Search for: All records

Abstract SummaryTarget identification by enzymes (TIE) problem aims to identify the set of enzymes in a given metabolic network, such that their inhibition eliminates a given set of target compounds associated with a disease while incurring minimum damage to the rest of the compounds. This is a NP-hard problem, and thus optimal solutions using classical computers fail to scale to large metabolic networks. In this article, we develop the first quantum optimization solution, called QuTIE (quantum optimization for target identification by enzymes), to this NP-hard problem. We do that by developing an equivalent formulation of the TIE problem in quadratic unconstrained binary optimization form. We then map it to a logical graph, and embed the logical graph on a quantum hardware graph. Our experimental results on 27 metabolic networks from Escherichia coli, Homo sapiens, and Mus musculus show that QuTIE yields solutions that are optimal or almost optimal. Our experiments also demonstrate that QuTIE can successfully identify enzyme targets already verified in wet-lab experiments for 14 major disease classes. Availability and implementationCode and sample data are available at: https://github.com/ngominhhoang/Quantum-Target-Identification-by-Enzymes. 

We study the problem of policy optimization (PO) with linear temporal logic (LTL) constraints. The language of LTL allows flexible description of tasks that may be unnatural to encode as a scalar cost function. We consider LTL-constrained PO as a systematic framework, decoupling task specification from policy selection, and as an alternative to the standard of cost shaping. With access to a generative model, we develop a model-based approach that enjoys a sample complexity analysis for guaranteeing both task satisfaction and cost optimality (through a reduction to a reachability problem). Empirically, our algorithm can achieve strong performance even in low-sample regimes. 

Minimizers are k-mer sampling schemes designed to generate sketches for large sequences that preserve sufficiently long matches between sequences. Despite their widespread application, learning an effective minimizer scheme with optimal sketch size is still an open question. Most work in this direction focuses on designing schemes that work well on expectation over random sequences, which have limited applicability to many practical tools. On the other hand, several methods have been proposed to construct minimizer schemes for a specific target sequence. These methods, however, require greedy approximations to solve an intractable discrete optimization problem on the permutation space of k-mer orderings. To address this challenge, we propose: (a) a reformulation of the combinatorial solution space using a deep neural network re-parameterization; and (b) a fully differentiable approximation of the discrete objective. We demonstrate that our framework, DEEPMINIMIZER, discovers minimizer schemes that significantly outperform state-of-the-art constructions on genomic sequences.