The majority of real-world networks are dynamic and extremely large (e.g., Internet Traffic, Twitter, Facebook, ...). To understand the structural behavior of nodes in these large dynamic networks, it may be necessary to model the dynamics of behavioral roles representing the main connectivity patterns over time. In this paper, we propose a dynamic behavioral mixed-membership model (DBMM) that captures the roles of nodes in the graph and how they evolve over time. Unlike other node-centric models, our model is scalable for analyzing large dynamic networks. In addition, DBMM is flexible, parameter-free, has no functional form or parameterization, and is interpretable (identifies explainable patterns). The performance results indicate our approach can be applied to very large networks while the experimental results show that our model uncovers interesting patterns underlying the dynamics of these networks.

This paper presents a new algorithm for online linear regression whose efficiency guarantees satisfy the requirements of the KWIK (Knows What It Knows) framework. The algorithm improves on the complexity bounds of the current state-of-the-art procedure in this setting. We explore several applications of this algorithm for learning compact reinforcement-learning representations. We show that KWIK linear regression can be used to learn the reward function of a factored MDP and the probabilities of action outcomes in Stochastic STRIPS and Object Oriented MDPs, none of which have been proven to be efficiently learnable in the RL setting before. We also combine KWIK linear regression with other KWIK learners to learn larger portions of these models, including experiments on learning factored MDP transition and reward functions together.

Message-passing algorithms have emerged as powerful techniques for approximate inference in graphical models. When these algorithms converge, they can be shown to find local (or sometimes even global) optima of variational formulations to the inference problem. But many of the most popular algorithms are not guaranteed to converge. This has lead to recent interest in convergent message-passing algorithms. In this paper, we present a unified view of convergent message-passing algorithms. We present a simple derivation of an abstract algorithm, tree-consistency bound optimization (TCBO) that is provably convergent in both its sum and max product forms. We then show that many of the existing convergent algorithms are instances of our TCBO algorithm, and obtain novel convergent algorithms "for free" by exchanging maximizations and summations in existing algorithms. In particular, we show that Wainwright's non-convergent sum-product algorithm for tree based variational bounds, is actually convergent with the right update order for the case where trees are monotonic chains.

The natural gradient allows for more efficient gradient descent by removing dependencies and biases inherent in a function's parameterization. Several papers present the topic thoroughly and precisely. It remains a very difficult idea to get your head around however. The intent of this note is to provide simple intuition for the natural gradient and its use. We review how an ill conditioned parameter space can undermine learning, introduce the natural gradient by analogy to the more widely understood concept of signal whitening, and present tricks and specific prescriptions for applying the natural gradient to learning problems.

Graph construction is a crucial step in spectral clustering (SC) and graph-based semi-supervised learning (SSL). Spectral methods applied on standard graphs such as full-RBF, $\epsilon$-graphs and $k$-NN graphs can lead to poor performance in the presence of proximal and unbalanced data. This is because spectral methods based on minimizing RatioCut or normalized cut on these graphs tend to put more importance on balancing cluster sizes over reducing cut values. We propose a novel graph construction technique and show that the RatioCut solution on this new graph is able to handle proximal and unbalanced data. Our method is based on adaptively modulating the neighborhood degrees in a $k$-NN graph, which tends to sparsify neighborhoods in low density regions. Our method adapts to data with varying levels of unbalancedness and can be naturally used for small cluster detection. We justify our ideas through limit cut analysis. Unsupervised and semi-supervised experiments on synthetic and real data sets demonstrate the superiority of our method.

