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Dimensionality reduction in 3D causal deep learning for neuroimage generation: an evaluation study

Journal of Medical Imaging 2025年第2期12卷

作者： Ohara, Erik Y. Vigneshwaran, Vibujithan Souza, Raissa Vamosi, Finn G. Wilms, Matthias Forkert, Nils D. University of Calgary Biomedical Engineering Graduate Program CalgaryAB Canada University of Calgary Department of Radiology CalgaryAB Canada University of Calgary Hotchkiss Brain Institute CalgaryAB Canada University of Calgary Alberta Children's Hospital Research Institute CalgaryAB Canada University of Calgary Department of Computer Science CalgaryAB Canada University of Calgary Departments of Pediatrics and Community Health Sciences CalgaryAB Canada

Purpose: Causal deep learning (DL) using normalizing flows allows the generation of true counterfactual images, which is relevant for many medical applications such as explainability of decisions, image harmonization, and in-silico studies. However, such models are computationally expensive when applied directly to high-resolution 3D images and, therefore, require image dimensionality reduction (DR) to efficiently process the data. The goal of this work was to compare how different DR methods affect counterfactual neuroimage generation. Approach: Five DR techniques [2D principal component analysis (PCA), 2.5D PCA, 3D PCA, autoencoder, and Vector Quantised-Variational AutoEncoder] were applied to 23,692 3D brain images to create low-dimensional representations for causal DL model training. Convolutional neural networks were used to quantitatively evaluate age and sex changes on the counterfactual neuroimages. Age alterations were measured using the mean absolute error (MAE), whereas sex changes were assessed via classification accuracy. Results: The 2.5D PCA technique achieved the lowest MAE of 4.16 when changing the age variable of an original image. When sex was changed, the autoencoder embedding led to the highest classification accuracy of 97.84% while also significantly impacting the age variable predictions, increasing the MAE to 5.24 years. Overall, 3D PCA provided the best balance, with an age prediction MAE of 4.57 years while maintaining 94.01% sex classification accuracy when altering the age variable and 94.73% sex classification accuracy and the lowest age prediction MAE (3.84 years) when altering the sex variable. Conclusions: 3D PCA appears to be the best-suited DR method for causal neuroimage analysis. © 2025 Society of Photo-Optical Instrumentation Engineers (SPIE).

关键词： Principal component analysis

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Synthetic Batik Pattern Generator Using Wasserstein Generative Adversarial Network with Gradient Penalty

Synthetic Batik Pattern Generator Using Wasserstein Generati...

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

作者： Kus Andriadi Yaya Heryadi Lukas Wayan Suparta Ilvico Sonata Computer Science Department Binus Graduate Program Doctor of Computer Science Bina Nusantara University Jakarta Indonesia Cognitive Engineering Research Group (CERG) Universitas Katolik Indonesia Atma Jaya Jakarta Indonesia Department of Electrical Engineering Faculty of Industrial Technology Institut Teknologi Nasional Yogyakarta Yogyakarta Indonesia

Batik is an Indonesian world cultural heritage. Batik consists of many kinds of patterns depending on where the batik comes from, Batik-making techniques continue to develop along with technology development. Among the batik making techniques that are widely used are hand-written, stamping, and printing. Batik motifs have been widely used as research material, especially in the field of artificial intelligence. The diverse appearance of batik motifs has attracted many researchers to carry out research on making synthetic batik patterns, one of which uses a Generative Adversarial Network. This paper presents a synthetic batik pattern model based on the Wasserstein Generative Adversarial Network with Gradient Penalty. This model has been proven to create new synthetic batik patterns quite well and almost identical with images provided in the dataset, with the notes if the dataset provided is large.

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Mobile Application Implementation as Agriculture 4.0 Strategy for Sugarcane Yield Prediction

Mobile Application Implementation as Agriculture 4.0 Strateg...

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HCI and UX Conference in Indonesia (CHIuXiD), International

作者： Hangger Gahara Mawandha Reza Rahutomo Teddy Suparyanto Bens Pardamean Faculty of Agricultural Technology Institut Pertanian Stiper Yogyakarta Indonesia Information Systems Department School of Information Systems Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798350304084

ISBN: (纸本)9798350304091

Information engineering strategies play a significant and transformative role in shaping the landscape of digital agriculture. It drives innovation and efficiency in modern farming practices, with a specific focus on enhancing the value of agricultural commodities, such as sugarcane. The application of mobile technology plays a crucial part in achieving increased sugarcane productivity. Mobile applications, equipped with advanced developer features, offer rapid and user-friendly access to vital information. Traditional methods of estimating sugarcane production relied on manual data recording on paper, followed by data transfer to computer systems, typically managed by sugar factory junior plant officers. This conventional approach presents several inherent weaknesses, including time and effort intensiveness during data recording and entry. Additionally, the potential for errors in calculation and data input is a concern. The storage capacity for paper-based documents is finite, and farmers are often unable to autonomously assess their production potential. The objective of this research is to confront these obstacles by creating a sugarcane production application for Android. This application functions as an information engineering approach focused on forecasting sugarcane yields for plantation owners and their assistants. The development procedure adhered to the systematic waterfall method, following the principles of the Software Development Life Cycle (SDLC) model. Data collection was carried out through observations, while interviews with junior plant officers provided valuable insights into sugarcane estimation techniques. Analysis involved the synthesis of observational and interview data to inform the design of the application’s interface and algorithmic system. The resulting application significantly simplifies the process of estimating production potential for farmers, enabling them to access sugarcane productivity data during harvest. Consequently, sugar

关键词： Productivity Operating systems Estimation Production facilities Raw materials Mobile applications Recording

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Challenges and Emerging Issues for Generative AI and Hyper Intelligence

Challenges and Emerging Issues for Generative AI and Hyper I...

