Layering as Optimization Decomposition: Questions and Answers

Network protocols in layered architectures have historically been obtained on an ad-hoc basis, and much of the recent cross-layer designs are conducted through piecemeal approaches. Network protocols may instead be holistically analyzed and systematically designed as distributed solutions to some global optimization problems in the form of generalized Network Utility Maximization (NUM), providing insight on what they optimize and on the structures of network protocol stacks. In the form of 10 Questions and Answers, this paper presents a short survey of the recent efforts towards a systematic understanding of "layering" as "optimization decomposition". The overall communication network is modeled by a generalized NUM problem, each layer corresponds to a decomposed subproblem, and the interfaces among layers are quantified as functions of the optimization variables coordinating the subproblems. Furthermore, there are many alternative decompositions, each leading to a different layering architecture. Industry adoption of this unifying framework has also started. Here we summarize the current status of horizontal decomposition into distributed computation and vertical decomposition into functional modules such as congestion control, routing, scheduling, random access, power control, and coding. We also discuss under-explored future research directions in this area. More importantly than proposing any particular crosslayer design, this framework is working towards a mathematical foundation of network architectures and the design process of modularization

Probabilistic Graphical Model Representation in Phylogenetics

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (1) reproducibility of an analysis, (2) model development and (3) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and non-specialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis-Hastings or Gibbs sampling of the posterior distribution

Inferring Regulatory Networks by Combining Perturbation Screens and Steady State Gene Expression Profiles

Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction problem. However, such data can be limited in size and/or are expensive to acquire. On the other hand, observational data of the organism in steady state (e.g. wild-type) are more readily available, but their informational content is inadequate for the task at hand. We develop a computational approach to appropriately utilize both data sources for estimating a regulatory network. The proposed approach is based on a three-step algorithm to estimate the underlying directed but cyclic network, that uses as input both perturbation screens and steady state gene expression data. In the first step, the algorithm determines causal orderings of the genes that are consistent with the perturbation data, by combining an exhaustive search method with a fast heuristic that in turn couples a Monte Carlo technique with a fast search algorithm. In the second step, for each obtained causal ordering, a regulatory network is estimated using a penalized likelihood based method, while in the third step a consensus network is constructed from the highest scored ones. Extensive computational experiments show that the algorithm performs well in reconstructing the underlying network and clearly outperforms competing approaches that rely only on a single data source. Further, it is established that the algorithm produces a consistent estimate of the regulatory network.Comment: 24 pages, 4 figures, 6 table

Speeding-up the decision making of a learning agent using an ion trap quantum processor

We report a proof-of-principle experimental demonstration of the quantum speed-up for learning agents utilizing a small-scale quantum information processor based on radiofrequency-driven trapped ions. The decision-making process of a quantum learning agent within the projective simulation paradigm for machine learning is implemented in a system of two qubits. The latter are realized using hyperfine states of two frequency-addressed atomic ions exposed to a static magnetic field gradient. We show that the deliberation time of this quantum learning agent is quadratically improved with respect to comparable classical learning agents. The performance of this quantum-enhanced learning agent highlights the potential of scalable quantum processors taking advantage of machine learning.Comment: 21 pages, 7 figures, 2 tables. Author names now spelled correctly; sections rearranged; changes in the wording of the manuscrip

Towards computationally efficient neural networks with adaptive and dynamic computations

