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Correction of Read Biases Induced by Complex Reference Genome Regions for Improving Copy Number Variation Detection Using a Gaussian Mixture Model

Correction of Read Biases Induced by Complex Reference Genom...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Xuwen Wang Zhili Chang Shenjie Wang Ruoyu Liu Yuqian Liu Xiaoyan Zhu Yang Shao Xin Lai Shuanying Yang Jiayin Wang Department of Respiratory Medicine The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an China School of Computer Science and Technology Xi'an Jiaotong University Xi'an China Shaanxi Engineering Research Center of Medical and Health Big Data Xi'an Jiaotong University Xi'an China Nanjing Geneseeq Technology INC.

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

Copy number variations are crucial in cancer research, but their detection through next-generation sequencing is often hindered by read biases, particularly in complex genomic regions. Existing bias-correction methods address common issues like GC content but often fail in regions with repetitive sequences or segmental duplications, leading to false-positive CNVs. We propose refMask, a hybrid Gaussian model-based method that dynamically identifies low-confidence regions in the reference genome, correcting read biases and improving CNV detection accuracy. By integrating features from hg38 and T2T genomes, refMask tailors a custom blacklist for each sequencing sample, enhancing the reliability of CNV detection across diverse conditions. Our method provides a more accurate and flexible solution compared to current fixed blacklists, offering improved performance in challenging genomic regions.

关键词： Sequential analysis Accuracy Genomics Feature extraction Blocklists Reliability Bioinformatics Next generation networking Gaussian mixture model Cancer

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Dear-DIA^(XMBD): Deep Autoencoder Enables Deconvolution of data-Independent Acquisition Proteomics

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research 2024年第1期6卷 707-720页

作者： Qingzu He Chuan-Qi Zhong Xiang Li Huan Guo Yiming Li Mingxuan Gao Rongshan Yu Xianming Liu Fangfei Zhang Donghui Guo Fangfu Ye Tiannan Guo Jianwei Shuai Jiahuai Han Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials ResearchXiamen UniversityXiamen 361005China Oujiang Laboratory(Zhejiang Lab for Regenerative Medicine Vision and Brain Health)and Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang 325001China School of Life Sciences Xiamen UniversityXiamen 361102China State Key Laboratory of Cellular Stress Biology Innovation Center for Cell Signaling NetworkXiamen 361102China Department of Computer Science Xiamen UniversityXiamen 361005China National Institute for Data Science in Health and Medicine School of MedicineXiamen UniversityXiamen 361102China Bruker(Beijing)Scientific Technology Co.Ltd. BeijingChina Westlake Laboratory of Life Sciences and Biomedicine Key Laboratory of Structural Biology of Zhejiang ProvinceSchool of Life SciencesWestlake University18 Shilongshan RoadHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced Study18 Shilongshan RoadHangzhou 310024China Westlake Omics Ltd. Yunmeng Road 1HangzhouChina Department of Electronic Engineering Xiamen UniversityXiamen 361005China

data-independent acquisition(DIA)technology for protein identification from mass spectrometry and related algorithms is developing *** spectrum-centric analysis of DIA data without the use of spectra library from data-dependent acquisition data represents a promising *** this paper,we proposed an untargeted analysis method,Dear-DIA^(XMBD),for direct analysis of DIA ***-DIA^(XMBD) first integrates the deep variational autoencoder and triplet loss to learn the representations of the extracted fragment ion chromatograms,then uses the k-means clustering algorithm to aggregate fragments with similar representations into the same classes,and finally establishes the inverted index tables to determine the precursors of fragment clusters between precursors and peptides and between fragments and *** show that Dear-DIA^(XMBD) performs superiorly with the highly complicated DIA data of different species obtained by different instrument platforms.

关键词： Deep Auto Independent

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Systematic Biases in LLM Simulations of Debates

arXiv

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arXiv 2024年

作者： Taubenfeld, Amir Dover, Yaniv Reichart, Roi Goldstein, Ariel The Hebrew University of Jerusalem School of Computer Science and Engineering Google Research United States The Hebrew University Business School Jerusalem Israel Federmann Center for the Study of Rationality Hebrew University Jerusalem Israel Faculty of Data and Decision Sciences Technion Department of Cognitive and Brain Sciences Hebrew University Jerusalem Israel

