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关键词： Poly(A) signals   Deep learning   Machine learning   Signal processing   Computer science   Bioinformatics   SITES   BIOINFORMATICS   RECOGNITION   SYSTEM   START  

摘要： Polyadenylation signals (PAS) are found in most protein-coding and some non-coding genes in eukaryotes. Their accurate recognition improves understanding gene regulation mechanisms and recognition of the 3'-end of transcribed gene regions where premature or alternate transcription ends may lead to various diseases. Although different methods and tools for in-silico prediction of genomic signals have been proposed, the correct identification of PAS in genomic DNA remains challenging due to a vast number of non-relevant hexamers identical to PAS hexamers. In this study, we developed a novel method for PAS recognition. The method is implemented in a hybrid PAS recognition model (HybPAS), which is based on deep neural networks (DNNs) and logistic regression models (LRMs). One of such models is developed for each of the 12 most frequent human PAS hexamers. DNN models appeared the best for eight PAS types (including the two most frequent PAS hexamers), while LRM appeared best for the remaining four PAS types. The new models use different combinations of signal processing based, statistical, and sequence-based features as input. The results obtained on human genomic data show that HybPAS outperforms the well-tuned state-of-the-art Omni-PolyA models, reducing the classification error for different PAS hexamers by up to 57.35% for 10 out of 12 PAS types, with Omni-PolyA models being better for two PAS types. For the most frequent PAS types, 'AATAAA' and 'ATTAAA', HybPAS reduced the error rate by 35.14% and 34.48%, respectively. On average, HybPAS reduces the error by 30.29%. HybPAS is implemented partly in Python and in MATLAB available at https://***/EMANG-KAUST/PolyA_PredictionLRM_DNN.

关键词： CHSH inequality   Quantum entanglement   Quantum structures   Corpuses of documents   Natural language processing  

摘要： We work out a quantum-theoretic model in complex Hilbert space of a recently performed test on co-occurrencies of two concepts and their combination in retrieval processes on specific corpuses of documents. The test violated the Clauser-Horne-Shimony-Holt version of Bell’s inequalities (‘CHSH inequality’), thus indicating the presence of entanglement between the combined concepts. We make use of a recently elaborated ‘entanglement scheme’ and represent the collected data in the tensor product of Hilbert spaces of the individual concepts, showing that the identified violation is due to the presence of a strong form of entanglement, involving both states and measurements and reflecting the meaning connection between the component concepts. These results provide a significant confirmation of the presence of quantum structures in corpuses of documents, like it is the case for the entanglement identified in human cognition.

ISBN: (纸本)9781450366496

摘要： The distinction between sciences is becoming increasingly more artificial - an approach from one area can be easily applied to the other. More exciting research nowadays is happening perhaps at the interfaces of disciplines like Physics, Mathematics and Computer Science. How do these interfaces emerge and interact? For instance, is there a specific pattern in which these fields cite each other? In this article, we investigate a collection of more than 1.2 million papers from three different scientific disciplines - Physics, Mathematics, and Computer Science. We show how over a timescale the citation patterns from the core science fields (Physics, Mathematics) to the applied and fast-growing field of Computer Science have drastically increased. Further, we observe how certain subfields in these disciplines are shrinking while others are becoming tremendously popular. For instance, an intriguing observation is that citations from Mathematics to the subfield of machine learning in Computer Science in recent times are exponentially increasing. Copyright © 2019, The Authors. All rights reserved.

关键词： Action research   lesson study   computer science   conflict management   engineering education   soft skills   GENDER  

摘要： This article explores one group's use of action research (AR) and lesson study in three US university-level computer science courses affecting 85 undergraduate computer science and engineering students. It offers an overview of three areas including AR, lesson study, and engineering soft skills. The research group identified a problem: undergraduate engineering student soft skill understanding. The group collaborated to enhance participant engagement with this problem by utilizing one lesson focused on soft skills over three research lesson iterations in three distinct university semesters (2017-2018). Field notes were the main data collection method. Observational field notes were recorded in the three research lesson iterations, and themes from the notes were identified. The group valued peer interactions, and the research lesson adaptations as well as pedagogical changes were based on evidence. Four themes were identified, and participant comments were considered as the lessons became more focused . The research group argues that AR and lesson study are separate and distinct ventures based on this yearlong experience, which is counter to some other literature presented. Implications are large for all stakeholders interested in AR, lesson study, soft skill utilization, conflict management, and participant learning impact. Possibilities for enhanced participant engagement exists with honed lesson pedagogy.

摘要： The article reports on the move by the Southern Indiana District Court to prepare as the U.S. Department of Defense moves forward with the resumption of executions. Doria Lynch, public information officer of the court, has issued a statement regarding the response by prisoners and their attorneys to the department's decision. U.S. Attorney General William Barr has directed the Federal Bureau of Prisons to clear the way for lethal injections.

关键词： Formal logic   Logic machines   Computer science  

摘要： I critically review Raymond Turner’s Computational Artifacts – Towards a Philosophy of Computer Science by placing beside his position a rather different one, according to which computer science is a branch of, and is therefore subsumed by, immaterial formal logic.

关键词： Computer science   DNA computing  

摘要： An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

关键词： 文献检索与计算机在材料科学中的应用   雨课堂   混合式教学  

摘要： “文献检索与计算机在材料科学中的应用”是材料科学类本科专业教学中重要的专业基础必修课程。针对传统课堂存在的问题,利用“雨课堂”对该门课程实施了混合式教学,从过程、结果和学生三个方面总结了利用“雨课堂”混合式教学的经验,为提高应用型专业课程的教学效果,增加学生综合运用知识的能力提供一些参考。