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International Conference on Cybernetics and Intelligent System (ICORIS)

作者： Mahmud Isnan Gregorius Natanael Elwirehardja Kuncahyo Setyo Nugroho Imelda Liana Ritonga Roby Pahala Januario Gultom Elida Afni Lubis Bens Pardamean Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Undergraduate of Nursing Program Universitas Imelda Medan Indonesia Medan Indonesia Undergraduate Pharmacy Program Universitas Imelda Medan Indonesia Medan Indonesia Clinical Pathology Unit Rumah Sakit Imelda Pekerja Indonesia Medan Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331539603

ISBN: (纸本)9798331539610

The need for an early screening and computer-Aided Diagnosis (CAD) system based on Artificial Intelligence (AI) for the field of radiology is essential to realize considering the large impact of lung diseases globally. However, developing AI requires a lot of data, which is a challenge because data in the health sector tends to be limited in quantity and has disparities between diagnostic categories (data imbalance). To overcome this issue, DINO ViT models was trained with the publicly available COVID-19 Radiography database in our previous study. The model was subsequently implemented into a web application, with this study focusing on the development of a prototype for the application. The study found this application can be useful for medical personnel and doctors in carrying out early screening and CAD. Meanwhile, it also highlighted the general unfamiliarity with AI applications among medical staff, emphasizing the need for increased education and training on AI's role in healthcare.

关键词： Training Solid modeling Design automation Pulmonary diseases Prototypes Radiology Predictive models computer aided diagnosis Artificial intelligence Medical diagnostic imaging

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An Exploratory Computational Approach for Elucidating a Nonstructural Protein Interaction in Dengue Virus 2

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Procedia computer science 2024年 245卷 470-479页

作者： Alam Ahmad Hidayat Rudi Nirwantono Bens Pardamean Mathematics Department School of Computer Science Bina Nusantara University Indonesia 11480 Biotechnology Department Faculty of Engineering Bina Nusantara University Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta Indonesia 11480

As the dengue infection still impacts hundreds of millions of people globally, unprecedented efforts in dengue drug development have been more progressive in recent decades. Computational methods provide a fast, sustainable, and efficient screening of active compounds and newly created drug molecules, including those specifically targeting nonstructural proteins (NS) of dengue viruses. In this work, protein modeling for the NS proteins of DENV-2/16681 strain was performed using a template-based homology modeling for the NS3 protein and an Artificial Intelligence (AI)-based prediction via AlphaFold for the NS4B protein. Moreover, the protein-protein interaction between the two structures was predicted using the HADDOCK server, which employs information about active and passive residues of the interaction interface to guide the docking process. After the modeling and its respective refinement process, the predicted structures of NS3 and NS4B improved their steric clashing scoring from MolProbity assessment. The refined models were then docked, and the resulting docking pose was analyzed to extract the interacting residues based on the polar contacts within the interface of the two proteins. Our result presents a preliminary study to create a dataset related to in silico molecular interactions of the NS3-NS4B interaction of different DENV types. It is helpful for building a computational pipeline for elucidating protein-ligand problems in dengue drug screenings.

关键词： bioinformatics computational biology dengue protein docking structural biology

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An Object Driven Fuzzy Decision Model for Sugarcane Yield Prediction in Indonesia’s Sugar Industry

An Object Driven Fuzzy Decision Model for Sugarcane Yield Pr...

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International Seminar on Research of Information Technology and Intelligent Systems (ISRITI)

作者： Ditdit Nugeraha Utama Muhammad Asrol Suharjito Christian Harito Napthaleni Muhammad Syafrudin Computer Science Department BINUS Graduate Program Master of Computer Science Bina Nusantara University Jakarta Indonesia Industrial Engineering Department BINUS Graduate Program Master of Industrial Engineering Bina Nusantara University Jakarta Indonesia Department of Artificial Intelligence and Data Science Sejong University Seoul South Korea

