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SMRI: A New Method for siRNA Design for COVID-19 Therapy

Journal of Computer Science & Technology 2022年第4期37卷 991-1002页

作者： Meng-Xin Chen Xiao-Dong Zhu Hao Zhang Zhen Liu Yuan-Ning Liu College of Software Jilin UniversityChangchun 130012China Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education Jilin UniversityChangchun 130012China College of Computer Science and Technology Jilin UniversityChangchun 130012China Graduate School of Engineering Nagasaki Institute of Applied ScienceNagasaki 851-0193Japan

First discovered in Wuhan, China, SARS-CoV-2 is a highly pathogenic novel coronavirus, which rapidly spreads globally and becomes a pandemic with no vaccine and limited distinctive clinical drugs available till March 13th, 2020. Ribonucleic Acid interference (RNAi) technology, a gene-silencing technology that targets mRNA, can cause damage to RNA viruses effectively. Here, we report a new efficient small interfering RNA (siRNA) design method named Simple Multiple Rules Intelligent Method (SMRI) to propose a new solution of the treatment of COVID-19. To be specific, this study proposes a new model named Base Preference and Thermodynamic Characteristic model (BPTC model) indicating the siRNA silencing efficiency and a new index named siRNA Extended Rules index (SER index) based on the BPTC model to screen high-efficiency siRNAs and filter out the siRNAs that are difficult to take effect or synthesize as a part of the SMRI method, which is more robust and efficient than the traditional statistical indicators under the same circumstances. Besides, to silence the spike protein of SARS-CoV-2 to invade cells, this study further puts forward the SMRI method to search candidate high-efficiency siRNAs on SARS-CoV-2's S gene. This study is one of the early studies applying RNAi therapy to the COVID-19 treatment. According to the analysis, the average value of predicted interference efficiency of the candidate siRNAs designed by the SMRI method is comparable to that of the mainstream siRNA design algorithms. Moreover, the SMRI method ensures that the designed siRNAs have more than three base mismatches with human genes, thus avoiding silencing normal human genes. This is not considered by other mainstream methods, thereby the five candidate high-efficiency siRNAs which are easy to take effect or synthesize and much safer for human body are obtained by our SMRI method, which provide a new safer, small dosage and long efficacy solution for the treatment of COVID-19.

关键词： COVID-19 SARS-CoV-2 RibonucleicAcid interference

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Caption-Aware Multimodal Relation Extraction with Mutual Information Maximization 24

Caption-Aware Multimodal Relation Extraction with Mutual Inf...

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32nd ACM International Conference on Multimedia, MM 2024

作者： Zhang, Zefan Zhang, Weiqi Li, Yanhui Bai, Tian College of Computer Science and Technology Jilin University Changchun China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Changchun China

ISBN: (纸本)9798400706868

Multimodal Relation Extraction (MRE) has achieved great improvements. However, modern MRE models are easily affected by irrelevant objects during multimodal alignment which are called error sensitivity issues. The main reason is that visual features are not fully aligned with textual features and the reasoning process may suppress redundant and noisy information at the risk of losing critical information. In light of this, we propose a Caption-Aware Multimodal Relation Extraction Network with Mutual Information Maximization (CAMIM). Specifically, we first generate detailed image captions through the Large Language Model (LLM). Then, the Caption-Aware Module (CAM) hierarchically aligns the fine-grained visual entities and textual entities for reasoning. In addition, for preserving crucial information within different modalities, we leverage a Mutual Information Maximization method to regulate the multimodal reasoning module. Experiments show that our model outperforms the state-of-the-art MRE models on the benchmark dataset MNRE. Further ablation studies prove the pluggable and effective performance of our Caption-Aware Module and Mutual Information Maximization method. Our code is available at https://***/zefanZhang-cn/CAMIM. © 2024 ACM.

关键词： Modeling languages

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A Method for Extracting Electronic Medical Record Entities by Fusing Multichannel Self-Attention Mechanism with Location Relationship Features 9th

A Method for Extracting Electronic Medical Record Entities b...

