-on” nature of inventive and productive praxis, necessitating a revision of methods of instruction and assessment that have traditionally privileged the acquisition of conceptual over experiential knowledge. The model of multimodality I construct from Merleau-Ponty’s phenomenology, ancient Sophistic rhetorical pedagogy, and current neuroscientific accounts of situated cognition insists on recognizing the significant role knowledges we acquire experientially play in our reading and writing, speaking and listening, discerning and designing practices.

Studies of CMS data access patterns with machine learning techniques

This thesis presents a study of the Grid data access patterns in distributed analysis in the CMS experiment at the LHC accelerator. This study ranges from the deep analysis of the historical patterns of access to the most relevant data types in CMS, to the exploitation of a supervised Machine Learning classification system to set-up a machinery able to eventually predict future data access patterns - i.e. the so-called dataset “popularity” of the CMS datasets on the Grid - with focus on specific data types. All the CMS workflows run on the Worldwide LHC Computing Grid (WCG) computing centers (Tiers), and in particular the distributed analysis systems sustains hundreds of users and applications submitted every day. These applications (or “jobs”) access different data types hosted on disk storage systems at a large set of WLCG Tiers. The detailed study of how this data is accessed, in terms of data types, hosting Tiers, and different time periods, allows to gain precious insight on storage occupancy over time and different access patterns, and ultimately to extract suggested actions based on this information (e.g. targetted disk clean-up and/or data replication). In this sense, the application of Machine Learning techniques allows to learn from past data and to gain predictability potential for the future CMS data access patterns. Chapter 1 provides an introduction to High Energy Physics at the LHC. Chapter 2 describes the CMS Computing Model, with special focus on the data management sector, also discussing the concept of dataset popularity. Chapter 3 describes the study of CMS data access patterns with different depth levels. Chapter 4 offers a brief introduction to basic machine learning concepts and gives an introduction to its application in CMS and discuss the results obtained by using this approach in the context of this thesis.

Learning data-driven models of non-verbal behaviors for building rapport using an intelligent virtual agent

There is a growing societal need to address the increasing prevalence of behavioral health issues, such as obesity, alcohol or drug use, and general lack of treatment adherence for a variety of health problems. The statistics, worldwide and in the USA, are daunting. Excessive alcohol use is the third leading preventable cause of death in the United States (with 79,000 deaths annually), and is responsible for a wide range of health and social problems. On the positive side though, these behavioral health issues (and associated possible diseases) can often be prevented with relatively simple lifestyle changes, such as losing weight with a diet and/or physical exercise, or learning how to reduce alcohol consumption. Medicine has therefore started to move toward finding ways of preventively promoting wellness, rather than solely treating already established illness.^ Evidence-based patient-centered Brief Motivational Interviewing (BMI) interventions have been found particularly effective in helping people find intrinsic motivation to change problem behaviors after short counseling sessions, and to maintain healthy lifestyles over the long-term. Lack of locally available personnel well-trained in BMI, however, often limits access to successful interventions for people in need. To fill this accessibility gap, Computer-Based Interventions (CBIs) have started to emerge. Success of the CBIs, however, critically relies on insuring engagement and retention of CBI users so that they remain motivated to use these systems and come back to use them over the long term as necessary.^ Because of their text-only interfaces, current CBIs can therefore only express limited empathy and rapport, which are the most important factors of health interventions. Fortunately, in the last decade, computer science research has progressed in the design of simulated human characters with anthropomorphic communicative abilities. Virtual characters interact using humans’ innate communication modalities, such as facial expressions, body language, speech, and natural language understanding. By advancing research in Artificial Intelligence (AI), we can improve the ability of artificial agents to help us solve CBI problems.^ To facilitate successful communication and social interaction between artificial agents and human partners, it is essential that aspects of human social behavior, especially empathy and rapport, be considered when designing human-computer interfaces. Hence, the goal of the present dissertation is to provide a computational model of rapport to enhance an artificial agent’s social behavior, and to provide an experimental tool for the psychological theories shaping the model. Parts of this thesis were already published in [LYL+12, AYL12, AL13, ALYR13, LAYR13, YALR13, ALY14].^

Collaborative filtering and deep learning based recommendation system for cold start items

Recommender system is a specific type of intelligent systems, which exploits historical user ratings on items and/or auxiliary information to make recommendations on items to the users. It plays a critical role in a wide range of online shopping, e-commercial services and social networking applications. Collaborative filtering (CF) is the most popular approaches used for recommender systems, but it suffers from complete cold start (CCS) problem where no rating record are available and incomplete cold start (ICS) problem where only a small number of rating records are available for some new items or users in the system. In this paper, we propose two recommendation models to solve the CCS and ICS problems for new items, which are based on a framework of tightly coupled CF approach and deep learning neural network. A specific deep neural network SADE is used to extract the content features of the items. The state of the art CF model, timeSVD++, which models and utilizes temporal dynamics of user preferences and item features, is modified to take the content features into prediction of ratings for cold start items. Extensive experiments on a large Netflix rating dataset of movies are performed, which show that our proposed recommendation models largely outperform the baseline models for rating prediction of cold start items. The two proposed recommendation models are also evaluated and compared on ICS items, and a flexible scheme of model retraining and switching is proposed to deal with the transition of items from cold start to non-cold start status. The experiment results on Netflix movie recommendation show the tight coupling of CF approach and deep learning neural network is feasible and very effective for cold start item recommendation. The design is general and can be applied to many other recommender systems for online shopping and social networking applications. The solution of cold start item problem can largely improve user experience and trust of recommender systems, and effectively promote cold start items.