ISBN: (数字)9798331519643

ISBN: (纸本)9798331519650

A sugarcane yield of one plantation area depends on several independent variables. Practically it is challenging to predict accurately by using conventional methods. This study aims to develop a decision model based on a combination of fuzzy logic and object-oriented methods to predict sugarcane yield. The research is conducted in four main stages, employing object-oriented methods for model design and fuzzy logic for model construction. Object and activity diagrams are used for the object-oriented model design. The fuzzy membership functions employed are a combination of trapezoidal and triangular shapes. The resulting decision model can simulate 2,225 data from plantation areas in Indonesia. Based on the 10 examples of plantation area data in Indonesia, plantation number one obtained the largest sugarcane yield, which was 4.79%, with a similarity value of 0.90 (when compared to manual calculations as its ground truth). This similarity value is a higher value when compared to the average similarity value, which is 0.89.

关键词： Fuzzy logic Seminars Shape Object oriented modeling Plantations Manuals Predictive models Sugar industry Intelligent systems Information technology

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Urban Sound Classification Using DNN, CNN LSTM a Comparative Approach

Urban Sound Classification Using DNN, CNN LSTM a Comparative...

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2021 International Conference on Innovation and Intelligence for Informatics, Computing, and Technologies, 3ICT 2021

作者： Bubashait, Mohamed Hewahi, Nabil Big Data Science and Analytics Master Program College of Science University of Bahrain Sakhier Bahrain University of Bahrain Department of Computer Science College of IT Sakhier Bahrain

ISBN: (纸本)9781665440325

Like air pollution, sound pollution has grown to be a major concern for city residents, designers, and developers. Detecting and recognizing sound types and sources in cities and suburban areas or any environment have become a necessity for the quality of life as well as security. In recent years, researchers have explored many models using Convolutional Neural Network (CNN), Long Short Term Memory (LSTM) Neural Network, and different combinations of these techniques, which produced promising results when combined with spectrogram images, or its different variations, to classify urban sounds. This research uses the DNN model performance as a baseline to compare the CNN and LSTM models' performance for classifying urban sound using Mel scale cepstral analysis (MEL) spectrum images using an open-source library called Librosa for sound processing. Models' performance was evaluated using the UrbanSound8k dataset. The CNN model underperformed with an accuracy rate of 87.15% and f1 score of 85.63% compared to both the DNN base model and the LSTM model. In contrast, comparing the LSTM model with CNN, LSTM shows better accuracy performance on test data with 90.15%, and f1 score of 90.15%. © 2021 IEEE.

关键词： Long short-term memory

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Cancer Prediction Using Clinical and Genomic data Fusion: A Systematic Review

Cancer Prediction Using Clinical and Genomic Data Fusion: A ...

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International Conference on Cybernetics and Intelligent System (ICORIS)

作者： Kelvin Julian Kuncahyo Setyo Nugroho Rudi Nirwantono Bens Pardamean Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Biotechnology Department Faculty of Engineering Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331539603

ISBN: (纸本)9798331539610

This systematic review provides a comprehensive overview of the methods used to integrate genomic and clinical data in cancer prediction. The review includes 19 studies across various cancers, including breast, colorectal, melanoma, lung, pancreatic, and thyroid. The studies employed different methods to combine genomic and clinical data, including weighted polygenic risk scores, genetic and non-genetic risk scores, and different machine learning algorithms. The results show significant improvements in model prediction performance accuracy across multiple studies. The review highlights the potential benefits of integrating genetic and phenotypic information to improve disease risk prediction models and inform personalized healthcare strategies.

关键词： Accuracy Machine learning algorithms Genomics data integration Medical services Predictive models data models Bioinformatics Cancer Systematic literature review

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Multi-Lingual ESG Impact Duration Inference 7

Multi-Lingual ESG Impact Duration Inference

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Joint Workshop of the 7th Financial Technology and Natural Language Processing, 5th Knowledge Discovery from Unstructured data in Financial Services and 4th Economics and Natural Language Processing, FinNLP-KDF-ECONLP 2024