The emergence of Large Language Models (LLMs), has opened exciting possibilities for constructing computational simulations designed to replicate human behavior accurately. Current research suggests that LLM-based agents become increasingly human-like in their performance, sparking interest in using these ai agents as substitutes for human participants in behavioral studies. However, LLMs are complex statistical learners without straightforward deductive rules, making them prone to unexpected behaviors. Hence, it is crucial to study and pinpoint the key behavioral distinctions between humans and LLM-based agents. In this study, we highlight the limitations of LLMs in simulating human interactions, particularly focusing on LLMs’ ability to simulate political debates on topics that are important aspects of people’s day-to-day lives and decision-making processes. Our findings indicate a tendency for LLM agents to conform to the model’s inherent social biases despite being directed to debate from certain political perspectives. This tendency results in behavioral patterns that seem to deviate from well-established social dynamics among humans. We reinforce these observations using an automatic self-fine-tuning method, which enables us to manipulate the biases within the LLM and demonstrate that agents subsequently align with the altered biases. These results underscore the need for further research to develop methods that help agents overcome these biases, a critical step toward creating more realistic simulations. © 2024, CC BY.

关键词： Digital elevation model

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Blister Package Classification Using ResNet-101 for Identification of Medication 25

Blister Package Classification Using ResNet-101 for Identifi...

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25th International computer science and engineering Conference, ICSEC 2021

作者： Hnoohom, Narit Maitrichit, Nagorn Chotivatunyu, Pitchaya Sornlertlamvanich, Virach Mekruksavanich, Sakorn Jitpattanakul, Anuchit Mahidol University Image Information and Intelligence Laboratory Department of Computer Engineering Faculty of Engineering Nakorn Pathom Thailand Musashino University Faculty of Data Science Tokyo Japan University of Phayao School of Information and Communication Technology Department of Computer Engineering Phayao Thailand Intelligent and Nonlinear Dynamic Innovations Research Center King Mongkut's University of Technology North Bangkok Faculty of Applied Science Department of Mathematics Bangkok Thailand

ISBN: (纸本)9781665411974

This research aimed to fine-Tune image classification with deep learning techniques to verify the dispensing of prescriptions in hospitals. The proposed approach will be able to help pharmacies reduce the errors that lead to patients receiving the wrong medications. The image classification model uses a double-side transformed image dataset with download from Highlighted Deep Learning (HDL) paper. The dataset collected two-hundred seventy-Two images for types of medicine blister packs, including 72 images of front-side and backside merged with a horizontal cropped background, which were used for training the model. The blister package image dataset uses a deep learning model with a ResNet-101 pre-Trained model from the TensorFlow framework. The experimental results indicated that the TensorFlow framework achieved higher precision, recall, and F1-score than the Caffe framework. A ResNet-101 model with histogram equalization in the front and backside has the highest accuracy at 100 percent. © 2021 IEEE.

关键词： Image classification

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Quantum reversible circuits for multiplicative inverse

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EPJ Quantum Technology 2022年第1期9卷 1-17页

作者： Luo, Qing-bin Yang, Guo-wu Li, Xiao-yu Li, Qiang Department of Computer Science and Technology School of Information Engineering Hubei Minzu University Enshi China School of Information and Software Engineering University of Electronic Science and Technology of China Chengdu China Big data research Center & School of Computer Science and Engineering University of Electronic Science and Technology of China Chengdu China Advanced Cryptography and System Security Key Laboratory of Sichuan Province Chengdu University of Information Technology Chengdu China

The synthesis of quantum circuits for multiplicative inverse over $\operatorname{GF}(2^{8})$ are discussed in this paper. We first convert the multiplicative inverse operation in $\operatorname{GF}(2^{8})$ to arithmetic operations in the composite field $\operatorname{GF}((2^{4})^{2})$ , and then discuss the expressions of the square calculation, the inversion calculation and the multiplication calculation separately in the finite field $\operatorname{GF}(2^{4})$ , where the expressions of multiplication calculation in $\operatorname{GF}(2^{4})$ are given directly in $\operatorname{GF}(2^{4})$ and given through being transformed into the composite field $\operatorname{GF}((2^{2})^{2})$ . Then the quantum circuits of these calculations are realized one by one. Finally, two quantum circuits for multiplicative inverse over $\operatorname{GF}(2^{8})$ are synthesized. They both use 21 qubits, the first quantum circuit uses 55 Toffoli gates and 107 CNOT gates and the second one uses 37 Toffoli gates and 209 CNOT gates. As an example of the application of multiplication inverse, we apply these quantum circuits to the implementations of the S-box quantum circuit of the AES cryptographic algorithm. Two quantum circuits for implementing the S-box of the AES cryptographic algorithm are presented. The first quantum circuit uses 21 qubits, 55 Toffoli gates, 131 CNOT gates and 4 NOT gates and the second one uses 21 qubits, 37 Toffoli gates, 233 CNOT gates and 4 NOT gates. Through the evaluation of quantum cost, the two quantum circuits of the S-box of AES cryptographic algorithm use less quantum resources than the existing schemes.