Collaborative filtering and deep learning based hybrid recommendation for cold start problem

Recommender systems (RS) are used by many social networking applications and online e-commercial services. Collaborative filtering (CF) is one of the most popular approaches used for RS. However traditional CF approach suffers from sparsity and cold start problems. In this paper, we propose a hybrid recommendation model to address the cold start problem, which explores the item content features learned from a deep learning neural network and applies them to the timeSVD++ CF model. Extensive experiments are run on a large Netflix rating dataset for movies. Experiment results show that the proposed hybrid recommendation model provides a good prediction for cold start items, and performs better than four existing recommendation models for rating of non-cold start items.

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.

Socratic flipped classroom : What types of questions and tasks promote learning?

Socratic questioning stresses the importance of questioning for learning. Flipped Classroom pedagogy generates a need for effective questions and tasks in order to promote active learning. This paper describes a project aimed at finding out how different kinds of questions and tasks support students’ learning in a flipped classroom context. In this study, during the flipped courses, both the questions and tasks were distributed together with video recordings. Answers and solutions were presented and discussed in seminars, with approximately 10 participating students in each seminar. Information Systems students from three flipped classroom courses at three different levels were interviewed in focus groups about their perceptions of how different kinds of questions and tasks supported their learning process. The selected courses were organized differently, with various kinds of questions and tasks. Course one included open questions that were answered and presented at the seminar. Students also solved a task and presented the solution to the group. Course two included open questions and a task. Answers and solutions were discussed at the seminars where students also reviewed each other’s answers and solutions. Course three included online single- and multiple choice questions with real-time feedback. Answers were discussed at the seminar, with the focus on any misconceptions. In this paper we categorized the questions in accordance with Wilson (2016) as factual, convergent, divergent, evaluative, or a combination of these. In all, we found that any comprehensible question that initiates a dialogue, preferably with a set of Socratic questions, is perceived as promoting learning. This is why seminars that allow such questions and discussion are effective. We found no differences between the different kinds of Socratic questions. They were seen to promote learning so long as they made students reflect and problematize the questions. To conclude, we found that questions and tasks promote learning when they are answered and solved in a process that is characterized by comprehensibility, variation, repetition and activity.

Healthcare Computer Reasoning Addressing Chronically Ill Societies Using IoT: Deep Learning AI to the Rescue of Home-Based Healthcare

The authors present a proposal to develop intelligent assisted living environments for home based healthcare. These environments unite the chronical patient clinical history sematic representation with the ability of monitoring the living conditions and events recurring to a fully managed Semantic Web of Things (SWoT). Several levels of acquired knowledge and the case based reasoning that is possible by knowledge representation of the health-disease history and acquisition of the scientific evidence will deliver, through various voice based natural interfaces, the adequate support systems for disease auto management but prominently by activating the less differentiated caregiver for any specific need. With these capabilities at hand, home based healthcare providing becomes a viable possibility reducing the institutionalization needs. The resulting integrated healthcare framework will provide significant savings while improving the generality of health and satisfaction indicators.

Analysis of Dyscalculia Evidences through Artificial Intelligence Systems

Dyscalculia is usually perceived of as a specific learning difficulty for mathematics or, more appropriately, arithmetic. Because definitions and diagnoses of dyscalculia are in their infancy and sometimes are contradictory. However, mathematical learning difficulties are certainly not in their infancy and are very prevalent and often devastating in their impact. Co-occurrence of learning disorders appears to be the rule rather than the exception. Co-occurrence is generally assumed to be a consequence of risk factors that are shared between disorders, for example, working memory. However, it should not be assumed that all dyslexics have problems with mathematics, although the percentage may be very high, or that all dyscalculics have problems with reading and writing. Because mathematics is very developmental, any insecurity or uncertainty in early topics will impact on later topics, hence to need to take intervention back to basics. However, it may be worked out in order to decrease its degree of severity. For example, disMAT, an app developed for android may help children to apply mathematical concepts, without much effort, that is turning in itself, a promising tool to dyscalculia treatment. Thus, this work will focus on the development of a Decision Support System to estimate children evidences of dyscalculia, based on data obtained on-the-fly with disMAT. The computational framework is built on top of a Logic Programming approach to Knowledge Representation and Reasoning, grounded on a Case-based approach to computing, that allows for the handling of incomplete, unknown, or even self-contradictory information.