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Cyber science and Technology Congress (CyberSciTech), IEEE

作者： Jianhua Ma Qun Jin Hui-Huang Hsu John Paul C. Vergara Antonio Guerrieri Claudio Miceli Ao Guo Faculty of Computer and Information Sciences Hosei University Japan Department of Human Informatics and Cognitive Sciences Waseda University Japan Department of Computer Science and Information Engineering Tamkang University Taiwan Department of Information Systems and Computer Science Ateneo de Manila University Philippines ICAR-CNR Italy Graduate Program in Systems Engineering and Computer Science Federal University of Rio de Janeiro Brazil Graduate School of Informatics Nagoya University Japan

ISBN: (数字)9798331532093

ISBN: (纸本)9798331532109

Generative Artificial Intelligence (GenAI) represents a significant milestone in the development of artificial intelligence, bringing sophisticated AI capabilities into daily life and work. As we approach the era of Hyper Intelligence (Hyper-I), a variety of critical challenges and emerging issues have come to light, ranging from computational complexity to ethical concerns. This paper explores the evolution of AI from the perspective of human learning, comparing machine and human intelligence, and identifying key considerations for the development of future AI systems. It also highlights the growing importance of regulating advanced AI models, such as Reinforcement Learning-based Long-Term Planning Agents, to ensure that Hyper-I remains under human control. Additionally, the paper discusses the computational complexity of transformer-based models, their applicability to intractable problems, and their role in cognitive building systems and resource-constrained environments through TinyML. By analyzing these pressing challenges, this work provides insights into the future of AI and the path toward responsible innovation in generative and hyper-intelligent systems.

关键词： Hyper-intelligent systems Ethics Technological innovation Generative AI Computational modeling Tiny machine learning Pressing Transformers Regulation Computational complexity

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Classification of Highly Similar Fish Species Using Machine Learning

Classification of Highly Similar Fish Species Using Machine ...

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International Conference on Systems, Signals and Image Processing, IWSSIP

作者： Leandro Magno C. Silva Franklin Cesar Flores Rosilene Luciana Delariva Gustavo Z. Felipe Yandre M. G. Da Costa Graduate Program in Computer Science State University of Maringá Federal Institute of Paraná Maringá Brazil Department of Informatics State University of Maringá Maringá Brazil Center for Biological and Health Sciences State University of Western Paraná Cascavel Brazil Graduate Program in Computer Science State University of Maringá Maringá Brazil

ISBN: (数字)9798350391886

ISBN: (纸本)9798350391893

Fish species inventory and monitoring is a timely concern due to the increasing environmental imbalance. In this sense, the development of machine learning strategies aiming to support automatic fish species identification is an important contribution, both in environmental and scientific terms. This study explores handcrafted features aiming to perform fish species identification in a quite challenging scenario, in which the inter-classes differences are minimal, as the species belong to the same family considering the hierarchy of biological classification (i.e. Characidae). For this purpose, it is proposed a set of features designed properly, aiming to capture visual properties closely related to each species that are difficult to be noted by experts in this domain of investigation. An additional contribution of this work is a dataset of 4870 images taken from 416 individuals from nine fish species. The Region of Interest (RoI) corresponding to the fish body is segmented, and horizontal and vertical histograms are collected from each sample, aiming to capture information related to the body shape, and other characteristics particular to each species. Experiments are performed using the Support Vector Machine (SVM), K-Nearest Neighbours (K-NN), Random Forest and Naive-Bayes classifiers and, in the best scenario, it is obtained an accuracy rate of 99%. This result corroborates the hypothesis that the use of handcrafted features specifically developed for this type of application can be quite effective in addressing this classification problem.

关键词： Support vector machines Image segmentation Visualization Histograms Image recognition Shape Fish

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Twitter-based text classification using svm for weather information system 6

Twitter-based text classification using svm for weather info...

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6th International Conference on Information Management and Technology, ICIMTech 2021

作者： Purwandari, Kartika Rahutomo, Reza Sigalingging, Join W. C. Ajy Kusuma, Mahisa Prasetyo, Aji Pardamean, Bens Research Center Bina Nusantara University Bioinformatics and Data Science Jakarta11480 Indonesia BMKG Meteorological Climatological and Geophysical Agency Database Center Division Jakarta10720 Indonesia Bina Nusantara University BINUS Graduate Program - Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665449373

The popularity of social media amplified the amount of text data that is used to enrich text classification research with machine learning approach. The modernization in weather information system is needed to produce real-time weather information using the involvement of Twitter users. GetOldTweets was used to cover data acquisition from Twitter. Support Vector Machine (SVM) was deployed as a machine learning model for text classification. The result was delivered in Esri Maps features. It facilitated a social sensing for Indonesia weather information system by using Twitter posts from Indonesian users with 93% accuracy. © 2021 IEEE.

