Bosheng Song

Bio: Bosheng Song is an academic researcher from Hunan University. The author has contributed to research in topics: Membrane computing & Computer science. The author has an hindex of 17, co-authored 56 publications receiving 694 citations. Previous affiliations of Bosheng Song include Huazhong University of Science and Technology.

Normal Forms for Some Classes of Sequential Spiking Neural P Systems

Abstract: Spiking neural P systems (SN P systems, for short) are a class of distributed parallel computing devices inspired from the way neurons communicate by means of spikes, where each neuron can have several spiking rules and forgetting rules and neurons work in parallel in the sense that each neuron that can fire should fire at each computation step. In this work, we consider SN P systems with the restrictions: 1) systems are simple (resp. almost simple) in the sense that each neuron has only one rule (resp. except for one neuron); 2) at each step the neuron(s) with the maximum number of spikes among the neurons that can spike will fire. These restrictions correspond to that the systems are simple or almost simple and a global view of the whole network makes the systems sequential. The computation power of simple SN P systems and almost simple SN P systems working in the sequential mode induced by maximum spike number is investigated. Specifically, we prove that such systems are Turing universal as both number generating and accepting devices. The results improve the corresponding ones in Theor. Comput. Sci., 410 (2009), 2982-2991.

MUFFIN: multi-scale feature fusion for drug–drug interaction prediction

Abstract: Motivation Adverse drug-drug interactions (DDIs) are crucial for drug research and mainly cause morbidity and mortality. Thus, the identification of potential DDIs is essential for doctors, patients, and the society. Existing traditional machine learning models rely heavily on handcraft features and lack generalization. Recently, the deep learning approaches that can automatically learn drug features from the molecular graph or drug-related network have improved the ability of computational models to predict unknown DDIs. However, previous works utilized large labeled data and merely considered the structure or sequence information of drugs without considering the relations or topological information between drug and other biomedical objects (e.g., gene, disease, and pathway), or considered knowledge graph (KG) without considering the information from the drug molecular structure. Results Accordingly, to effectively explore the joint effect of drug molecular structure and semantic information of drugs in knowledge graph for DDI prediction, we propose a multi-scale feature fusion deep learning model named MUFFIN. MUFFIN can jointly learn the drug representation based on both the drug-self structure information and the KG with rich bio-medical information. In MUFFIN, we designed a bi-level cross strategy that includes cross- and scalar-level components to fuse multi-modal features well. MUFFIN can alleviate the restriction of limited labeled data on deep learning models by crossing the features learned from large-scale KG and drug molecular graph. We evaluated our approach on three datasets and three different tasks including binary-class, multi-class, and multi-label DDI prediction tasks. The results showed that MUFFIN outperformed other state-of-the-art baselines. Availability The source code and data are available at https://github.com/xzenglab/MUFFIN. Supplementary information Supplementary data are available at Bioinformatics online.

Cell-like P systems with evolutional symport/antiport rules and membrane creation

Abstract: Cell-like P systems with symport/antiport rules are computing models inspired by the conservation law, in the sense that they compute by changing the places of objects with respect to the membranes, and not by changing the objects themselves. In this work, a variant of these kinds of membrane systems, called cell-like P systems with evolutional symport/antiport rules, where objects can evolve in the execution of such rules, is introduced. Besides, inspired by the autopoiesis process (ability of a system to maintain itself), membrane creation rules are considered as an efficient mechanism to provide an exponential workspace in terms of membranes. The presumed efficiency of these computing models (ability to solve computationally hard problems in polynomial time and uniform way) is explored. Specifically, an efficient solution to the SAT problem is provided by means of a family of recognizer cell-like P systems with evolutional symport/antiport rules and membrane creation which make use of communication rules involving a restricted number of objects.

Monodirectional Tissue P Systems With Promoters

Abstract: Tissue $P$ systems with promoters provide nondeterministic parallel bioinspired devices that evolve by the interchange of objects between regions, determined by the existence of some special objects called promoters . However, in cellular biology, the movement of molecules across a membrane is transported from high to low concentration. Inspired by this biological fact, in this article, an interesting type of tissue $P$ systems, called monodirectional tissue $P$ systems with promoters , where communication happens between two regions only in one direction, is considered. Results show that finite sets of numbers are produced by such $P$ systems with one cell, using any length of symport rules or with any number of cells, using a maximal length 1 of symport rules, and working in the maximally parallel mode. Monodirectional tissue $P$ systems are Turing universal with two cells, a maximal length 2, and at most one promoter for each symport rule, and working in the maximally parallel mode or with three cells, a maximal length 1, and at most one promoter for each symport rule, and working in the flat maximally parallel mode. We also prove that monodirectional tissue $P$ systems with two cells, a maximal length 1, and at most one promoter for each symport rule (under certain restrictive conditions) working in the flat maximally parallel mode characterizes regular sets of natural numbers. Besides, the computational efficiency of monodirectional tissue $P$ systems with promoters is analyzed when cell division rules are incorporated. Different uniform solutions to the Boolean satisfiability problem (SAT problem) are provided. These results show that with the restrictive condition of “monodirectionality,” monodirectional tissue $P$ systems with promoters are still computationally powerful. With the powerful computational power, developing membrane algorithms for monodirectional tissue $P$ systems with promoters is potentially exploitable.

Computers And Intractability A Guide To The Theory Of Np Completeness

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RA-UNet: A hybrid deep attention-aware network to extract liver and tumor in CT scans

Abstract: Automatic extraction of liver and tumor from CT volumes is a challenging task due to their heterogeneous and diffusive shapes. Recently, 2D and 3D deep convolutional neural networks have become popular in medical image segmentation tasks because of the utilization of large labeled datasets to learn hierarchical features. However, 3D networks have some drawbacks due to their high cost on computational resources. In this paper, we propose a 3D hybrid residual attention-aware segmentation method, named RA-UNet, to precisely extract the liver volume of interests (VOI) and segment tumors from the liver VOI. The proposed network has a basic architecture as a 3D U-Net which extracts contextual information combining low-level feature maps with high-level ones. Attention modules are stacked so that the attention-aware features change adaptively as the network goes "very deep" and this is made possible by residual learning. This is the first work that an attention residual mechanism is used to process medical volumetric images. We evaluated our framework on the public MICCAI 2017 Liver Tumor Segmentation dataset and the 3DIRCADb dataset. The results show that our architecture outperforms other state-of-the-art methods. We also extend our RA-UNet to brain tumor segmentation on the BraTS2018 and BraTS2017 datasets, and the results indicate that RA-UNet achieves good performance on a brain tumor segmentation task as well.