Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Likelihood-based inference of B-cell clonal families

The human immune system depends on a highly diverse collection of antibody-making B cells. B cell receptor sequence diversity is generated by a random recombination process called "rearrangement" forming progenitor B cells, then a Darwinian process of lineage diversification and selection called "affinity maturation." The resulting receptors can be sequenced in high throughput for research and diagnostics. Such a collection of sequences contains a mixture of various lineages, each of which may be quite numerous, or may consist of only a single member. As a step to understanding the process and result of this diversification, one may wish to reconstruct lineage membership, i.e. to cluster sampled sequences according to which came from the same rearrangement events. We call this clustering problem "clonal family inference." In this paper we describe and validate a likelihood-based framework for clonal family inference based on a multi-hidden Markov Model (multi-HMM) framework for B cell receptor sequences. We describe an agglomerative algorithm to find a maximum likelihood clustering, two approximate algorithms with various trade-offs of speed versus accuracy, and a third, fast algorithm for finding specific lineages. We show that under simulation these algorithms greatly improve upon existing clonal family inference methods, and that they also give significantly different clusters than previous methods when applied to two real data sets

Feature Selection For The Fuzzy Artmap Neural Network Using A Hybrid Genetic Algorithm And Tabu Search

Prestasi pengelas rangkaian neural amat bergantung kepada set data yang digunakan dalam process pembelajaran. The performance of Neural-Network (NN)-based classifiers is strongly dependent on the data set used for learning

Predictive User Modeling with Actionable Attributes

Different machine learning techniques have been proposed and used for modeling individual and group user needs, interests and preferences. In the traditional predictive modeling instances are described by observable variables, called attributes. The goal is to learn a model for predicting the target variable for unseen instances. For example, for marketing purposes a company consider profiling a new user based on her observed web browsing behavior, referral keywords or other relevant information. In many real world applications the values of some attributes are not only observable, but can be actively decided by a decision maker. Furthermore, in some of such applications the decision maker is interested not only to generate accurate predictions, but to maximize the probability of the desired outcome. For example, a direct marketing manager can choose which type of a special offer to send to a client (actionable attribute), hoping that the right choice will result in a positive response with a higher probability. We study how to learn to choose the value of an actionable attribute in order to maximize the probability of a desired outcome in predictive modeling. We emphasize that not all instances are equally sensitive to changes in actions. Accurate choice of an action is critical for those instances, which are on the borderline (e.g. users who do not have a strong opinion one way or the other). We formulate three supervised learning approaches for learning to select the value of an actionable attribute at an instance level. We also introduce a focused training procedure which puts more emphasis on the situations where varying the action is the most likely to take the effect. The proof of concept experimental validation on two real-world case studies in web analytics and e-learning domains highlights the potential of the proposed approaches

Linking Policy Research and Practice in 'STIG Systems': Many Obstacles, but Some Ways Forward

This paper reflects on the relevance of systems thinking about the interdependent policy issues bearing on the dynamics of science, technology and innovation in their relationship to economic growth. Considering the approach that characterizes much of the current economics literatures treatment of technology and growth policies, we pose the critical question: what kind of systems paradigm is likely to prove particularly fruitful in that particular problem-domain: Evolutionary, neo-Schumpeterian, and complex system dynamics approaches are conceptually attractive and we analyze their respective virtues while also acknowledging their more serious problematic features. Those become visible quickly when trying connect systems-relevant research with practical policy-making in this field. Not content to have simply identified some significant obstructions in the path toward that goal, the paper also suggests some potentially feasible ways forward.Techonological Change, systems paradigm, STIG systems,

