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Added by
Jose Frederico Simoes Bravo Ferreira
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Nuclear Magnetic Resonance (NMR) Spectroscopy is the second most used technique (after X-ray crystallography) for structural determination of proteins. A computational challenge in this technique involves solving a discrete optimization problem that assigns the resonance frequency to each atom in the protein. This paper introduces LIAN (LInear programming Assignment for NMR), a novel linear programming formulation of the problem which yields state-of-the-art results in simulated and experimental datasets.
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We consider the problem of mapping a logical quantum circuit onto a given hardware with limited two-qubit connectivity. We model this problem as an integer linear program, using a network flow formulation with binary variables that includes the initial allocation of qubits and their routing. We consider several cost functions: an approximation of the fidelity of the circuit, its total depth, and a measure of cross-talk, all of which can be incorporated in the model. Numerical experiments on synthetic data and different hardware topologies indicate that the error rate and depth can be optimized simultaneously without significant loss. We test our algorithm on a large number of quantum volume circuits, optimizing for error rate and depth; our algorithm significantly reduces the number of CNOTs compared to Qiskits default transpiler SABRE, and produces circuits that, when executed on hardware, exhibit higher fidelity.
Nuclear magnetic resonance (NMR) spectroscopy is a powerful method for the investigation of three-dimensional structures of biological molecules such as proteins. Determining a protein structure is essential for understanding its function and alterations in function which lead to disease. One of the major challenges of the post-genomic era is to obtain structural and functional information on the many unknown proteins encoded by thousands of newly identified genes. The goal of this research is to design an algorithm capable of automating the analysis of backbone protein NMR data by implementing AI strategies such as greedy and A* search.
Recent advancements in procedural content generation via machine learning enable the generation of video-game levels that are aesthetically similar to human-authored examples. However, the generated levels are often unplayable without additional editing. We propose a generate-then-repair framework for automatic generation of playable levels adhering to specific styles. The framework constructs levels using a generative adversarial network (GAN) trained with human-authored examples and repairs them using a mixed-integer linear program (MIP) with playability constraints. A key component of the framework is computing minimum cost edits between the GAN generated level and the solution of the MIP solver, which we cast as a minimum cost network flow problem. Results show that the proposed framework generates a diverse range of playable levels, that capture the spatial relationships between objects exhibited in the human-authored levels.
In this paper, we develop a simple and fast online algorithm for solving a class of binary integer linear programs (LPs) arisen in general resource allocation problem. The algorithm requires only one single pass through the input data and is free of doing any matrix inversion. It can be viewed as both an approximate algorithm for solving binary integer LPs and a fast algorithm for solving online LP problems. The algorithm is inspired by an equivalent form of the dual problem of the relaxed LP and it essentially performs (one-pass) projected stochastic subgradient descent in the dual space. We analyze the algorithm in two different models, stochastic input and random permutation, with minimal technical assumptions on the input data. The algorithm achieves $Oleft(m sqrt{n}right)$ expected regret under the stochastic input model and $Oleft((m+log n)sqrt{n}right)$ expected regret under the random permutation model, and it achieves $O(m sqrt{n})$ expected constraint violation under both models, where $n$ is the number of decision variables and $m$ is the number of constraints. The algorithm enjoys the same performance guarantee when generalized to a multi-dimensional LP setting which covers a wider range of applications. In addition, we employ the notion of permutational Rademacher complexity and derive regret bounds for two earlier online LP algorithms for comparison. Both algorithms improve the regret bound with a factor of $sqrt{m}$ by paying more computational cost. Furthermore, we demonstrate how to convert the possibly infeasible solution to a feasible one through a randomized procedure. Numerical experiments illustrate the general applicability and effectiveness of the algorithms.
Recently a novel framework has been proposed for designing the molecular structure of chemical compounds using both artificial neural networks (ANNs) and mixed integer linear programming (MILP). In the framework, we first define a feature vector $f(C)$ of a chemical graph $C$ and construct an ANN that maps $x=f(C)$ to a predicted value $eta(x)$ of a chemical property $pi$ to $C$. After this, we formulate an MILP that simulates the computation process of $f(C)$ from $C$ and that of $eta(x)$ from $x$. Given a target value $y^*$ of the chemical property $pi$, we infer a chemical graph $C^dagger$ such that $eta(f(C^dagger))=y^*$ by solving the MILP. In this paper, we use linear regression to construct a prediction function $eta$ instead of ANNs. For this, we derive an MILP formulation that simulates the computation process of a prediction function by linear regression. The results of computational experiments suggest our method can infer chemical graphs with around up to 50 non-hydrogen atoms.
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