Ces dernières années, l'intelligence artificielle a été considérablement avancée et l'apprentissage en profondeur, où des réseaux de neurones profonds sont utilisés pour tenter d'imiter vaguement le cerveau humain, y a contribué de manière significative. Les réseaux de neurones profonds sont désormais capables d'obtenir un grand succès sur la base d'une grande quantité de données et de ressources de calcul suffisantes. Malgré leur succès, leur capacité à s'adapter rapidement à de nouveaux concepts, tâches et environnements est assez limitée voire inexistante. Dans cette thèse, nous nous intéressons à la façon dont les réseaux de neurones profonds peuvent s'adapter à des circonstances en constante évolution ou totalement nouvelles, de la même manière que l'intelligence humaine, et introduisons en outre des modules architecturaux adaptatifs et dynamiques ou des cadres de méta-apprentissage pour que cela se produise de manière efficace sur le plan informatique. Cette thèse consiste en une série d'études proposant des méthodes pour utiliser des calculs adaptatifs et dynamiques pour aborder les problèmes d'adaptation qui sont étudiés sous différentes perspectives telles que les adaptations au niveau de la tâche, au niveau temporel et au niveau du contexte. Dans le premier article, nous nous concentrons sur l'adaptation rapide des tâches basée sur un cadre de méta-apprentissage. Plus précisément, nous étudions l'incertitude du modèle induite par l'adaptation rapide à une nouvelle tâche avec quelques exemples. Ce problème est atténué en combinant un méta-apprentissage efficace basé sur des gradients avec une inférence variationnelle non paramétrique dans un cadre probabiliste fondé sur des principes. C'est une étape importante vers un méta-apprentissage robuste que nous développons une méthode d'apprentissage bayésienne à quelques exemples pour éviter le surapprentissage au niveau des tâches. Dans le deuxième article, nous essayons d'améliorer les performances de la prédiction de la séquence (c'est-à-dire du futur) en introduisant une prédiction du futur sauteur basée sur la taille du pas adaptatif. C'est une capacité critique pour un agent intelligent d'explorer un environnement qui permet un apprentissage efficace avec une imagination sauteur futur. Nous rendons cela possible en introduisant le modèle hiérarchique d'espace d'état récurrent (HRSSM) qui peut découvrir la structure temporelle latente (par exemple, les sous-séquences) tout en modélisant ses transitions d'état stochastiques de manière hiérarchique. Enfin, dans le dernier article, nous étudions un cadre qui peut capturer le contexte global dans les données d'image de manière adaptative et traiter davantage les données en fonction de ces informations. Nous implémentons ce cadre en extrayant des concepts visuels de haut niveau à travers des modules d'attention et en utilisant un raisonnement basé sur des graphes pour en saisir le contexte global. De plus, des transformations au niveau des caractéristiques sont utilisées pour propager le contexte global à tous les descripteurs locaux de manière adaptative.Over the past few years, artificial intelligence has been greatly advanced, and deep learning, where deep neural networks are used to attempt to loosely emulate the human brain, has significantly contributed to it. Deep neural networks are now able to achieve great success based on a large amount of data and sufficient computational resources. Despite their success, their ability to quickly adapt to new concepts, tasks, and environments is quite limited or even non-existent. In this thesis, we are interested in how deep neural networks can become adaptive to continually changing or totally new circumstances, similarly to human intelligence, and further introduce adaptive and dynamic architectural modules or meta-learning frameworks to make it happen in computationally efficient ways. This thesis consists of a series of studies proposing methods to utilize adaptive and dynamic computations to tackle adaptation problems that are investigated from different perspectives such as task-level, temporal-level, and context-level adaptations. In the first article, we focus on task-level fast adaptation based on a meta-learning framework. More specifically, we investigate the inherent model uncertainty that is induced from quickly adapting to a new task with a few examples. This problem is alleviated by combining the efficient gradient-based meta-learning with nonparametric variational inference in a principled probabilistic framework. It is an important step towards robust meta-learning that we develop a Bayesian few-shot learning method to prevent task-level overfitting. In the second article, we attempt to improve the performance of sequence (i.e. future) prediction by introducing a jumpy future prediction that is based on the adaptive step size. It is a critical ability for an intelligent agent to explore an environment that enables efficient option-learning and jumpy future imagination. We make this possible by introducing the Hierarchical Recurrent State Space Model (HRSSM) that can discover the latent temporal structure (e.g. subsequences) while also modeling its stochastic state transitions hierarchically. Finally, in the last article, we investigate a framework that can capture the global context in image data in an adaptive way and further process the data based on that information. We implement this framework by extracting high-level visual concepts through attention modules and using graph-based reasoning to capture the global context from them. In addition, feature-wise transformations are used to propagate the global context to all local descriptors in an adaptive way