Inferring the structure of gene regulatory networks (GRN) from gene expression data has many applications, from the elucidation of complex biological processes to the identification of potential drug targets. It is however a notoriously difficult problem, for which the many existing methods reach limited accuracy. In this paper, we formulate GRN inference as a sparse regression problem and investigate the performance of a popular feature selection method, least angle regression (LARS) combined with stability selection. We introduce a novel, robust and accurate scoring technique for stability selection, which improves the performance of feature selection with LARS. The resulting method, which we call TIGRESS (Trustful Inference of Gene REgulation using Stability Selection), was ranked among the top methods in the DREAM5 gene network reconstruction challenge. We investigate in depth the influence of the various parameters of the method and show that a fine parameter tuning can lead to significant improvements and state-of-the-art performance for GRN inference. TIGRESS reaches state-of-the-art performance on benchmark data. This study confirms the potential of feature selection techniques for GRN inference. Code and data are available on http://cbio.ensmp.fr/~ahaury. Running TIGRESS online is possible on GenePattern: http://www.broadinstitute.org/cancer/software/genepattern/.

In latent Dirichlet allocation (LDA), topics are multinomial distributions over the entire vocabulary. However, the vocabulary usually contains many words that are not relevant in forming the topics. We adopt a variable selection method widely used in statistical modeling as a dimension reduction tool and combine it with LDA. In this variable selection model for LDA (vsLDA), topics are multinomial distributions over a subset of the vocabulary, and by excluding words that are not informative for finding the latent topic structure of the corpus, vsLDA finds topics that are more robust and discriminative. We compare three models, vsLDA, LDA with symmetric priors, and LDA with asymmetric priors, on heldout likelihood, MCMC chain consistency, and document classification. The performance of vsLDA is better than symmetric LDA for likelihood and classification, better than asymmetric LDA for consistency and classification, and about the same in the other comparisons.

In this paper we propose a class of prior distributions on decomposable graphs, allowing for improved modeling flexibility. While existing methods solely penalize the number of edges, the proposed work empowers practitioners to control clustering, level of separation, and other features of the graph. Emphasis is placed on a particular prior distribution which derives its motivation from the class of product partition models; the properties of this prior relative to existing priors is examined through theory and simulation. We then demonstrate the use of graphical models in the field of agriculture, showing how the proposed prior distribution alleviates the inflexibility of previous approaches in properly modeling the interactions between the yield of different crop varieties.

We present a simple and fast geometric method for modeling data by a union of affine subspaces. The method begins by forming a collection of local best-fit affine subspaces, i.e., subspaces approximating the data in local neighborhoods. The correct sizes of the local neighborhoods are determined automatically by the Jones' $\beta_2$ numbers (we prove under certain geometric conditions that our method finds the optimal local neighborhoods). The collection of subspaces is further processed by a greedy selection procedure or a spectral method to generate the final model. We discuss applications to tracking-based motion segmentation and clustering of faces under different illuminating conditions. We give extensive experimental evidence demonstrating the state of the art accuracy and speed of the suggested algorithms on these problems and also on synthetic hybrid linear data as well as the MNIST handwritten digits data; and we demonstrate how to use our algorithms for fast determination of the number of affine subspaces.

Domain knowledge is crucial for effective performance in autonomous control systems. Typically, human effort is required to encode this knowledge into a control algorithm. In this paper, we present an approach to language grounding which automatically interprets text in the context of a complex control application, such as a game, and uses domain knowledge extracted from the text to improve control performance. Both text analysis and control strategies are learned jointly using only a feedback signal inherent to the application. To effectively leverage textual information, our method automatically extracts the text segment most relevant to the current game state, and labels it with a task-centric predicate structure. This labeled text is then used to bias an action selection policy for the game, guiding it towards promising regions of the action space. We encode our model for text analysis and game playing in a multi-layer neural network, representing linguistic decisions via latent variables in the hidden layers, and game action quality via the output layer. Operating within the Monte-Carlo Search framework, we estimate model parameters using feedback from simulated games. We apply our approach to the complex strategy game Civilization II using the official game manual as the text guide. Our results show that a linguistically-informed game-playing agent significantly outperforms its language-unaware counterpart, yielding a 34% absolute improvement and winning over 65% of games when playing against the built-in AI of Civilization.