Human-aware space sharing and navigation for an interactive robot

Les méthodes de planification de mouvements robotiques se sont développées à un rythme accéléré ces dernières années. L'accent a principalement été mis sur le fait de rendre les robots plus efficaces, plus sécurisés et plus rapides à réagir à des situations imprévisibles. En conséquence, nous assistons de plus en plus à l'introduction des robots de service dans notre vie quotidienne, en particulier dans les lieux publics tels que les musées, les centres commerciaux et les aéroports. Tandis qu'un robot de service mobile se déplace dans l'environnement humain, il est important de prendre en compte l'effet de son comportement sur les personnes qu'il croise ou avec lesquelles il interagit. Nous ne les voyons pas comme de simples machines, mais comme des agents sociaux et nous nous attendons à ce qu'ils se comportent de manière similaire à l'homme en suivant les normes sociétales comme des règles. Ceci a créé de nouveaux défis et a ouvert de nouvelles directions de recherche pour concevoir des algorithmes de commande de robot, qui fournissent des comportements de robot acceptables, lisibles et proactifs. Cette thèse propose une méthode coopérative basée sur l'optimisation pour la planification de trajectoire et la navigation du robot avec des contraintes sociales intégrées pour assurer des mouvements de robots prudents, conscients de la présence de l'être humain et prévisibles. La trajectoire du robot est ajustée dynamiquement et continuellement pour satisfaire ces contraintes sociales. Pour ce faire, nous traitons la trajectoire du robot comme une bande élastique (une construction mathématique représentant la trajectoire du robot comme une série de positions et une différence de temps entre ces positions) qui peut être déformée (dans l'espace et dans le temps) par le processus d'optimisation pour respecter les contraintes données. De plus, le robot prédit aussi les trajectoires humaines plausibles dans la même zone d'exploitation en traitant les chemins humains aussi comme des bandes élastiques. Ce système nous permet d'optimiser les trajectoires des robots non seulement pour le moment présent, mais aussi pour l'interaction entière qui se produit lorsque les humains et les robots se croisent les uns les autres. Nous avons réalisé un ensemble d'expériences avec des situations interactives humains-robots qui se produisent dans la vie de tous les jours telles que traverser un couloir, passer par une porte et se croiser sur de grands espaces ouverts. La méthode de planification coopérative proposée se compare favorablement à d'autres schémas de planification de la navigation à la pointe de la technique. Nous avons augmenté le comportement de navigation du robot avec un mouvement synchronisé et réactif de sa tête. Cela permet au robot de regarder où il va et occasionnellement de détourner son regard vers les personnes voisines pour montrer que le robot va éviter toute collision possible avec eux comme prévu par le planificateur. À tout moment, le robot pondère les multiples critères selon le contexte social et décide de ce vers quoi il devrait porter le regard. Grâce à une étude utilisateur en ligne, nous avons montré que ce mécanisme de regard complète efficacement le comportement de navigation ce qui améliore la lisibilité des actions du robot. Enfin, nous avons intégré notre schéma de navigation avec un système de supervision plus large qui peut générer conjointement des comportements du robot standard tel que l'approche d'une personne et l'adaptation de la vitesse du robot selon le groupe de personnes que le robot guide dans des scénarios d'aéroport ou de musée.The methods of robotic movement planning have grown at an accelerated pace in recent years. The emphasis has mainly been on making robots more efficient, safer and react faster to unpredictable situations. As a result we are witnessing more and more service robots introduced in our everyday lives, especially in public places such as museums, shopping malls and airports. While a mobile service robot moves in a human environment, it leaves an innate effect on people about its demeanor. We do not see them as mere machines but as social agents and expect them to behave humanly by following societal norms and rules. This has created new challenges and opened new research avenues for designing robot control algorithms that deliver human-acceptable, legible and proactive robot behaviors. This thesis proposes a optimization-based cooperative method for trajectoryplanning and navigation with in-built social constraints for keeping robot motions safe, human-aware and predictable. The robot trajectory is dynamically and continuously adjusted to satisfy these social constraints. To do so, we treat the robot trajectory as an elastic band (a mathematical construct representing the robot path as a series of poses and time-difference between those poses) which can be deformed (both in space and time) by the optimization process to respect given constraints. Moreover, we also predict plausible human trajectories in the same operating area by treating human paths also as elastic bands. This scheme allows us to optimize the robot trajectories not only for the current moment but for the entire interaction that happens when humans and robot cross each other's paths. We carried out a set of experiments with canonical human-robot interactive situations that happen in our everyday lives such as crossing a hallway, passing through a door and intersecting paths on wide open spaces. The proposed cooperative planning method compares favorably against other stat-of-the-art human-aware navigation planning schemes. We have augmented robot navigation behavior with synchronized and responsive movements of the robot head, making the robot look where it is going and occasionally diverting its gaze towards nearby people to acknowledge that robot will avoid any possible collision with them. At any given moment the robot weighs multiple criteria according to the social context and decides where it should turn its gaze. Through an online user study we have shown that such gazing mechanism effectively complements the navigation behavior and it improves legibility of the robot actions. Finally, we have integrated our navigation scheme with a broader supervision system which can jointly generate normative robot behaviors such as approaching a person and adapting the robot speed according to a group of people who the robot guides in airports or museums