Bayesian network models are finding success in characterizing enzyme-catalyzed reactions, slow conformational changes, predicting enzyme inhibition, and genomics. In this work, we apply them to statistical modeling of peptides by simultaneously identifying amino acid sequence motifs and using a motif-based model to clarify the role motifs may play in antimicrobial activity. We construct models of increasing sophistication, demonstrating how chemical knowledge of a peptide system may be embedded without requiring new derivation of model fitting equations after changing model structure. These models are used to construct classifiers with good performance (94% accuracy, Matthews correlation coefficient of 0.87) at predicting antimicrobial activity in peptides, while at the same time being built of interpretable parameters. We demonstrate use of these models to identify peptides that are potentially both antimicrobial and antifouling, and show that the background distribution of amino acids could play a greater role in activity than sequence motifs do. This provides an advancement in the type of peptide activity modeling that can be done and the ease in which models can be constructed.

The Centers for Disease Control and Prevention (CDC) coordinates a labor-intensive process to measure the prevalence of autism spectrum disorder (ASD) among children in the United States. Random forests methods have shown promise in speeding up this process, but they lag behind human classification accuracy by about 5 percent. We explore whether newer document classification algorithms can close this gap. We applied 6 supervised learning algorithms to predict whether children meet the case definition for ASD based solely on the words in their evaluations. We compared the algorithms? performance across 10 random train-test splits of the data, and then, we combined our top 3 classifiers to estimate the Bayes error rate in the data. Across the 10 train-test cycles, the random forest, neural network, and support vector machine with Naive Bayes features (NB-SVM) each achieved slightly more than 86.5 percent mean accuracy. The Bayes error rate is estimated at approximately 12 percent meaning that the model error for even the simplest of our algorithms, the random forest, is below 2 percent. NB-SVM produced significantly more false positives than false negatives. The random forest performed as well as newer models like the NB-SVM and the neural network. NB-SVM may not be a good candidate for use in a fully-automated surveillance workflow due to increased false positives. More sophisticated algorithms, like hierarchical convolutional neural networks, would not perform substantially better due to characteristics of the data. Deep learning models performed similarly to traditional machine learning methods at predicting the clinician-assigned case status for CDC's autism surveillance system. While deep learning methods had limited benefit in this task, they may have applications in other surveillance systems.

We present a probabilistic model of an intrusion in a marked renewal process. Given a process and a sequence of events, an intrusion is a subsequence of events that is not produced by the process. Applications of the model are, for example, online payment fraud with the fraudster taking over a user's account and performing payments on the user's behalf, or unexpected equipment failures due to unintended use. We adopt Bayesian approach to infer the probability of an intrusion in a sequence of events, a MAP subsequence of events constituting the intrusion, and the marginal probability of each event in a sequence to belong to the intrusion. We evaluate the model for intrusion detection on synthetic data, as well as on anonymized data from an online payment system.

Modern neural networks are highly overparameterized, with capacity to substantially overfit to training data. Nevertheless, these networks often generalize well in practice. It has also been observed that trained networks can often be "compressed" to much smaller representations. The purpose of this paper is to connect these two empirical observations. Our main technical result is a generalization bound for compressed networks based on the compressed size. Combined with off-the-shelf compression algorithms, the bound leads to state of the art generalization guarantees; in particular, we provide the first non-vacuous generalization guarantees for realistic architectures applied to the ImageNet classification problem. As additional evidence connecting compression and generalization, we show that compressibility of models that tend to overfit is limited: We establish an absolute limit on expected compressibility as a function of expected generalization error, where the expectations are over the random choice of training examples. The bounds are complemented by empirical results that show an increase in overfitting implies an increase in the number of bits required to describe a trained network.

This paper addresses the problem of planning a safe (i.e., collision-free) trajectory from an initial state to a goal region when the obstacle space is a-priori unknown and is incrementally revealed online, e.g., through line-of-sight perception. Despite its ubiquitous nature, this formulation of motion planning has received relatively little theoretical investigation, as opposed to the setup where the environment is assumed known. A fundamental challenge is that, unlike motion planning with known obstacles, it is not even clear what an optimal policy to strive for is. Our contribution is threefold. First, we present a notion of optimality for safe planning in unknown environments in the spirit of comparative (as opposed to competitive) analysis, with the goal of obtaining a benchmark that is, at least conceptually, attainable. Second, by leveraging this theoretical benchmark, we derive a pseudo-optimal class of policies that can seamlessly incorporate any amount of prior or learned information while still guaranteeing the robot never collides. Finally, we demonstrate the practicality of our algorithmic approach in numerical experiments using a range of environment types and dynamics, including a comparison with a state of the art method. A key aspect of our framework is that it automatically and implicitly weighs exploration versus exploitation in a way that is optimal with respect to the information available.

