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Bio-Inspired computing: theories and Applications 1

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丛书名： Communications in Computer and Information Science

1000年

作者： Linqiang Pan Jianqing Lin Yong Wang

ISBN: (数字)9789819722754

ISBN: (纸本)9789819722747

the two-volume set CCIS 2061 and 2062 constitutes the refereed post-conference proceedings of the 18th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2023, held in Changsha, China, during December 15–17, 2023.;the 64 revised full papers presented in these proceedings were carefully reviewed and selected from 168 submissions. the papers are organized in the following topical sections:;Volume I: Evolutionary Computation and Swarm Intelligence; and Membrane computing and dna computing;Volume II: Machine Learning and Applications; and Intelligent Control and Application.

关键词： Artificial Intelligence theory of Computation Computer Communication Networks Special Purpose and Application-Based Systems Computer System Implementation Mathematics of computing

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Learning Protein-dna Interaction Landscapes by Integrating Experimental Data through Computational Models

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18th Annual international conference on Research in Computational molecular Biology (RECOMB)

作者： Zhong, Jianling Wasson, Todd Hartemink, Alexander J. Duke Univ Durham NC 27708 USA Lawrence Livermore Natl Lab Livermore CA 94550 USA Duke Univ Dept Comp Sci Durham NC 27708 USA

ISBN: (纸本)9783319052694;9783319052687

Transcriptional regulation is directly enacted by the interactions between dna and many proteins, including transcription factors, nucleosomes, and polymerases. A critical step in deciphering transcriptional regulation is to infer, and eventually predict, the precise locations of these interactions, along with their strength and frequency. While recent datasets yield great insight into these interactions, individual data sources often provide only noisy information regarding one specific aspect of the complete interaction landscape. For example, chromatin immunoprecipitation (ChIP) reveals the precise binding positions of a protein, but only for one protein at a time. In contrast, nucleases like MNase and dnase reveal binding positions for many different proteins at once, but cannot easily determine the identities of those proteins. Here, we develop a novel statistical framework that integrates different sources of experimental information within a thermodynamic model of competitive binding to jointly learn a holistic view of the in vivo protein-dna interaction landscape. We show that our framework learns an interaction landscape with increased accuracy, explaining multiple sets of data in accordance with thermodynamic principles of competitive dna binding. the resulting model of genomic occupancy provides a precise, mechanistic vantage point from which to explore the role of protein-dna interactions in transcriptional regulation.

关键词： protein-dna interaction landscape thermodynamic modeling genomic data integration competitive binding COMPETE

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A circuit simplification mechanism based on dna combinatorial strands displacement 12th

A circuit simplification mechanism based on DNA combinatoria...

引用

12th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2017

作者： Zhang, Xuncai Han, Feng Wang, Yanfeng College of Electrical and Electronic Engineering Zhengzhou University of Light Industry Zhengzhou450002 China

ISBN: (纸本)9789811071782

through extensive application of dna strand displacement technology in the field of molecular computing, we know that the dna strand of the toehold domain and the branch migration domain are covalently connected to form logical gates in traditional dna strand displacement circuits. In this paper, we will adopt a composite strand mechanism that the toehold domain and branch migration domain in different single strand form displacing complex, and construct logical gates with combinatorial strand displacement mechanism. After that, a logic gate model is constructed, and the mechanism is verified by the design and simulation of the logical molecular model of the encoder. When the dna signal strand is input, the signal strand molecule can be output by combination of molecular specific hybridization reaction and intermolecular strand displacement reaction. the results of Visual DSD simulation show the feasibility and accuracy of the encoder logic calculation model designed in this article. © Springer Nature Singapore Pte Ltd 2017.

关键词： Timing circuits

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the decoder based on dna strand displacement with improved "AND" gate and "OR" gate 1

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12th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2017

作者： Han, Weixuan Zhou, Changjun Wang, Xiaojun Zhang, Qiang Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education Dalian University Dalian116622 China

ISBN: (数字)9789811071799

ISBN: (纸本)9789811071782

In the computational biology, dna strand displacement technique is used to construct the logic gate model and molecular circuits. But with the increase of number of the reaction strands, the basic logic gates cannot meet the accuracy in the reaction process. this paper improved the logical unit OR gate, AND gate to solve this problem on the basic of the seesaw model and the mechanism of dna strand displacement reaction. Since the basic circuit of the decoder is an array of AND gates, the improvement module is applied to the decoder. the molecular circuit of decoder is constructed to realize the dynamic link between the input signal and the output signal. It is concluded that the sensitivity and accuracy of the improved decoder in the molecular circuit is improved by the Visual DSD software. the improvement module laid the foundation for the development of molecular circuits. © Springer Nature Singapore Pte Ltd 2017.

关键词： Logic gates

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molecular Characterization and dna-sensing using Graphene Electrochemical Devices under Illumination 18

Molecular Characterization and DNA-sensing using Graphene El...