作者： Chen, Chung-Chi Tseng, Yu-Min Kang, Juyeon Lhuissier, Anaïs Seki, Yohei Lee, Hanwool Day, Min-Yuh Tu, Teng-Tsai Chen, Hsin-Hsi AIST Japan Data Science Degree Program National Taiwan University Academia Sinica Taiwan 3DS Outscale France University of Tsukuba Japan NCSOFT Korea Republic of Graduate Institute of Information Management National Taipei University Taiwan Graduate Institute of International Business National Taipei University Taiwan Department of Computer Science and Information Engineering National Taiwan University Taiwan

ISBN: (纸本)9782493814197

To accurately assess the dynamic impact of a company’s activities on its Environmental, Social, and Governance (ESG) scores, we have initiated a series of shared tasks, named ML-ESG. These tasks adhere to the MSCI guidelines for annotating news articles across various languages. This paper details the third iteration of our series, ML-ESG-3, with a focus on impact duration inference—a task that poses significant challenges in estimating the enduring influence of events, even for human analysts. In ML-ESG-3, we provide datasets in five languages (Chinese, English, French, Korean, and Japanese) and share insights from our experience in compiling such subjective datasets. Additionally, this paper reviews the methodologies proposed by ML-ESG-3 participants and offers a comparative analysis of the models’ performances. Concluding the paper, we introduce the concept for the forthcoming series of shared tasks, namely multi-lingual ESG promise verification, and discuss its potential contributions to the field. © 2024 ELRA Language Resource Association.

关键词： Iterative methods

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Aggregating Structural Features for Computational Analysis of Mutations in BRCT Domains of BRCA1 Protein

Aggregating Structural Features for Computational Analysis o...

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International Conference on Informatics, Multimedia, Cyber and Information System (ICIMCIS)

作者： Alam Ahmad Hidayat Rudi Nirwantono Mahmud Isnan Joko Pebrianto Trinugroho Bens Pardamean Mathematics Department School of Computer Science Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Biotechnology Department Faculty of Engineering Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department Bioinformatics and Data Science Research Center BINUS Graduate Program Jakarta Indonesia

Understanding the mechanistic interpretability of mutation effects in a protein can help predict the clinical implications of the genetic variants. Hence, computational variant effect predictions that involve protein structural features of the protein mutations might be suitable in this case. In this work, we focus on BRCT domains of BRCA1 gene that is widely studied in breast cancer studies. We retrieved 88 selected missense variants found in BRCT domains annotated in both ClinVar and gnomAD databases. To computationally characterize the pathogenic property of the mutations we used two types of features extracted from protein structures: a change in free Gibbs energy and a set of features derived from molecular dynamics simulations of each mutant. Using a dimensional reduction and Gaussian mixture model (GMM)-based clustering we demonstrate that the variants are segregated into two regions that may correspond to their pathogenic status. This method can be a potential computational pipeline for providing the preliminary mechanistic interpretation of mutation effects in terms of their thermodynamic and structural features.

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ZIP-FIT: EMBEDDING-FREE data SELECTION VIA COMPRESSION-BASED ALIGNMENT

arXiv

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arXiv 2024年

作者： Obbad, Elyas Mlauzi, Iddah Miranda, Brando Schaeffer, Rylan Obbad, Kamal Bedi, Suhana Koyejo, Sanmi Department of Computer Science Stanford University United States Department of Biomedical Data Science Stanford School of Medicine United States Stanford Biophysics Program Stanford School of Medicine United States

data selection is crucial for optimizing language model (LM) performance on specific tasks, yet most existing methods fail to effectively consider the target task distribution. Current approaches either ignore task-specific requirements entirely or rely on approximations that fail to capture the nuanced patterns needed for tasks like Autoformalization or code generation. Methods that do consider the target distribution often rely on simplistic, sometimes noisy, representations, like hashed n-gram features, which can lead to collisions and introduce noise. We introduce ZIP-FIT, a data selection framework that uses gzip compression to directly measure alignment between potential training data and the target task distribution. Our key insight is that compression-based similarity captures both syntactic and structural patterns relevant to the target task, enabling more precise selection of truly task-relevant data. In extensive evaluations on Autoformalization and Python code generation, ZIP-FIT significantly outperforms leading baselines like DSIR and D4. Models trained on ZIP-FIT-selected data achieve their lowest cross-entropy loss up to 85.1% faster than baselines, demonstrating that better task alignment leads to more efficient learning. In addition, ZIP-FIT performs selection up to 65.8% faster than DSIR and two orders of magnitude faster than D4. Notably, ZIP-FIT shows that smaller, well-aligned datasets often outperform larger but less targeted ones, demonstrating that a small amount of higher quality data is superior to a large amount of lower quality data. Our results imply that task-aware data selection is crucial for efficient domain adaptation, and that compression offers a principled way to measure task alignment. By showing that targeted data selection can dramatically improve task-specific performance, our work provides new insights into the relationship between data quality, task alignment, and model learning efficiency. © 2024, CC BY.