A common mechanism to assess trust in crowdworkers is to have them answer gold tasks. However, assigning gold tasks to all workers reduces the efficiency of the platform. We propose a mechanism that exploits transitivity so that a worker can be certified as trusted by other trusted workers who solve common tasks. Thus, trust can be derived from a smaller number of gold tasks assignment through multiple layers of peer relationship among the workers, a model we call deep trust. We use the derived trust to incentivize workers for high quality work and show that the resulting mechanism is dominant strategy incentive compatible. We also show that the mechanism satisfies a notion of fairness in that the trust assessment (and thus the reward) of a worker in the limit is independent of the quality of other workers.

With a new era of cloud and big data, Database Management Systems (DBMSs) have become more crucial in numerous enterprise business applications in all the industries. Accordingly, the importance of their proactive and preventive maintenance has also increased. However, detecting problems by predefined rules or stochastic modeling has limitations, particularly when analyzing the data on high-dimensional Key Performance Indicators (KPIs) from a DBMS. In recent years, Deep Learning (DL) has opened new opportunities for this complex analysis. In this paper, we present two complementary DL approaches to detect anomalies in SAP HANA. A temporal learning approach is used to detect abnormal patterns based on unlabeled historical data, whereas a spatial learning approach is used to classify known anomalies based on labeled data. We implement a system in SAP HANA integrated with Google TensorFlow. The experimental results with real-world data confirm the effectiveness of the system and models.

This paper considers parametric Markov decision processes (pMDPs) whose transitions are equipped with affine functions over a finite set of parameters. The synthesis problem is to find a parameter valuation such that the instantiated pMDP satisfies a specification under all strategies. We show that this problem can be formulated as a quadratically-constrained quadratic program (QCQP) and is non-convex in general. To deal with the NP-hardness of such problems, we exploit a convex-concave procedure (CCP) to iteratively obtain local optima. An appropriate interplay between CCP solvers and probabilistic model checkers creates a procedure --- realized in the open-source tool PROPhESY --- that solves the synthesis problem for models with thousands of parameters.

Bayesian approaches have been used extensively in scientific and engineering research to quantify uncertainty and extract information. However, its model-dependent nature means that when the a priori model is incomplete or unavailable, there is a severe risk that Bayesian approaches will yield misleading results. Here, we propose a universal model-free information extraction approach, capable of reliably recovering target signals from complex responses. This breakthrough leverages on a data-centric approach, whereby measured data is reconfigured to create an enriched observable space, which in turn is mapped to a well-adapted manifold, thereby detecting crucial information via a reconstructed low-rank phase-space. A Koopman operator is used to transform hidden and complex nonlinear dynamics to linear one, which enables us to detect hidden event of interest from rapidly evolving systems, and relate it to either unobservable stimulus or anomalous behaviour. Thanks to its data-driven nature, our method excludes completely any prior knowledge on governing dynamics. We benchmark the astonishing accuracy of our method on three diverse and challenging problems in: biology, medicine, and engineering. In all cases, our approach outperforms existing state-of-the-art methods, of both Bayesian and non-Bayesian type. By creating a new reliable information analysis paradigm, it is suitable for ubiquitous nonlinear dynamical systems or end-users with little expertise, which permits the unbiased understanding of various mechanisms in the real world.

The fundamental problem in short-text classification is \emph{feature sparseness} -- the lack of feature overlap between a trained model and a test instance to be classified. We propose \emph{ClassiNet} -- a network of classifiers trained for predicting missing features in a given instance, to overcome the feature sparseness problem. Using a set of unlabeled training instances, we first learn binary classifiers as feature predictors for predicting whether a particular feature occurs in a given instance. Next, each feature predictor is represented as a vertex $v_i$ in the ClassiNet where a one-to-one correspondence exists between feature predictors and vertices. The weight of the directed edge $e_{ij}$ connecting a vertex $v_i$ to a vertex $v_j$ represents the conditional probability that given $v_i$ exists in an instance, $v_j$ also exists in the same instance. We show that ClassiNets generalize word co-occurrence graphs by considering implicit co-occurrences between features. We extract numerous features from the trained ClassiNet to overcome feature sparseness. In particular, for a given instance $\vec{x}$, we find similar features from ClassiNet that did not appear in $\vec{x}$, and append those features in the representation of $\vec{x}$. Moreover, we propose a method based on graph propagation to find features that are indirectly related to a given short-text. We evaluate ClassiNets on several benchmark datasets for short-text classification. Our experimental results show that by using ClassiNet, we can statistically significantly improve the accuracy in short-text classification tasks, without having to use any external resources such as thesauri for finding related features.