引用

18th IEEE Nanotechnology Materials and Devices conference, NMDC 2023

作者： Alpuim, Pedro Pinzón, Edgar Lopes, Laís C. Domingues, Telma Borme, Jérôme Godoy, Erika Raposo, M. Manuela M. Bueno, Paulo R. Av. Mestre José Veiga Braga Portugal Centro de Física Universidade Do Minho Braga Portugal Araraquara Brazil Centro de Química Universidade Do Minho Braga Portugal

ISBN: (纸本)9798350335460

In the AC-electrochemical mode, the signal of quantum capacitance (Cq) of individual graphene channels was resolved as a function of a superimposed DC bias potential through electrochemical impedance spectroscopy (EIS). this capacitive response was used to study the electronic states of push-pull molecules immobilized on the graphene surface in the dark and under visible illumination in the 400 to 580 nm range. the same technique will be further used in the molecular detection of target dna by functionalizing the graphene surface with complementary probe-dna and monitoring the Cq-minimum (Dirac point) changes for different target-dna concentrations in the dark and under visible illumination. © 2023 IEEE.

关键词： Graphene

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Joint conferences on 18th international conference on Intelligent Systems Design and Applications, ISDA 2018 and 10th World Congress on Nature and Biologically Inspired computing , NaBIC 2018

Joint Conferences on 18th International Conference on Intell...

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Joint conferences on 18th international conference on Intelligent Systems Design and Applications, ISDA 2018 and 10th World Congress on Nature and Biologically Inspired computing , NaBIC 2018

ISBN: (纸本)9783030166564

the proceedings contain 214 papers. the special focus in this conference is on Intelligent Systems Design and Applications. the topics include: A robust speech encryption system based on dna addition and chaotic maps;efficient energy attentive and fault recognition mechanism in distributed wireless sensor networks: A review;Digital color documents authentication using QR code based on digital watermarking;comparative study of regression models and deep learning models for insurance cost prediction;extending borda rule under q-rung orthopair fuzzy set for multi-attribute group decision-making;a novel approach for operational performance based mail sorting facility layout selection using grey relational analysis: A case on India speed post service industry;recognition of handwritten meitei mayek and english alphabets using combination of spatial features;a self-adaptive differential evolution with local search applied to multimodal optimization;Simulation of friction stir welding of aluminium alloy AA5052 – tailor welded blanks;Information systems success: Extending the theoretical model from IT business value perspective;towards an automatic detection of sensitive information in mongo database;Business growth using open source e-commerce and ERP in small business;directional multiscale feature extraction for biomedical image indexing and retrieval using contourlet transform;Link quality and QoE aware predictive vertical handoff mechanism for video streaming in urban VANET;Performance comparison of PID and ANFIS controller for stabilization of x and x-y inverted pendulums;modeling hybrid indicators for stock index prediction;XOR encryption techniques of video steganography: A comparative analysis;Intention to use m–banking: the role of E–WOM;background modeling using deep-variational autoencoder.

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18th international conference on Computational Methods in Systems Biology, CMSB 2020

18th International Conference on Computational Methods in Sy...

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18th international conference on Computational Methods in Systems Biology, CMSB 2020

ISBN: (纸本)9783030603267

the proceedings contain 22 papers. the special focus in this conference is on Computational Methods in Systems Biology. the topics include: Tutorial: the colomoto interactive notebook, accessible and reproducible computational analyses for qualitative biological networks;integrating experimental pharmacology and systems biology for gpcr drug discovery;control Strategy Identification via Trap Spaces in Boolean Networks;comparing Probabilistic and Logic programming Approaches to Predict the Effects of Enzymes in a Neurodegenerative Disease Model;growth Dependent Computation of Chokepoints in Metabolic Networks;what is a Cell Cycle Checkpoint? the TotemBioNet Answer;stationary Distributions and Metastable Behaviour for Self-regulating Proteins with General Lifetime Distributions;core Models of Receptor Reactions to Evaluate Basic Pathway Designs Enabling Heterogeneous Commitments to Apoptosis;Parallel Parameter Synthesis for Multi-affine Hybrid Systems from Hybrid CTL Specifications;classifier Construction in Boolean Networks Using Algebraic Methods;qualitative Analysis of Mammalian Circadian Oscillations: Cycle Dynamics and Robustness;on the Complexity of Quadratization for Polynomial Differential Equations;interval Constraint Satisfaction and Optimization for Biological Homeostasis and Multistationarity;Accelerating Reactions at the dna Can Slow Down Transient Gene Expression;eBCSgen: A Software Tool for Biochemical Space Language;fnyzer: A Python Package for the Analysis of Flexible Nets;modRev - Model Revision Tool for Boolean Logical Models of Biological Regulatory Networks;synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision;graphical Conditions for Rate Independence in Chemical Reaction Networks;ABC(SMC)2: Simultaneous Inference and Model Checking of Chemical Reaction Networks;sequential Temporary and Permanent Control of Boolean Networks.