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A Classification-by-Retrieval Framework for Few-Shot Anomaly Detection to Detect API Injection Attacks

arXiv

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arXiv 2024年

作者： Aharon, Udi Dubin, Ran Dvir, Amit Hajaj, Chen School of Computer Science Ariel University Golan Heights 1 Ariel4077625 Israel Ariel Cyber Innovation Center Ariel University Golan Heights 1 Ariel4077625 Israel Data Science and Artificial Intelligence Research Center Ariel University Golan Heights 1 Ariel4077625 Israel Department of Industrial Engineering & Management Ariel University Golan Heights 1 Ariel4077625 Israel

application Programming Interface (API) Injection attacks refer to the unauthorized or malicious use of APIs, which are often exploited to gain access to sensitive data or manipulate online systems for illicit purposes. Identifying actors that deceitfully utilize an API poses a demanding problem. Although there have been notable advancements and contributions in the field of API security, there remains a significant challenge when dealing with attackers who use novel approaches that don’t match the well-known payloads commonly seen in attacks. Also, attackers may exploit standard functionalities unconventionally and with objectives surpassing their intended boundaries. Thus, API security needs to be more sophisticated and dynamic than ever, with advanced computational intelligence methods, such as machine learning models that can quickly identify and respond to abnormal behavior. In response to these challenges, we propose a novel unsupervised few-shot anomaly detection framework composed of two main parts: First, we train a dedicated generic language model for API based on FastText embedding. Next, we use Approximate Nearest Neighbor search in a classification-by-retrieval approach. Our framework allows for training a fast, lightweight classification model using only a few examples of normal API requests. We evaluated the performance of our framework using the CSIC 2010 and ATRDF 2023 datasets. The results demonstrate that our framework improves API attack detection accuracy compared to the state-of-the-art (SOTA) unsupervised anomaly detection baselines. © 2024, CC BY-NC-ND.

关键词： Anomaly detection

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Prediction New Cases of COVID-19 in Indonesia Using Vector Autoregression (VAR) and Long-Short Term Memory (LSTM) Methods

Prediction New Cases of COVID-19 in Indonesia Using Vector A...

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2021 International Conference on Artificial Intelligence and Big data Analytics, ICaiBDA 2021

作者： Danistya, Daffa Rahmansyah Qaulifa, Fahira Ramadani, Yovi Adhi Nurma Yulita, Intan Ardisasmita, Mulya Nurmansyah Agustian, Dwi Research Center for Artificial Intelligence and Big Data Padjadjaran University Bandung Indonesia Department of Electrical Engineering Brawijaya University Malang Indonesia Department of Electrical Engineering Telkom University Bandung Indonesia Department of Informatics Engineering Semarang University Semarang Indonesia Department of Computer Science Padjadjaran University Bandung Indonesia Department of Public Health Padjadjaran University Bandun Indonesia

ISBN: (纸本)9781665408905

The addition of Covid-19 cases is still uncontrolled, especially in Indonesia. Often the addition of Covid-19 cases in Indonesia always experiences a significant upward trend after a slightly loose government policy. This is because the government does not think there will be a spike in cases after cases go down. This is where the importance of predicting new cases of Covid-19 in Indonesia to be a reference for the government in taking policy. With deep learning, the prediction results will be more accurate. The implementation of vector autoregression (VAR) and long-short term memory (LSTM) methods can reach an accretion rate of up to 98%. With this method, the prediction results can be used for the government in anticipating if there is a surge in new cases per day because it has been predicted from the beginning. In fact, this method can predict new cases for up to a year. © 2021 IEEE.

关键词： Long short-term memory

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Tackling data Sparsity and Combinatorial Challenges in Rare Disease Matching with Medical Informed Machine Learning

Tackling Data Sparsity and Combinatorial Challenges in Rare ...

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IEEE International Conference on Big data

作者： Armin Berger Tom Anglim Lagones Lorenz Grigull Lara Fendrich Thiago Bell Henriette Högl Gundula Ernst Ralf Schmidt David Bascom Rafet Sifa Max Lübbering Department of Media Engineering Fraunhofer IAIS Germany Department of Computer Science University of Bonn Germany West-AI - Federal Ministry of Education and Research Germany Department of Health Queensland Australia Griffith University - School of Medicine Australia University Hospital Bonn - Center for Rare Diseases Germany Children’s Network for Chronic Illnesses and Disabilities Germany Department of Medical Psychology Medical School Hannover Germany

ISBN: (数字)9798350362480

ISBN: (纸本)9798350362497

With over 7,000 known rare diseases and a prevalence of less than one in a thousand, rare diseases pose substantial challenges to advanced medical support networks. This study investigates the efficacy of ***, a novel social networking platform designed for individuals affected by rare diseases, including patients, their family members, and medical professionals, addressing data sparsity and combinatorial complexities in user matching. We demonstrate that simple matching heuristics already serve as a decent basis for collecting user feedback on match quality. Leveraging over 10,000 user matching feedback scores from more than 2,000 active users, we evaluate algorithms including collaborative filtering and user embedding similarity with state-of-the-art Large Language Models (LLMs). With a top-10 and top-5 hit-rate of 55% and 37%, respectively, we show that a combination of medical data augmentation and embeddings significantly enhances performance beyond the initial heuristic baseline.

