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A drug recommendation system based on response prediction: Integrating gene expression and K-mer fragmentation of drug SMILES using LightGBM

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Intelligence-Based Medicine 2025年 11卷 100206-100206页

作者： Naveed, Sajid Husnain, Mujtaba Department of Computer Science Faculty of Computing The Islamia University of Bahawalpur 63100 Pakistan Department of Software Engineering Faculty of Computing The Islamia University of Bahawalpur 63100 Pakistan

Medical experts and physicians examine the gene expression abnormality in glioblastoma (GBM) cancer patients to identify the drug response. The main objective of this research is to build a machine learning (ML) based model for improve the outcome of cancer medication to save the time and effort of medical practitioners. Developing a drug response recommendation system is our goal that uses the gene expression data of cancer cell lines to predict the response of anticancer drugs in terms of half-maximal inhibitory concentration (IC50). Genetic data from a GBM cancer patient is used as input into a system to predict and recommend the response of multiple anticancer drugs in a particular cancer sample. In this research, we used K-mer molecular fragmentation to process drug SMILES in a novel way, which enabled us to build a competent model that provides drug response. We used the Light Gradient Boosting Machine (LightGBM) regression algorithm and Genomics of Drug Sensitivity of Cancer (GDSC) data for this proposed recommendation system. The results showed that all predicted IC50 values are fall within the range of the real values when examining GBM data. Two drugs, temozolomide and carmustine, were predicted with a Mean Squared Error (MSE) of 0.10 and 0.11 respectively, and 0.41 in unseen test samples. These recommended responses were then verified by expert doctors, who confirmed that the responses to these drugs were very close to the actual response. These recommendation are also effective in slowing the growth of these tumors and improving patients quality of life by monitoring medication effects. © 2025 The Authors

关键词： Drug response recommendation system Drug SMILES Gene expression Glioblastoma K-mer fragmentation LightGBM

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Analyses of Parametric Relation in Ant Colony Approach for Robot Path Planning Problem

Analyses of Parametric Relation in Ant Colony Approach for R...

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IEEE Workshop on Advanced Robotics and its Social Impacts, ARSO

作者： Sudeep Sharan Anh Tong Ngoc Minh Juan José Domínguez-Jiménez Peter Nauth Faculty of Computer Science and Engineering Frankfurt University of Applied Sciences Frankfurt am Main Germany UCASE Software Engineering Group School of Engineering University of Cádiz Cádiz Spain

ISBN: (数字)9798350344639

ISBN: (纸本)9798350344646

One of the most challenging areas of robotics research is the mobile robot vehicle in a complicated obstacle environment. Recently, algorithms for autonomous mobile vehicles have largely been influenced by nature-based algorithms. The swarm behavior of many different organisms, such as ants, fireflies, honey bees, and foxes, is simulated by several algorithms in mobile robot research, and the results are highly interesting and inspiring. In this paper, we took the inspired algorithm as an ant colony which is used to solve the path planning problems for any mobile vehicle/robots. While studying and using the ant colony approaches to solve the problem, we found that the parameter selections are one of the important expects to make the results of any application worse or better. Therefore, we decided to perform the study on the parametric relation in an ant colony approach. The importance of utilization of the Ant Colony optimization (ACO) approach is to control the parameters. In this paper, we analysed/investigated the relationship between the different control parameters of the ACO algorithm and their performance in the resolution of path planning problem. Simulation is performed with different parameter values and by the result analysis, a selection of parameter is presented.

关键词： Ant colony optimization Path planning Organisms Mobile robots

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Development of Low Resource Machine Learning Models for Child Cognitive Ability Assessments 4

Development of Low Resource Machine Learning Models for Chil...

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4th International Conference on Advancements in Computing, ICAC 2022

作者： Kahawanugoda, Adithya Gnanarathna, Kulanika Meegoda, Nilan Monarawila, Randika Samarasinghe, Pradeepa Lindamulage, Asiri Gawesha Department of Computer Science and Software Engineering Faculty of Computing Sri Lanka Institute of Information Technology Malabe Sri Lanka Department of Information Technology Faculty of Computing Sri Lanka Institute of Information Technology Malabe Sri Lanka

