Spectral Sequence Motif Discovery

Sequence discovery tools play a central role in several fields of computational biology. In the framework of Transcription Factor binding studies, motif finding algorithms of increasingly high performance are required to process the big datasets produced by new high-throughput sequencing technologies. Most existing algorithms are computationally demanding and often cannot support the large size of new experimental data. We present a new motif discovery algorithm that is built on a recent machine learning technique, referred to as Method of Moments. Based on spectral decompositions, this method is robust under model misspecification and is not prone to locally optimal solutions. We obtain an algorithm that is extremely fast and designed for the analysis of big sequencing data. In a few minutes, we can process datasets of hundreds of thousand sequences and extract motif profiles that match those computed by various state-of-the-art algorithms.Comment: 20 pages, 3 figures, 1 tabl

Stochastic Control via Entropy Compression

We consider an agent trying to bring a system to an acceptable state by repeated probabilistic action. Several recent works on algorithmizations of the Lovasz Local Lemma (LLL) can be seen as establishing sufficient conditions for the agent to succeed. Here we study whether such stochastic control is also possible in a noisy environment, where both the process of state-observation and the process of state-evolution are subject to adversarial perturbation (noise). The introduction of noise causes the tools developed for LLL algorithmization to break down since the key LLL ingredient, the sparsity of the causality (dependence) relationship, no longer holds. To overcome this challenge we develop a new analysis where entropy plays a central role, both to measure the rate at which progress towards an acceptable state is made and the rate at which noise undoes this progress. The end result is a sufficient condition that allows a smooth tradeoff between the intensity of the noise and the amenability of the system, recovering an asymmetric LLL condition in the noiseless case.Comment: 18 page

Conditions for duality between fluxes and concentrations in biochemical networks

Mathematical and computational modelling of biochemical networks is often done in terms of either the concentrations of molecular species or the fluxes of biochemical reactions. When is mathematical modelling from either perspective equivalent to the other? Mathematical duality translates concepts, theorems or mathematical structures into other concepts, theorems or structures, in a one-to-one manner. We present a novel stoichiometric condition that is necessary and sufficient for duality between unidirectional fluxes and concentrations. Our numerical experiments, with computational models derived from a range of genome-scale biochemical networks, suggest that this flux-concentration duality is a pervasive property of biochemical networks. We also provide a combinatorial characterisation that is sufficient to ensure flux-concentration duality. That is, for every two disjoint sets of molecular species, there is at least one reaction complex that involves species from only one of the two sets. When unidirectional fluxes and molecular species concentrations are dual vectors, this implies that the behaviour of the corresponding biochemical network can be described entirely in terms of either concentrations or unidirectional fluxes

On the Computational Complexity of Stochastic Controller Optimization in POMDPs

We show that the problem of finding an optimal stochastic 'blind' controller in a Markov decision process is an NP-hard problem. The corresponding decision problem is NP-hard, in PSPACE, and SQRT-SUM-hard, hence placing it in NP would imply breakthroughs in long-standing open problems in computer science. Our result establishes that the more general problem of stochastic controller optimization in POMDPs is also NP-hard. Nonetheless, we outline a special case that is convex and admits efficient global solutions.Comment: Corrected error in the proof of Theorem 2, and revised Section

Optimal and Approximate Q-value Functions for Decentralized POMDPs

Decision-theoretic planning is a popular approach to sequential decision making problems, because it treats uncertainty in sensing and acting in a principled way. In single-agent frameworks like MDPs and POMDPs, planning can be carried out by resorting to Q-value functions: an optimal Q-value function Q* is computed in a recursive manner by dynamic programming, and then an optimal policy is extracted from Q*. In this paper we study whether similar Q-value functions can be defined for decentralized POMDP models (Dec-POMDPs), and how policies can be extracted from such value functions. We define two forms of the optimal Q-value function for Dec-POMDPs: one that gives a normative description as the Q-value function of an optimal pure joint policy and another one that is sequentially rational and thus gives a recipe for computation. This computation, however, is infeasible for all but the smallest problems. Therefore, we analyze various approximate Q-value functions that allow for efficient computation. We describe how they relate, and we prove that they all provide an upper bound to the optimal Q-value function Q*. Finally, unifying some previous approaches for solving Dec-POMDPs, we describe a family of algorithms for extracting policies from such Q-value functions, and perform an experimental evaluation on existing test problems, including a new firefighting benchmark problem