关键词： Social networking (online) Large language models Collaborative filtering Machine learning Big data data augmentation data models Complexity theory Diseases

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Interpreting Industrial IoT data Streams Through Fuzzy Querying With Hysteretic Fuzzy Sets on Apache Kafka

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IEEE Transactions on Fuzzy Systems 2024年第8期32卷 4671-4684页

作者： Bożena Małysiak-Mrozek Bartłomiej Ryba Marek Molęda Che-Lun Hung Witold Pedrycz Weiping Ding Dariusz Mrozek Department of Distributed Systems and Informatic Devices Silesian University of Technology Gliwice Poland Department of Applied Informatics Silesian University of Technology Gliwice Poland Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei City Taiwan Department of Electrical and Computer Engineering University of Alberta Edmonton AB Canada Department of Measurements and Control Systems Silesian University of Technology Gliwice Poland Research Center of Performance and Productivity Analysis Istinye University Istanbul Türkiye School of Artificial Intelligence and Computer Science Nantong University Nantong China Faculty of Data Science City University of Macau Macau China

In industrial settings, querying data streams from Internet of Things (IoT) devices benefits from utilizing elastic criteria to enhance the interpretability of the current state of the monitored environment. Fuzzy sets provide this elasticity, enabling the aggregation and representation of similar values in a human-comprehensible manner. However, many sensor signals exhibit temporal oscillations, leading to varying interpretations of the signal based on its current trend (rising or falling). This hysteresis in signal (and subsequently of the production device) interpretation inspired us to introduce this phenomenon into data stream processing, resulting in the novel concept of hysteretic fuzzy sets. This article demonstrates how fuzzy searching and grouping can be applied to IoT sensor signals in flexible Big data stream processing on Apache Kafka. We illustrate the impact of data stream querying with KSQL queries involving fuzzy sets (encompassing fuzzy filtering of data stream events, fuzzy transformation of data stream attributes, fuzzy grouping, and joining) on the flexibility of executed operations and computational resources utilized by the Kafka processing engine. Finally, our experiments with hysteretic fuzzy sets while analyzing sensor signals in power plants demonstrate that this novel approach effectively reduces the number of alarms while monitoring the state of the production machine.

关键词： Streams Fuzzy sets Internet of Things Big data Monitoring Production Real-time systems

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Estimating Smart Grid Stability with Hybrid RNN+LSTM Deep Learning Approach

Estimating Smart Grid Stability with Hybrid RNN+LSTM Deep Le...

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International Smart Grid Workshop and Certificate Program (ISGWCP)

作者： Saadin Oyucu Şeref Sağıroğlu Ahmet Aksöz Emre Biçer Department of Computer Engineering Faculty of Engineering Adıyaman Türkiye Gazi University Artificial Intelligence and Big Data Analytics Security R&D Center Ankara Türkiye Mobilers Team Sivas Cumhuriyet University Sivas Türkiye Faculty of Engineering and Natural Sciences Battery Research Laboratory Sivas University of Science and Technology Sivas Türkiye

ISBN: (数字)9798350361612

ISBN: (纸本)9798350361629

Smart grids are faced with a range of challenges, such as the development of communication infrastructure, cybersecurity threats, data privacy, and the protection of user information, due to their complex structure. Another key challenge faced by smart grids is the stability issues arising from variable energy sources and consumption patterns. In these complex grid systems where energy demand and supply need to be balanced instantly, stability predictions play a significant role in foreseeing potential disruptions and optimizing energy flow. Therefore, within the scope of this study, a hybrid structure utilizing Recurrent Neural Networks (RNN) and Long Short-Term Memory (LSTM) networks is employed for stability classification to predict grid stability. This hybrid model combines the ability of RNN to recognize relationships between consecutive data points with LSTM’s capability to preserve long-term dependencies. The results obtained indicate that the model exhibited stable performance with accuracy rates of 98.06% and 98.02% at 50 and 100 epochs, respectively. The findings of this study contribute valuable insights to research on the management and stability of smart grids, enabling energy systems to be operated more reliably and efficiently.

关键词： Deep learning data privacy Recurrent neural networks Power system stability Stability analysis data models Smart grids

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