ISBN: (纸本)9798350398090

Automated cognitive assessment tools are state-of-the-art in assessing cognition development. Due to the low availability of resources, building automated cognitive ability evaluation tools is challenging. This study focuses on developing machine learning models using a limited amount of data to assess Reasoning IQ, Knowledge IQ, Mental Chronometry and Attention-levels of Sinhala-speaking children between the age of 7 to 9 years. Our solution includes Sinhala speech recognition systems, image classification models, gaze estimation, blink count detection and facial expression recognition models to evaluate the above four cognitive ability measuring factors. Open domain speech recognition has been used to evaluate complex Sinhala child verbal responses and limited vocabulary responses were assessed using an end-to-end speech recognition system, respectively achieving 40.1% WER and 97.14% accuracy. Additionally, the image classification models for handwritten Sinhala letter recognition and two shape recognition models have gained 97%, 89% and 99% accuracy. The linear regression model for attention level evaluation that utilizes the inputs from a combination of eye-gaze estimation, facial expression recognition and blink rate detection models has gained 85% accuracy. © 2022 IEEE.

关键词： Image classification

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GraphMU: Repairing Robustness of Graph Neural Networks via Machine Unlearning

arXiv

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arXiv 2024年

作者： Wu, Tao Cao, Xinwen Wang, Chao Qiao, Shaojie Xian, Xingping Yuan, Lin Cui, Canyixing Liu, Yanbing The School of Cybersecurity and Information Law Chongqing University of Posts and Telecommunications Chongqing400065 China The School of Software Engineering Chengdu University of Information Technology Chengdu610225 China The School of Computer and Information Science Chongqing Normal University Chongqing401331 China Yunnan Key Laboratory of Software Engineering Yunnan650504 China

Graph Neural Networks (GNNs) have demonstrated significant application potential in various fields. However, GNNs are still vulnerable to adversarial attacks. Numerous adversarial defense methods on GNNs are proposed to address the problem of adversarial attacks. However, these methods can only serve as a defense before poisoning, but cannot repair poisoned GNN. Therefore, there is an urgent need for a method to repair poisoned GNN. In this paper, we address this gap by introducing the novel concept of model repair for GNNs. We propose a repair framework, Repairing Robustness of Graph Neural Networks via Machine Unlearning (GraphMU), which aims to fine-tune poisoned GNN to forget adversarial samples without the need for complete retraining. We also introduce a unlearning validation method to ensure that our approach effectively forget specified poisoned data. To evaluate the effectiveness of GraphMU, we explore three fine-tuned subgraph construction scenarios based on the available perturbation information: (i) Known Perturbation Ratios, (ii) Known Complete Knowledge of Perturbations, and (iii) Unknown any Knowledge of Perturbations. Our extensive experiments, conducted across four citation datasets and four adversarial attack scenarios, demonstrate that GraphMU can effectively restore the performance of poisoned GNN. Copyright © 2024, The Authors. All rights reserved.

关键词： Graph neural networks

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Accurate Real-World Co-ordinate Finding and the Object Classification for the Robot Manipulator

Accurate Real-World Co-ordinate Finding and the Object Class...

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Embedded Systems and Artificial Intelligence (ESAI), International Conference on

作者： Sudeep Sharan Hung Do Thanh Peter Nauth Juan José Domínguez-Jiménez Faculty of Computer Science and Engineering Frankfurt University of Applied Sciences Frankfurt am Main Germany UCASE Software Engineering Group School of Engineering University of Cádiz Cádiz Spain

ISBN: (数字)9798331522056

ISBN: (纸本)9798331522063

This paper presents an object detection and classification of the objects using Deep Learning (DL). The integration of object detection algorithms and depth camera developed is capable of providing robots, such as self developed assistive intelligent robot called “ROSWITHA” (RObot System WITH Autonomy) with the ability to detect an object and interpret their surrounding environment. It also provides the real-world coordinates/position of the object in that environment, which helps the robot to perform some applications, such as grabbing and serving, etc. You Only Look Once (YOLO) is one of the most popular object detection algorithms which is treated as a single regression problem and is processed by a single neural network. In this work, the YOLOv5 (YOLO version 5) network is implemented on a depth camera “RealSense” for processing object detection and estimating the position of the objects. The model is trained on reduced/filtered application-required objects (e.g. bottle and cup) from the available COCO dataset, and the training outcome alongside the performance of the overall system was evaluated. The results exhibited a satisfactory performance of the model in accurately detecting and classifying the objects with a high confidence score ranging from the least to $\mathbf{7 2 \%}$ to the highest of $\mathbf{9 0 \%}$. The confidence score could also be adjusted by the user on the developed GUI to attain the most certain predictions.