关键词： Data acquisition

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Design and Implementation of Business Intelligence Dashboard for Project Control at the Port Harbor-Company 12th

Design and Implementation of Business Intelligence Dashboard...

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12th Asian Conference on Intelligent Information and Database Systems, ACIIDS 2020

作者： Lumban Gaol, Ford Syahir, Arsyan Matsuo, Tokuro Computer Science Department BINUS Graduate Program – Doctor of Computer Science Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program – Master of Information System Bina Nusantara University Jakarta Indonesia Advanced Institute of Industry Technology Tokyo Japan

ISBN: (纸本)9789811533792

This study aims to assist resource management and the project controller at Port Harbor Company. Port Harbor Company is an IT Consulting. Problems that often occur in IT Consulting are related to the project cost, resource management and control of each project. Problems that occur at the Port Harbor Company are poor resource management, spending costs that exceed a predetermined budget and how to see the status of ongoing projects. Using Business Intelligence and the dashboard as a front end will help the project controller and resource management manage resources, manage project costs and monitor ongoing projects. In this study, the development and implementation of Business Intelligence and dashboards using the ASAP method are expected to be more structured and can solve the Port Harbor Company problem. © 2020, Springer Nature Singapore Pte Ltd.

关键词： Project management

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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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IoT-Based portable modules for energy consumption monitoring in smart home system 3

IoT-Based portable modules for energy consumption monitoring...

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3rd International Conference on Vocational Education and Technology, IConVET 2020

作者： Bayu, J.P. Aryanto, K.A.A. Suweken, G. Aryanto, K.Y.E. Study Program of Computer Science Graduate Program Universitas Pendidikan Ganesha Singaraja-Bali Indonesia Department of Computer System Stikom Bali Denpasar-Bali Indonesia

Energy consumption has become one of the major problems in Indonesia. The use of recent technology is highly beneficial since various automation could be done even in simple devices. In this research, portable smart home modules based on the internet of things (IoT) technology to monitor the power consumption in household electrical devices were built. The module consisted of current sensors, voltage sensors, and IoT Wi-Fi Development Board. It communicated with the server, built using the Raspberry Pi, using the MQTT protocol. The server was equipped with web pages that allowed users to monitor the devices' electrical power usage. Therefore, all of the connected modules could be monitored to provide information regarding an electric household device's defect. The results had shown that the prototypes of the modules had been successfully built. It was shown that very slight differences were found between the system measurements compared to the manual one using the 60 seconds interval measurements. The power consumed by the module was very low, where the current sensor uses 0.125 Watt while the voltage sensor uses 0.001 Watt. The portable devices were developed in the shape of small boxes;therefore, it could be easy to move and install. © Published under licence by IOP Publishing Ltd.

关键词： Internet of things

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A Bioinformatics Analysis and Homology 3D Modeling of Dihydroxy-orotate-dehydrogenase of Plasmodium ovale

A Bioinformatics Analysis and Homology 3D Modeling of Dihydr...

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

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

The infection of Plasmodium vivax is relatively less virulent than the deathliest Plasmodium falciparum. However, it still can lead to a fatal case and often induces recurring malaria due to dormant parasites in the liver. Thus, the research to study the drug to treat Plasmodium vivax is essential, where the enzyme dihydroorotate dehydrogenase (DHODH) has recently become a new drug target. However, the drug-enzyme interaction study has only recently been conducted in Plasmodium falciparum (pfDHODH) due to the lack of the 3D structure of enzyme DHODH from Plasmodium vivax that is crucial for the study. Therefore, this study aimed to perform the modelling study of Plasmodium vivax DHODH (PvDHODH) to create a 3D structure as a basis for drug-protein interaction study in upcoming studies. Sequence pvDHODH (Accession: SCO68359.1) was used in homology modelling using Modeller 10.2 with the crystal structure of DHODH from DHODH (Accession: 7KZY) as a template. Overall, the model generated from the homology modelling was considered a good model, and the 3D structure was close to the native state according to several parameters, including DOPE score, GA341 score, QMEAN4 value, 3D-1D score, ERRAT2 score, and ProSA score. Ramachandran plot also revealed that almost all amino acids were distributed in the desirable and allowed area (99.1%), and only 0.9% were in generously allowed regions. Superimposition of the model with the template also indicated that the model has an almost similar structure and amino acids positioning, including in the binding pocket and active site. Therefore, the model can be used for downstream analysis in drug-protein interaction studies. Nevertheless, some improvements can still be performed to upgrade the quality of the model by deleting unaligned residues on the C-terminal and realigning the residues at the doubting site.

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