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Impossibility of Sufficiently Simple Chemical Reaction Network Implementations in dna Strand Displacement 1

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18th international conference on Unconventional Computation and Natural Computation (UCNC)

作者： Johnson, Robert F. CALTECH Bioengn Pasadena CA 91125 USA

ISBN: (数字)9783030193119

ISBN: (纸本)9783030193119;9783030193102

dna strand displacement (DSD) has recently become a common technology for constructing molecular devices, with a number of useful systems experimentally demonstrated. To help with DSD system design, various researchers are developing formal definitions to model dna strand displacement systems. With these models a DSD system can be defined, described by a Chemical Reaction Network, simulated, and otherwise analyzed. Meanwhile, the research community is trying to use DSD to do increasingly complex tasks, while also trying to make DSD systems simpler and more robust. I suggest that formal modeling of DSD systems can be used not only to analyze DSD systems, but to guide their design. For instance, one might prove that a DSD system that implements a certain function must use a certain mechanism. As an example, I show that a physically reversible DSD system with no pseudoknots, no effectively trimolecular reactions, and using 4-way but not 3-way branch migration, cannot be a systematic implementation of reactions of the form A reversible arrow B that uses a constant number of toehold domains and does not crosstalk when multiple reactions of that type are combined. this result is a tight lower bound in the sense that, for most of those conditions, removing just that one condition makes the desired DSD system possible. I conjecture that a system with the same restrictions using both 3-way and 4-way branch migration still cannot systematically implement the reaction A + B reversible arrow C.

关键词： dna

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Comprehensive Evaluation of BERT Model for dna-Language for Prediction of dna Sequence Binding Specificities in Fine-Tuning Phase 18th

Comprehensive Evaluation of BERT Model for DNA-Language for ...

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18th international conference on Intelligent computing (ICIC)

作者： Tan, Xianbao Yuan, Changan Wu, Hongjie Zhao, Xingming Tongji Univ Sch Elect & Informat Engn Inst Machine Learning & Syst Biol Shanghai 201804 Peoples R China Guangxi Acad Sci Nanning 530007 Peoples R China Guangxi Acad Sci Guangxi Key Lab Human Machine Interact & Intellig Nanning Peoples R China Suzhou Univ Sci & Technol Sch Elect & Informat Engn Suzhou 215009 Peoples R China Fudan Univ Inst Sci & Technol Brain Inspired Intelligence IS Shanghai 200433 Peoples R China

ISBN: (纸本)9783031138294;9783031138287

Deciphering the language of dna has always been one of the difficult problems that informatics methods need to deal with. In order to meet this challenge, many deep learning models have been proposed. Among them, dna-language models based on pre-trained Bidirectional Encoder Representations from Transformers (BERT) is one of the methods with excellent performance in recognition accuracy. At the same time, most studies focus on the design of the model structure, while for pre-trained dna-language models such as BERT, there are relatively few studies on the influence of the fine-tuning stage on model performance. To this end, we select dnaBERT, the first pre-trained BERT model for dna-language, to analysis its fine-tuning performances with different parameters settings in motif mining tasks, which are one of the most classic missions for prediction of dna sequence binding specificities. Furthermore, we compare the fine-tuning results to the performances of previously existing models by dividing different types of datasets. the results show that in fine-tuning phase, different hyper-parameters combinations and types of dataset do have significant impact on model performance.

关键词： Motif mining Sequence binding specificities Fine-tuning analysis dna-language model BERT

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Parallel Solutions to the k-difference Primer Problem 18th

Parallel Solutions to the <i>k</i>-difference Primer Problem

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18th international conference on Computational Science (ICCS)

作者： Feuser, Leandro Moreano, Nahri Univ Fed Mato Grosso do Sul Sch Comp Campo Grande MS Brazil

ISBN: (纸本)9783319936987;9783319936970

this paper presents parallel solutions to the k-difference primer problem, targeting multicore processors and GPUs. this problem consists of finding the shortest substrings of one sequence with at least k differences from another sequence. the sequences found in the solution are candidate regions to contain primers used by biologists to amplify a dna sequence in laboratory. To the authors' knowledge, these are the first parallel solutions proposed for the k-difference primer problem. We identified two forms, coarse- and fine-grained, of exploiting parallelism while solving the problem. Several optimizations were applied to the solutions, such as synchronization overhead reduction, tiling, and speculative prefetch, allowing the analysis of very long sequences in a reduced execution time. In an experimental performance evaluation using real dna sequences, the best OpenMP (in a quad-core processor) and CUDA solutions produced speedups up to 5.6 and 72.8, respectively, when compared to the best sequential solution. Even when the sequences length and the number of differences k increase, the performance is not affected. the best sequential, OpenMP, and CUDA solutions achieved the throughput of 0.16, 0.94, and 11.85 billions symbol comparisons per second, respectively, emphasizing the performance gain of the CUDA solution, which reached 100% of GPU occupancy.

关键词： Inexact matching High performance computing Parallelism Multicore processor GPU

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