A fundamental aspect of biological information processing is the ubiquity of sequence-function relationships -- functions that map the sequence of DNA, RNA, or protein to a biochemically relevant activity. Most sequence-function relationships in biology are quantitative, but only recently have experimental techniques for effectively measuring these relationships been developed. The advent of such "massively parallel" experiments presents an exciting opportunity for the concepts and methods of statistical physics to inform the study of biological systems. After reviewing these recent experimental advances, we focus on the problem of how to infer parametric models of sequence-function relationships from the data produced by these experiments. Specifically, we retrace and extend recent theoretical work showing that inference based on mutual information, not the standard likelihood-based approach, is often necessary for accurately learning the parameters of these models. Closely connected with this result is the emergence of "diffeomorphic modes" -- directions in parameter space that are far less constrained by data than likelihood-based inference would suggest. Analogous to Goldstone modes in physics, diffeomorphic modes arise from an arbitrarily broken symmetry of the inference problem. An analytically tractable model of a massively parallel experiment is then described, providing an explicit demonstration of these fundamental aspects of statistical inference. This paper concludes with an outlook on the theoretical and computational challenges currently facing studies of quantitative sequence-function relationships.

As a model for an on-line classification setting we consider a stochastic process $(X_{-n},Y_{-n})_{n}$, the present time-point being denoted by 0, with observables $ \ldots,X_{-n},X_{-n+1},\ldots, X_{-1}, X_0$ from which the pattern $Y_0$ is to be inferred. So in this classification setting, in addition to the present observation $X_0$ a number $l$ of preceding observations may be used for classification, thus taking a possible dependence structure into account as it occurs e.g. in an ongoing classification of handwritten characters. We treat the question how the performance of classifiers is improved by using such additional information. For our analysis, a hidden Markov model is used. Letting $R_l$ denote the minimal risk of misclassification using $l$ preceding observations we show that the difference $\sup_k |R_l - R_{l+k}|$ decreases exponentially fast as $l$ increases. This suggests that a small $l$ might already lead to a noticeable improvement. To follow this point we look at the use of past observations for kernel classification rules. Our practical findings in simulated hidden Markov models and in the classification of handwritten characters indicate that using $l=1$, i.e. just the last preceding observation in addition to $X_0$, can lead to a substantial reduction of the risk of misclassification. So, in the presence of stochastic dependencies, we advocate to use $ X_{-1},X_0$ for finding the pattern $Y_0$ instead of only $X_0$ as one would in the independent situation.

Transferring knowledge across a sequence of related tasks is an important challenge in reinforcement learning (RL). Despite much encouraging empirical evidence, there has been little theoretical analysis. In this paper, we study a class of lifelong RL problems: the agent solves a sequence of tasks modeled as finite Markov decision processes (MDPs), each of which is from a finite set of MDPs with the same state/action sets and different transition/reward functions. Motivated by the need for cross-task exploration in lifelong learning, we formulate a novel online coupon-collector problem and give an optimal algorithm. This allows us to develop a new lifelong RL algorithm, whose overall sample complexity in a sequence of tasks is much smaller than single-task learning, even if the sequence of tasks is generated by an adversary. Benefits of the algorithm are demonstrated in simulated problems, including a recently introduced human-robot interaction problem.

Classification and clustering are both important topics in statistical learning. A natural question herein is whether predefined classes are really different from one another, or whether clusters are really there. Specifically, we may be interested in knowing whether the two classes defined by some class labels (when they are provided), or the two clusters tagged by a clustering algorithm (where class labels are not provided), are from the same underlying distribution. Although both are challenging questions for the high-dimensional, low-sample size data, there has been some recent development for both. However, when it is costly to manually place labels on observations, it is often that only a small portion of the class labels is available. In this article, we propose a significance analysis approach for such type of data, namely partially labeled data. Our method makes use of the whole data and tries to test the class difference as if all the labels were observed. Compared to a testing method that ignores the label information, our method provides a greater power, meanwhile, maintaining the size, illustrated by a comprehensive simulation study. Theoretical properties of the proposed method are studied with emphasis on the high-dimensional, low-sample size setting. Our simulated examples help to understand when and how the information extracted from the labeled data can be effective. A real data example further illustrates the usefulness of the proposed method.

Protein-protein interaction (PPI) prediction is an important problem in machine learning and computational biology. However, there is no data set for training or evaluation purposes, where all the instances are accurately labeled. Instead, what is available are instances of positive class (with possibly noisy labels) and no instances of negative class. The non-availability of negative class data is typically handled with the observation that randomly chosen protein-pairs have a nearly 100% chance of being negative class, as only 1 in 1,500 protein pairs expected is expected to be an interacting pair. In this paper, we focused on the problem that non-availability of accurately labeled testing data sets in the domain of protein-protein interaction (PPI) prediction may lead to biased evaluation results. We first showed that not acknowledging the inherent skew in the interactome (i.e. rare occurrence of positive instances) leads to an over-estimated accuracy of the predictor. Then we show that, with the belief that positive interactions are a rare category, sampling random pairs of proteins excluding known interacting proteins set as the negative testing data set could lead to an under-estimated evaluation result. We formalized those two problems to validate the above claim, and based on the formalization, we proposed a balancing method to cancel out the over-estimation with under-estimation. Finally, our experiments validated the theoretical aspects and showed that this balancing evaluation could evaluate the exact performance without availability of golden standard data sets.

