A Novel Model for DNA Sequence Similarity Analysis Based on Graph Theory

Determination of sequence similarity is one of the major steps in computational phylogenetic studies. As we know, during evolutionary history, not only DNA mutations for individual nucleotide but also subsequent rearrangements occurred. It has been one of major tasks of computational biologists to develop novel mathematical descriptors for similarity analysis such that various mutation phenomena information would be involved simultaneously. In this paper, different from traditional methods (eg, nucleotide frequency, geometric representations) as bases for construction of mathematical descriptors, we construct novel mathematical descriptors based on graph theory. In particular, for each DNA sequence, we will set up a weighted directed graph. The adjacency matrix of the directed graph will be used to induce a representative vector for DNA sequence. This new approach measures similarity based on both ordering and frequency of nucleotides so that much more information is involved. As an application, the method is tested on a set of 0.9-kb mtDNA sequences of twelve different primate species. All output phylogenetic trees with various distance estimations have the same topology, and are generally consistent with the reported results from early studies, which proves the new method\u27s efficiency; we also test the new method on a simulated data set, which shows our new method performs better than traditional global alignment method when subsequent rearrangements happen frequently during evolutionary history

Tensor-network-assisted variational quantum algorithm

Near-term quantum devices generally suffer from shallow circuit depth and hence limited expressivity due to noise and decoherence. To address this, we propose tensor-network-assisted parametrized quantum circuits, which concatenate a classical tensor-network operator with a quantum circuit to effectively increase the circuit's expressivity without requiring a physically deeper circuit. We present a framework for tensor-network-assisted variational quantum algorithms that can solve quantum many-body problems using shallower quantum circuits. We demonstrate the efficiency of this approach by considering two examples of unitary matrix-product operators and unitary tree tensor networks, showing that they can both be implemented efficiently. Through numerical simulations, we show that the expressivity of these circuits is greatly enhanced with the assistance of tensor networks. We apply our method to two-dimensional Ising models and one-dimensional time-crystal Hamiltonian models with up to 16 qubits and demonstrate that our approach consistently outperforms conventional methods using shallow quantum circuits.Comment: 12 pages, 8 figures, 37 reference

Linearizability Problem of Resonant Degenerate Singular Point for Polynomial Differential Systems

The linearizability (or isochronicity) problem is one of the open problems for polynomial differential systems which is far to be solved in general. A progressive way to find necessary conditions for linearizability is to compute period constants. In this paper, we are interested in the linearizability problem of p : −q resonant degenerate singular point for polynomial differential systems. Firstly, we transform degenerate singular point into the origin via a homeomorphism. Moreover, we establish a new recursive algorithm to compute the so-called generalized period constants for the origin of the transformed system. Finally, to illustrate the effectiveness of our algorithm, we discuss the linearizability problems of 1 : −1 resonant degenerate singular point for a septic system. We stress that similar results are hardly seen in published literatures up till now. Our work is completely new and extends existing ones

Mutual Information Learned Regressor: an Information-theoretic Viewpoint of Training Regression Systems

As one of the central tasks in machine learning, regression finds lots of applications in different fields. An existing common practice for solving regression problems is the mean square error (MSE) minimization approach or its regularized variants which require prior knowledge about the models. Recently, Yi et al., proposed a mutual information based supervised learning framework where they introduced a label entropy regularization which does not require any prior knowledge. When applied to classification tasks and solved via a stochastic gradient descent (SGD) optimization algorithm, their approach achieved significant improvement over the commonly used cross entropy loss and its variants. However, they did not provide a theoretical convergence analysis of the SGD algorithm for the proposed formulation. Besides, applying the framework to regression tasks is nontrivial due to the potentially infinite support set of the label. In this paper, we investigate the regression under the mutual information based supervised learning framework. We first argue that the MSE minimization approach is equivalent to a conditional entropy learning problem, and then propose a mutual information learning formulation for solving regression problems by using a reparameterization technique. For the proposed formulation, we give the convergence analysis of the SGD algorithm for solving it in practice. Finally, we consider a multi-output regression data model where we derive the generalization performance lower bound in terms of the mutual information associated with the underlying data distribution. The result shows that the high dimensionality can be a bless instead of a curse, which is controlled by a threshold. We hope our work will serve as a good starting point for further research on the mutual information based regression.Comment: 28 pages, 2 figures, presubmitted to AISTATS2023 for reviewin