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Quantum annealing versus classical machine learning applied to a simplified computational biology problem.

ABSTRACT: Transcription factors regulate gene expression, but how these proteins recognize and specifically bind to their DNA targets is still debated. Machine learning models are effective means to reveal interaction mechanisms. Here we studied the ability of a quantum machine learning approach to predict binding specificity. Using simplified datasets of a small number of DNA sequences derived from actual binding affinity experiments, we trained a commercially available quantum annealer to classify and rank transcription factor binding. The results were compared to state-of-the-art classical approaches for the same simplified datasets, including simulated annealing, simulated quantum annealing, multiple linear regression, LASSO, and extreme gradient boosting. Despite technological limitations, we find a slight advantage in classification performance and nearly equal ranking performance using the quantum annealer for these fairly small training data sets. Thus, we propose that quantum annealing might be an effective method to implement machine learning for certain computational biology problems.

SUBMITTER: Li RY

PROVIDER: S-EPMC5891835 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Quantum annealing versus classical machine learning applied to a simplified computational biology problem.

Li Richard Y RY Di Felice Rosa R Rohs Remo R Lidar Daniel A DA

NPJ quantum information 20180221

Transcription factors regulate gene expression, but how these proteins recognize and specifically bind to their DNA targets is still debated. Machine learning models are effective means to reveal interaction mechanisms. Here we studied the ability of a quantum machine learning approach to predict binding specificity. Using simplified datasets of a small number of DNA sequences derived from actual binding affinity experiments, we trained a commercially available quantum annealer to classify and r ...[more]

PMID: 29652405

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Project description:A hybrid quantum-classical method for learning Boltzmann machines (BM) for a generative and discriminative task is presented. BM are undirected graphs with a network of visible and hidden nodes where the former is used as the reading site. In contrast, the latter is used to manipulate visible states' probability. In Generative BM, the samples of visible data imitate the probability distribution of a given data set. In contrast, the visible sites of discriminative BM are treated as Input/Output (I/O) reading sites where the conditional probability of output state is optimized for a given set of input states. The cost function for learning BM is defined as a weighted sum of Kullback-Leibler (KL) divergence and Negative conditional Log-likelihood (NCLL), adjusted using a hyper-parameter. Here, the KL Divergence is the cost for generative learning, and NCLL is the cost for discriminative learning. A Stochastic Newton-Raphson optimization scheme is presented. The gradients and the Hessians are approximated using direct samples of BM obtained through quantum annealing. Quantum annealers are hardware representing the physics of the Ising model that operates on low but finite temperatures. This temperature affects the probability distribution of the BM; however, its value is unknown. Previous efforts have focused on estimating this unknown temperature through regression of theoretical Boltzmann energies of sampled states with the probability of states sampled by the actual hardware. These approaches assume that the control parameter change does not affect the system temperature; however, this is usually untrue. Instead of using energies, the probability distribution of samples is employed to estimate the optimal parameter set, ensuring that the optimal set can be obtained from a single set of samples. The KL divergence and NCLL are optimized for the system temperature, and the result is used to rescale the control parameter set. The performance of this approach, as tested against the theoretically expected distributions, shows promising results for Boltzmann training on quantum annealers.

Dataset Information

Quantum annealing versus classical machine learning applied to a simplified computational biology problem.

Publications

Quantum annealing versus classical machine learning applied to a simplified computational biology problem.

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