关键词： YOLO Training Accuracy Robot kinematics Current measurement Robot vision systems Cameras Manipulators Distance measurement Robots

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Smart UML - Assignment Management Tool for UML Diagrams 4

Smart UML - Assignment Management Tool for UML Diagrams

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4th International Conference on Advancements in Computing, ICAC 2022

作者： Weerasinghe, D.N.H. Thiwanka, K.A.T. Jayasith, H.B.C. Onella Natalie, P.A.D. Samantha Rajapaksha, U.U. Karunasena, Anuradha Department of Computer Science and Software Engineering Faculty of Computing Sri Lanka Institute of Information Technology Malabe Sri Lanka Department of Information Technology Faculty of Computing Sri Lanka Institute of Information Technology Malabe Sri Lanka

ISBN: (纸本)9798350398090

The great majority of manual processes have been automated in the current day. Nonetheless, there is no reliable approach for evaluating UML diagrams for plagiarism and correctness. Unified Modeling Language (UML) provides the basis for UML diagrams. UML Diagrams are typically used to graphically express a system's stakeholders, activities, objects, and classes to get a deep knowledge of a particular system. UML diagrams are widely used by industry experts as well as beginners. Class diagrams and use case diagrams are the most commonly used diagrams in UML. Though most computer science-related students get assessed in UML modelling, diagram plagiarism isn't considered in most exams since it's a tedious task to perform. The proposed system automates capturing details in UML diagram components and generating a model answer from the given question scenario to compare the diagrams and calculate the plagiarism percentage with the correction percentage. © 2022 IEEE.

关键词： Unified Modeling Language

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Voice Enabled Intelligent Programming Assistant 4

Voice Enabled Intelligent Programming Assistant

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4th International Conference on Advancements in Computing, ICAC 2022

作者： Wataketiya, Ravindu Chandrasiri, Navinda Kithsiri, Ramesh Malwatta, Hirush Nadeeshani, Madhuka Siriwardana, Samanthi Department of Computer Science and Software Engineering Faculty of Computing Sri Lanka Institute of Information Technology Malabe Sri Lanka Department of Information Technology Faculty of Computing Sri Lanka Institute of Information Technology Malabe Sri Lanka

ISBN: (纸本)9798350398090

In modern era where software development is of vital importance, software developers are challenged with conditions like Repetitive Strain Injury (RSI) which hinders their ability to work effectively. Furthermore, people with difficulties with using their hands also find it challenging to program in the traditional manner. As a solution, coding with one's voice has been experimented with, but current solutions lack interactivity and are harder to use and setup leaving much room for improvement in this domain. In this research work, by using input classifier models with accuracies over 90%, intent classifiers with accuracies over 70%, code parsing and various human computer interaction techniques, we developed a conversationally interactive, programming language agnostic, easy to setup and easy to use Voice Coding Assistant. This will potentially help a global audience of programmers to achieve their goals and improve productivity and lead a healthier life. We have named the system thus developed, "Venic". © 2022 IEEE.

关键词： Human computer interaction

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Smart Farmer Education System for Disease Identification, Severity Assessment and Infestation Management (Brinjal) 17

Smart Farmer Education System for Disease Identification, Se...

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17th IEEE International Conference on Industrial and Information Systems, ICIIS 2023

作者： Bandara, Keshara Vidhanaarachchi, Samitha Nanayakkara, A.A.E. Kulasinghe, Kavindu Rajapakshe, Sanka Wickramasinghe, Asela Yapa, Kanishka Sri Lanka Institute of Information Technology Department of Information Technology New Kandy Road Malabe Sri Lanka Sri Lanka Institute of Information Technology Department of Computer Science and Software Engineering Malabe Sri Lanka University of Ruhuna Faculty of Agriculture Department of Soil Science Mapalana Kamburupitiya Sri Lanka Sri Lanka Institute of Information Technology Department of Computer Systems Engineering Malabe Sri Lanka

ISBN: (纸本)9798350323634

The agriculture industry is one of the most significant sources of foreign exchange and employment in the Sri Lankan market. Therefore, small crops play a crucial role in ensuring the food security of the population as they are integral components of Sri Lankan cuisine. However, industry experts have identified inefficient disease and pest management as a hindrance to production. This issue requires immediate attention and proper action, which can be effectively addressed through the utilization of ICT technologies. Consequently, this research paper proposes a smart system that aims to assist farmers and agriculture professionals by providing them with farmer education, disease and infestation management tools, as well as progression level calculations. The implementation of this system aims to uplift the agriculture industry in Sri Lanka. The developed 'AI-based mobile application system for Brinjal Diseases,' which is based on analyzing the eating patterns of leafhopper damage, presents an innovative approach to identify the most significant threats to Brinjal, specifically focusing on leafhopper damage. This proposed system effectively informs various stakeholders, including the Area Agricultural Research Officer, Seed Certification and Plant Protection Center (SCPPC), Agricultural Service Center, Office of the Register of Pesticides (ROP), Plant Protection Service (PPS), as well as farmers, regarding the dispersion and prevention of brinjal diseases and pest infections. © 2023 IEEE.

