An investigation of coupled natural human systems using a two-way coupled agent-based modeling framework
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Zmuidzinas, Jonas ; Gao, Jian-Rong (Ed.)
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Abstract Predicting the interactions between drugs and targets plays an important role in the process of new drug discovery, drug repurposing (also known as drug repositioning). There is a need to develop novel and efficient prediction approaches in order to avoid the costly and laborious process of determining drug–target interactions (DTIs) based on experiments alone. These computational prediction approaches should be capable of identifying the potential DTIs in a timely manner. Matrix factorization methods have been proven to be the most reliable group of methods. Here, we first propose a matrix factorization-based method termed ‘Coupled Matrix–Matrix Completion’ (CMMC). Next, in order to utilize more comprehensive information provided in different databases and incorporate multiple types of scores for drug–drug similarities and target–target relationship, we then extend CMMC to ‘Coupled Tensor–Matrix Completion’ (CTMC) by considering drug–drug and target–target similarity/interaction tensors. Results: Evaluation on two benchmark datasets, DrugBank and TTD, shows that CTMC outperforms the matrix-factorization-based methods: GRMF, $L_{2,1}$-GRMF, NRLMF and NRLMF$\beta $. Based on the evaluation, CMMC and CTMC outperform the above three methods in term of area under the curve, F1 score, sensitivity and specificity in a considerably shorter run time.more » « less
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The chemistry community has long sought the exact relationship between the conventional and the unitary coupled cluster ansatz for a single-reference system, especially given the interest in performing quantum chemistry on quantum computers. In this work, we show how one can use the operator manipulations given by the exponential disentangling identity and the Hadamard lemma to relate the factorized form of the unitary coupled-cluster approximation to a factorized form of the conventional coupled cluster approximation (the factorized form is required, because some amplitudes are operator-valued and do not commute with other terms). By employing the Trotter product formula, one can then relate the factorized form to the standard form of the unitary coupled cluster ansatz. The operator dependence of the factorized form of the coupled cluster approximation can also be removed at the expense of requiring even more higher-rank operators, finally yielding the conventional coupled cluster. The algebraic manipulations of this approach are daunting to carry out by hand, but can be automated on a computer for small enough systems.more » « less
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1016/j.envsoft.2022.105451