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9th International Conference of Pioneering Computer Scientists, Engineers and Educators, ICPCSEE 2023

作者： Xu, Hongyan Wang, Hong Feng, Yong Wang, Rongbing Zhang, Yonggang College of Information Liaoning University Shenyang110036 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun130012 China

ISBN: (纸本)9789819959709

With the implementation of the "Internet+" strategy, electronic medical records are generally applied in the medical field. Deep mining of electronic medical record content data is an effective means to obtain medical knowledge and analyse patients’ states, but the existing methods for extracting entities from electronic medical records have problems of redundant information, overlapping entities, and low accuracy rates. Therefore, this paper proposes an entity extraction method for electronic medical records based on the network framework of BERT-BiLSTM, which incorporates a multichannel self-attention mechanism and location relationship features. First, the text input sequence was encoded using the BERT-BiLSTM network framework, and the global semantic information of the sentence was mined more deeply using the multichannel self-attention mechanism. Then, the position relation characteristic was used to extract the local semantic message of the text, and the position relation characteristic of the word and the position embedding matrix of the whole sentence were obtained. Next, the extracted global semantic information was stitched with the positional embedding matrix of the sentence to obtain the current entity classification matrix. Finally, the proposed method was validated on the dataset of Chinese medical text entity relationship extraction and the 2010i2b2/VA relationship corpus, and the experimental results indicate that the proposed method surpasses existing methods in terms of precision, recall, F1 value and training time. © 2023, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

关键词： Location

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K-means on commodity GPUs with CUDA

K-means on commodity GPUs with CUDA

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2009 WRI World Congress on Computer Science and Information engineering, CSIE 2009

作者： Bai, Hong-Tao He, Li-Li Ouyang, Dan-Tong Li, Zhan-Shan Li, He College of Computer Science and Technology Jilin University 130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University 130012 China

ISBN: (纸本)9780769535074

K-means algorithm is one of the most famous unsupervised clustering algorithms. Many theoretical improvements for the performance of original algorithms have been put forward, while almost all of them are based on Single Instruction Single Data (SISD) architecture processors (CPUs), which partly ignored the inherent paralleled characteristic of the algorithms. In this paper, a novel Single Instruction Multiple Data (SIMD) architecture processors (GPUs) based k-means algorithm is proposed. In this algorithm, in order to accelerate compute-intensive portions of traditional k-means, both data objects assignment and k centroids recalculation are off-loaded to the GPU in parallel. We have implemented this GPU-based k-means on the newest generation GPU with Compute Unified Device Architecture (CUDA). The numerical experiments demonstrated that the speed of GPU-based k-means could reach as high as 40 times of the CPU-based k-means. © 2008 IEEE.

关键词： Graphics processing unit

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A novel approach for modeling Direction Relations between Uncertain Regions

A novel approach for modeling Direction Relations between Un...

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2010 International Conference on Machine Vision and Human-Machine Interface, MVHI 2010

作者： Dong, Yiqun Liu, Dayou Wang, Fang Tian, Ye College of Computer Science and Technology Jilin University Changchun China Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Changchun China

ISBN: (纸本)9780769540092

Conventional models based on crisp regions can not deal with the Direction Relations between Uncertain Regions (DRUR). Using broad boundary to represent the uncertain boundary, a novel approach is proposed based on model SK for modeling DRUR in this paper. DRUR are described as the combinations of basic cardinal direction relations, then we study the composition of DRUR, and a method is put forward for calculating this composition. © 2010 IEEE.

关键词： Board boundary Composition Direction relations Model SK Uncertain regions Plant uncertain Uncertainty Modeling Boundary

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A study on parallel semantics of constraint logic rograms

A study on parallel semantics of constraint logic rograms

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International Conference on Machine Learning and Cybernetics, ICMLC 2005

作者： Sun, Ji.-Gui Zhang, Yong-Gang College of Computer Science and Technology Jilin University Changchun 130012 China Key Laboratory for Symbolic Computation and Knowledge Engineering Ministry of Education Changchun 130012 China

ISBN: (纸本)078039092X

This paper presents two parallel semantics of constraint logic programs: multiset answer constraint semantics and game semantics, which differ entirely from the traditional semantics. When giving the first semantics, it adopts the s-semantics approach, whose aim is to find notions of models which really capture the operational semantics. And it defines the program equivalence based on multiset answer constraint. Then it investigates the game semantics and proves that it is consistent with traditional operational semantics. On the basis of these two semantics, programmers can comprehend the programs deeply and develop more sound parallel constraint logic programming systems. Finally, it gives the conclusions and future work. © 2005 IEEE.