Adaptive and Maladaptive Implications of Reinforcement Learning Processes: Fronto-Striatal Loops and Behavioural Correlates

That humans and animals learn from interaction with the environment is a foundational idea underlying nearly all theories of learning and intelligence. Learning that certain outcomes are associated with specific actions or stimuli (both internal and external), is at the very core of the capacity to adapt behaviour to environmental changes. In the present work, appetitive and aversive reinforcement learning paradigms have been used to investigate the fronto-striatal loops and behavioural correlates of adaptive and maladaptive reinforcement learning processes, aiming to a deeper understanding of how cortical and subcortical substrates interacts between them and with other brain systems to support learning. By combining a large variety of neuroscientific approaches, including behavioral and psychophysiological methods, EEG and neuroimaging techniques, these studies aim at clarifying and advancing the knowledge of the neural bases and computational mechanisms of reinforcement learning, both in normal and neurologically impaired population.

Challenges and Opportunities of Machine Learning for Clinical and Omics Data

Clinical and omics data are a promising field of application for machine learning techniques even though these methods are not yet systematically adopted in healthcare institutions. Despite artificial intelligence has proved successful in terms of prediction of pathologies or identification of their causes, the systematic adoption of these techniques still presents challenging issues due to the peculiarities of the analysed data. The aim of this thesis is to apply machine learning algorithms to both clinical and omics data sets in order to predict a patient's state of health and get better insights on the possible causes of the analysed diseases. In doing so, many of the arising issues when working with medical data will be discussed while possible solutions will be proposed to make machine learning provide feasible results and possibly become an effective and reliable support tool for healthcare systems.

Sperimentazione di Deep Metric Loss per Self-Supervised Information Retrieval Systems su CORD19.

Dopo lo sviluppo dei primi casi di Covid-19 in Cina nell’autunno del 2019, ad inizio 2020 l’intero pianeta è precipitato in una pandemia globale che ha stravolto le nostre vite con conseguenze che non si vivevano dall’influenza spagnola. La grandissima quantità di paper scientifici in continua pubblicazione sul coronavirus e virus ad esso affini ha portato alla creazione di un unico dataset dinamico chiamato CORD19 e distribuito gratuitamente. Poter reperire informazioni utili in questa mole di dati ha ulteriormente acceso i riflettori sugli information retrieval systems, capaci di recuperare in maniera rapida ed efficace informazioni preziose rispetto a una domanda dell'utente detta query. Di particolare rilievo è stata la TREC-COVID Challenge, competizione per lo sviluppo di un sistema di IR addestrato e testato sul dataset CORD19. Il problema principale è dato dal fatto che la grande mole di documenti è totalmente non etichettata e risulta dunque impossibile addestrare modelli di reti neurali direttamente su di essi. Per aggirare il problema abbiamo messo a punto nuove soluzioni self-supervised, a cui abbiamo applicato lo stato dell'arte del deep metric learning e dell'NLP. Il deep metric learning, che sta avendo un enorme successo soprattuto nella computer vision, addestra il modello ad "avvicinare" tra loro immagini simili e "allontanare" immagini differenti. Dato che sia le immagini che il testo vengono rappresentati attraverso vettori di numeri reali (embeddings) si possano utilizzare le stesse tecniche per "avvicinare" tra loro elementi testuali pertinenti (e.g. una query e un paragrafo) e "allontanare" elementi non pertinenti. Abbiamo dunque addestrato un modello SciBERT con varie loss, che ad oggi rappresentano lo stato dell'arte del deep metric learning, in maniera completamente self-supervised direttamente e unicamente sul dataset CORD19, valutandolo poi sul set formale TREC-COVID attraverso un sistema di IR e ottenendo risultati interessanti.

Machine Learning Unsupervised Methods in the Design of an On-board Health Monitoring System for Satellite Applications

The dissertation starts by providing a description of the phenomena related to the increasing importance recently acquired by satellite applications. The spread of such technology comes with implications, such as an increase in maintenance cost, from which derives the interest in developing advanced techniques that favor an augmented autonomy of spacecrafts in health monitoring. Machine learning techniques are widely employed to lay a foundation for effective systems specialized in fault detection by examining telemetry data. Telemetry consists of a considerable amount of information; therefore, the adopted algorithms must be able to handle multivariate data while facing the limitations imposed by on-board hardware features. In the framework of outlier detection, the dissertation addresses the topic of unsupervised machine learning methods. In the unsupervised scenario, lack of prior knowledge of the data behavior is assumed. In the specific, two models are brought to attention, namely Local Outlier Factor and One-Class Support Vector Machines. Their performances are compared in terms of both the achieved prediction accuracy and the equivalent computational cost. Both models are trained and tested upon the same sets of time series data in a variety of settings, finalized at gaining insights on the effect of the increase in dimensionality. The obtained results allow to claim that both models, combined with a proper tuning of their characteristic parameters, successfully comply with the role of outlier detectors in multivariate time series data. Nevertheless, under this specific context, Local Outlier Factor results to be outperforming One-Class SVM, in that it proves to be more stable over a wider range of input parameter values. This property is especially valuable in unsupervised learning since it suggests that the model is keen to adapting to unforeseen patterns.