关键词： data consistency

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Implementation of Face Patterns and Smile Recognition for Intelligent Class Attendance Systems

Implementation of Face Patterns and Smile Recognition for In...

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International Conference of computer and Informatics Engineering (IC2IE)

作者： Miftakhurrokhmat Teddy Suparyanto Gregorius Natanael Elwirehardja Shofiyati Nur Karimah Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia Department of Informatics Faculty of Computer Science Universitas Amikom Yogyakarta Yogyakarta Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia

Students “attendance in class is one important success parameter in face-to-face learning processes. Conventional attendance systems, such as paper-based attendance sheets or identity card systems, require a long time in the manual recapitulation process. Without additional verifications, even computer vision-based methods are prone to fraudulent practices by the students instead of gaining their excitement and attention in a class. To stimulate students” attention in a class, this work designs an intelligent class attendance system, in which facial pattern and smile recognition are implemented by using the latter as an additional task-based verification to reduce the risks of fake attendance. For the face recognition module, this pilot study used FaceNet as a feature extractor combined with SVM for classification, whereas the Haar cascade algorithm is used for recognizing smiles. This face recognition pipeline was implemented as a service installed on minicomputers or Internet of Things (IoT) devices in each classroom and connected to an IP camera. Every recorded attendance will be sent as a notification to a mobile application for students that requires their active participation to confirm it with a smiling self-photo. The proposed pipeline obtained 92.86% accuracy on the test data, and 66.67% accuracy when evaluated in a real-life simulation setting through the implemented system. The lower accuracy in the simulation indicated that further improvements are indispensable, especially since the model obtained 28.57% False Negative Rate. Future studies will need to acquire more data and experiment with more efficient methods of attendance verification.

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A machine learning and neural network approach for classifying multidrug-resistant bacterial infections

Healthcare Analytics

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Healthcare Analytics 2025年 7卷 100388-100388页

作者： Mengsiri, Preeda Ungcharoen, Ratchadaporn Gertphol, Sethavidh Biomedical Data Science Program Faculty of Science Kasetsart University Thailand Faculty of Public Health Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus Thailand Department of Computer Science Faculty of Science Kasetsart University Thailand

Antimicrobial resistance (AMR) represents a major public health challenge, significantly complicating infection prevention and treatment. This study employs machine learning and neural network techniques to classify multidrug-resistant Gram-negative bacterial (MDR-GNB) infections using electronic health records from 624 patients at Thatphanom Crown Prince Hospital in Thailand. We compared several algorithms, including Logistic Regression, Random Forest, Support Vector Machine (SVM), Extreme Gradient Boosting (XGBoost), K-Nearest Neighbors (KNN), Multilayer Perceptron (MLP), and Light Gradient Boosting Machine (LightGBM), with the MLP model exhibiting the highest accuracy and specificity. Performance was further enhanced by integrating feature selection methods such as Sequential Forward Selection (SFS), Recursive Feature Elimination with Cross-Validation (RFE-CV), and SelectKBest with data augmentation techniques, including ADASYN and SMOTE variants. Utilizing SHapley Additive exPlanations (SHAP) provided valuable insights into the most influential predictors for MDR-GNB. Notably, the MLP model achieved an AUC of 0.70, surpassing prior studies and highlighting its potential to advance clinical decision-making in managing MDR-GNB infections. © 2025 The Authors

关键词： Electronic health records Gram-negative bacteria Machine learning Multidrug resistance Neural network

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