关键词： Crowdsourcing

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ETHACA - A Container-Based Cyber Range for Research and Education 29

ETHACA - A Container-Based Cyber Range for Research and Educ...

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29th IEEE International Workshop on computer Aided Modeling and Design of Communication Links and Networks, CAMAD 2024

作者： Chouliaras, Nestoras Kantzavelou, Ioanna Pantziou, Grammati Maglaras, Leandros Chouliara-Sidera, Panagiota Adamakos, Antonis Chalatsakos, Panagiotis University of West Attica Department of Informatics and Computer Engineering Athens Greece School of Computing Edinburgh Napier University EdinburghEH10 5DT United Kingdom University of Thessaly Department of Computer Science and Biomedical Infromatics Lamia Greece Senior Software Engineer at *** Athens Greece Open University of Cyprus Faculty of Pure and Applied Sciences Nicosia Cyprus

ISBN: (纸本)9798350377644

The advent of Industry 4.0 and the Industrial Internet of Things (IIoT) has revolutionized manufacturing and production systems, enhancing efficiency and communication through the integration of advanced technologies such as IoT devices and AI. However, this increased digitization has also led to heightened cybersecurity risks, with a notable rise in the frequency and complexity of cyber-attacks. Cyber Ranges emerges as a critical solution in addressing these challenges, offering a controlled environment for simulating cyber-attack scenarios, training cybersecurity teams, and developing robust defense strategies. The escalating demand for cybersecurity professionals has highlighted the crucial need for effective training solutions. This article presents an open-source Cyber Range constructed on container-based architecture, meticulously engineered for efficient operation with minimal resource consumption. In response to the scarcity of cybersecurity experts, this platform prioritizes extensive scalability and robust isolation between exercises, ensuring secure learning environments, and also integrates a complex developed exercise series aimed at strengthening cybersecurity learning experiences. These exercises encompass a variety of scenarios and challenges, catering to professionals at different skill levels. Each exercise replicates real-world cyber threats, offering practical, hands-on learning opportunities. Additionally, a comprehensive questionnaire accompanies these exercises, designed to gather feedback on participants' experiences. © 2024 IEEE.

关键词： Cyber attacks

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Recognition of Handwritten Tamazight Characters Using ResNet, MobileNet and VGG Transfer Learning 23

Recognition of Handwritten Tamazight Characters Using ResNet...

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23rd International Conference on New Trends in Intelligent software Methodologies, Tools and Techniques, SoMeT 2024

作者： Fattahi, Jaouhar Sghaier, Feriel Mejri, Mohamed Manai, Elyes Ghayoula, Ridha Department of Computer Science and Software Engineering Laval University 2325 rue de l'Université QuébecQCG1V 0A6 Canada Ecole Nationale d'Ingénieurs de Carthage Université de Carthage Tunis Tunisia Faculty of Engineering Information Systems Department University of Moncton New Brunswick Canada

ISBN: (纸本)9781643685380

The Tamazight civilization stands as a significant cultural entity, marked by its linguistic diversity, historical legacy, and scriptural traditions, which collectively enrich the cultural tapestry of North Africa. Among these traditions, the Tamazight handwritten script assumes particular importance, embodying centuries of cultural identity and artistic expression. Recognizing the imperative of safeguarding this cultural heritage, our study focuses on Tamazight handwritten character recognition. Leveraging the strategic application of Transfer Learning, we explore its efficacy in this domain. Transfer Learning presents a robust framework wherein pre-existing models are adapted for specific tasks despite limited data availability. Our research employs three prominent Transfer Learning architectures: VGG, ResNet, and MobileNet. Through a rigorous comparative analysis, we discern the efficacy of these methodologies in the context of Tamazight handwritten character recognition. Our findings underscore the potential of Transfer Learning to significantly augment the accuracy and efficiency of script recognition systems, thereby advancing the overarching objective of preserving and propagating the Tamazight cultural heritage. © 2024 IOS Press. All rights reserved.

关键词： Transfer learning

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