This paper presents a case study of a recommender system that can be used to save energy in smart homes without lowering the comfort of the inhabitants. We present an algorithm that uses consumer behavior data only and uses machine learning to suggest actions for inhabitants to reduce the energy consumption of their homes. The system mines for frequent and periodic patterns in the event data provided by the Digitalstrom home automation system. These patterns are converted into association rules, prioritized and compared with the current behavior of the inhabitants. If the system detects an opportunities to save energy without decreasing the comfort level it sends a recommendation to the residents.

Motivated by large-scale Collaborative-Filtering applications, we present a Non-Commuting Latent Factor (NCLF) tensor-completion approach for modeling three-way arrays, which is diagonal like the standard PARAFAC, but wherein different terms distinguish different kinds of three-way relations of co-clusters, as determined by permutations of latent factors. The first key component of the algebraic representation is the usage of two non-commutative real trilinear operations as the building blocks of the approximation. These operations are the standard three dimensional triple-product and a trilinear product on a two-dimensional real vector space, which is a representation of the real Clifford Algebra Cl(1,1) (a certain Majorana spinor). Both operations are purely ternary in that they cannot be decomposed into two group-operations on the relevant spaces. The second key component of the method is combining these operations using permutation-symmetry preserving linear combinations. We apply the model to the MovieLens and Fannie Mae datasets, and find that it outperforms the PARAFAC model. We propose some future directions, such as unsupervised-learning.

This paper covers the two approaches for sentiment analysis: i) lexicon based method; ii) machine learning method. We describe several techniques to implement these approaches and discuss how they can be adopted for sentiment classification of Twitter messages. We present a comparative study of different lexicon combinations and show that enhancing sentiment lexicons with emoticons, abbreviations and social-media slang expressions increases the accuracy of lexicon-based classification for Twitter. We discuss the importance of feature generation and feature selection processes for machine learning sentiment classification. To quantify the performance of the main sentiment analysis methods over Twitter we run these algorithms on a benchmark Twitter dataset from the SemEval-2013 competition, task 2-B. The results show that machine learning method based on SVM and Naive Bayes classifiers outperforms the lexicon method. We present a new ensemble method that uses a lexicon based sentiment score as input feature for the machine learning approach. The combined method proved to produce more precise classifications. We also show that employing a cost-sensitive classifier for highly unbalanced datasets yields an improvement of sentiment classification performance up to 7%.

A model of an Ant System where ants are controlled by a spiking neural circuit and a second order pheromone mechanism in a foraging task is presented. A neural circuit is trained for individual ants and subsequently the ants are exposed to a virtual environment where a swarm of ants performed a resource foraging task. The model comprises an associative and unsupervised learning strategy for the neural circuit of the ant. The neural circuit adapts to the environment by means of classical conditioning. The initially unknown environment includes different types of stimuli representing food and obstacles which, when they come in direct contact with the ant, elicit a reflex response in the motor neural system of the ant: moving towards or away from the source of the stimulus. The ants are released on a landscape with multiple food sources where one ant alone would have difficulty harvesting the landscape to maximum efficiency. The introduction of a double pheromone mechanism yields better results than traditional ant colony optimization strategies. Traditional ant systems include mainly a positive reinforcement pheromone. This approach uses a second pheromone that acts as a marker for forbidden paths (negative feedback). This blockade is not permanent and is controlled by the evaporation rate of the pheromones. The combined action of both pheromones acts as a collective stigmergic memory of the swarm, which reduces the search space of the problem. This paper explores how the adaptation and learning abilities observed in biologically inspired cognitive architectures is synergistically enhanced by swarm optimization strategies. The model portraits two forms of artificial intelligent behaviour: at the individual level the spiking neural network is the main controller and at the collective level the pheromone distribution is a map towards the solution emerged by the colony.

A major problem in road network analysis is discovery of important crossroads, which can provide useful information for transport planning. However, none of existing approaches addresses the problem of identifying network-wide important crossroads in real road network. In this paper, we propose a novel data-driven based approach named CRRank to rank important crossroads. Our key innovation is that we model the trip network reflecting real travel demands with a tripartite graph, instead of solely analysis on the topology of road network. To compute the importance scores of crossroads accurately, we propose a HITS-like ranking algorithm, in which a procedure of score propagation on our tripartite graph is performed. We conduct experiments on CRRank using a real-world dataset of taxi trajectories. Experiments verify the utility of CRRank.