关键词： Semantics

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A Morphology Focused Cell Detection Model for Histopathology Images

A Morphology Focused Cell Detection Model for Histopathology...

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2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023

作者： Wang, Zhe Wei, Fangyue Guo, Shuyu Che, Xiaoting Bai, Tian Jilin University College of Computer Science and Technology Changchun China Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Changchun China

ISBN: (纸本)9798350337488

The accurate automatic recognition of cell locations is of great significance for downstream tasks in pathology. Due to the various size and distribution of different cell types, previous cell detection methods applied fixed circles as labels to localize cell position by default, which makes less precise and more difficult to adapt various cell morphology. In this paper, we integrate adaptive areas of interests based on morphology to address the limitation in detecting cells with irregular shapes in pathological images. Moreover, a EGSI module is proposed to extract global distribution of cells in slices, which enables model to acquire more rich semantic information. We exhibit favorable F1 score of our method on four public datasets. Experimental results demonstrate that the proposed method could detect cells more accurately in those images with different cell morphologies and dense cell distribution. © 2023 IEEE.

关键词： cell detection cellular morphology digital pathology medical image analysis

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Singleton arc consistency based on failure-first principle

Singleton arc consistency based on failure-first principle

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International Conference on Machine Learning and Cybernetics

作者： Li, Zhan-Shan Xing, Shi-Mei Yang, Feng-Jie Du, Hui-Ying Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Changchun 130012 China College of Computer Science and Technology Changchun 130012 China

ISBN: (纸本)9781424465262

Constraint satisfaction problems play a significant role in the field of Artificial Intelligence. Reducing the search space can improve the efficiency of solving the problems before the search of solutions. Applying in preprocessing step, arc consistency technique can remove some values which are arc inconsistent, so that it can reduce the search space. Using heuristic strategies can improve the efficiency of the algorithms. In this paper we propose a new singleton arc consistency algorithm based on failure-first principle, which improves the practical time efficiency through the earlier detection of variables which contain null values and removal of the values which are arc inconsistency during the preprocessing step. © 2010 IEEE.

关键词： Constraint satisfaction problems

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Solving SAT problem with a revised hitting set algorithm

Solving SAT problem with a revised hitting set algorithm

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2010 2nd International Conference on Future Computer and Communication, ICFCC 2010

作者： Xu, Youjun Ouyang, Dantong Ye, Yuxin He, Jialiang College of Computer Science and Technology Jilin University Changchun China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun China

ISBN: (纸本)9781424458226

The satisfiability(SAT) problem is a core problem of artificial intelligence. Research findings in SAT are widely used in many areas. The main methods solving SAT problem are resolution principle, tableau calculus and extension rule. Besides methods mentioned above, we find that the SAT problem can be solved with hitting set algorithms. If a set of clause is satisfiable, there must be a hitting set of the clause set which containing no complementary pairs of literals. Algorithm NEWHS-tree is an efficient hitting set algorithm proposed by Ouyang. RNHST proposed in this paper is a revised algorithm in respect of NEWHS-tree. It judges the satisfiability of a clause set by confirming the existence of the set's hitting set without complementary pairs of literals. The test result shows that RNHST is an efficient algorithm. ©2010 IEEE.

关键词： Forestry

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Quasi-periodic Solutions of the General Nonlinear Beam Equations

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Communications in Mathematical Research 2012年第1期28卷 51-64页

作者： GAO YI-XIAN College of Mathematics and Statistics Northeast Normal University Changchun 130024 Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun 130012

In this paper, one-dimensional （1D） nonlinear beam equations of the form utt - uxx ＋ uxxxx ＋ mu = f （u） with Dirichlet boundary conditions are considered, where the nonlinearity f is an analytic, odd function and f（u） = O（u3）. It is proved that for all m ∈ （0, M＊]  R （M＊ is a fixed large number）, but a set of small Lebesgue measure, the above equations admit small-amplitude quasi-periodic solutions corresponding to finite dimensional invariant tori for an associated infinite dimensional dynamical system. The proof is based on an infinite dimensional KAM theory and a partial Birkhoff normal form technique.

关键词： beam equation KAM theorem quasi-periodic solution partial Birkhoffnormal form

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