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1st International Conference on Smart Technology, Applied Informatics, and Engineering, APICS 2022

作者： Indriani, Nyimas Muthia Arif, Azeli Carissa Arin, Ikrar Adinata School of Information Systems Bina Nusantara University Information System Department Jakarta Indonesia School of Information Systems Bina Nusantara University Computer Science Department Binus Graduate Program Computer Science Information System Department Jakarta Indonesia

ISBN: (数字)9781665489850

ISBN: (纸本)9781665489850

The advancement and application of information technology have provided significant benefits to society. Complete and quality information is needed to achieve efficiency and make it easier for people to find the right and trusted vacation partner. One way that can be done is to create an information system to find vacation companions or travel companions to travel to the same destination at the same time. This study aims to design and build a mobile application. Travemate is a mobile application that helps travelers find the right and trustworthy friends or partners to travel to the same destination. The development of this information system is expected to help the community, especially solo travelers, reduce the time spent looking for the right partner or traveler who meets their criteria. This application is built using a mobile apps platform that can be installed on devices connected to the internet via smartphones and also with the features available on travemate to facilitate and optimize user activities in finding partners for their travels so that with this application, all activities will be easy, fun, and efficient. In the long term, the application programs we create can touch people all over the world, making it easier for people to find friends to travel with. © 2022 IEEE.

关键词： Information systems

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Implementation of Fine-Tuned BERT for Enzyme Classification Based on Gene Ontology

Implementation of Fine-Tuned BERT for Enzyme Classification ...

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International Conference of Advanced Informatics: Concept, Theory and Application (ICAICTA)

作者： Matthew Martianus Henry Christian Kenneth Bens Pardamean 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)9798331520311

ISBN: (纸本)9798331520328

Enzymes are biocatalysts with vital roles in biological functions and many industrial applications. Diverse enzymes are classified using Enzyme Commission (EC) nomenclature, making differentiation challenging. On the other hand, another biological information, gene ontology (GO), can describe the biological aspects of enzymes, covering related biological processes (BP), molecular functions (MF), and their locations within cells (CC). This study proposes a novel EC class and subclass classification of enzymes within the ontology subclass based on their GO semantics using a Bidirectional Encoder Representation of Transformer (BERT). The BERT model is first fine-tuned using the preprocessed GO term name and definition, with the enzymes in each ontology class (BP, MF, or CC) are also divided based on how the GO assigned, either through manual annotation (NONIEA) or electronically inferred (IEA). BERT successfully obtained 0.93, 0.60, 0.99, 0.90, 0.40, and 0.35 F1 scores during fine-tuning for BP IEA, BP NONIEA, MF IEA, MF NONIEA, CC IEA, and CC NONIEA, respectively. On the test set, the fine-tuned BERT significantly outperformed GOntoSim, a framework to calculate semantic similarity based on classical information theory, in EC class classification across all metrics with less inference time in all ontology subclass. Expanded further to the EC subclass, BERT can classify the enzyme on the EC subclass level in BP IEA and MF IEA ontology subclass. However, longer epochs are needed in fine-tuning. This result shows that the names and definitions of GO terms are distinguishable features in classifying enzymes as an alternative to the information content approach.

关键词： Measurement Enzymes Semantics Bidirectional control Manuals Ontologies Transformers Encoding Biological information theory Informatics

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Disentangling Interpretable Factors with Supervised Independent Subspace Principal Component Analysis 38

Disentangling Interpretable Factors with Supervised Independ...

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38th Conference on Neural Information Processing Systems, NeurIPS 2024

作者： Su, Jiayu Knowles, David A. Rabadan, Raul Program for Mathematical Genomics United States Department of Systems Biology Columbia University United States Department of Biomedical Informatics Columbia University United States Department of Computer Science Columbia University United States New York Genome Center United States

The success of machine learning models relies heavily on effectively representing high-dimensional data. However, ensuring data representations capture human-understandable concepts remains difficult, often requiring the incorporation of prior knowledge and decomposition of data into multiple subspaces. Traditional linear methods fall short in modeling more than one space, while more expressive deep learning approaches lack interpretability. Here, we introduce Supervised Independent Subspace Principal Component Analysis (sisPCA), a PCA extension designed for multi-subspace learning. Leveraging the Hilbert-Schmidt Independence Criterion (HSIC), sisPCA incorporates supervision and simultaneously ensures subspace disentanglement. We demonstrate sisPCA's connections with autoencoders and regularized linear regression and showcase its ability to identify and separate hidden data structures through extensive applications, including breast cancer diagnosis from image features, learning aging-associated DNA methylation changes, and single-cell analysis of malaria infection. Our results reveal distinct functional pathways associated with malaria colonization, underscoring the essentiality of explainable representation in high-dimensional data analysis. © 2024 Neural information processing systems foundation. All rights reserved.

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SpikingSoft: A Spiking Neuron Controller for Bio-inspired Locomotion with Soft Snake Robots

arXiv

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arXiv 2025年

作者： Zhang, Chuhan Wang, Cong Pan, Wei Della Santina, Cosimo The Department of Cognitive Robotics Faculty of Mechanical Engineering Delft University of Technology Delft Netherlands The Department of Computer Science The University of Manchester Manchester United Kingdom

Inspired by the dynamic coupling of moto-neurons and physical elasticity in animals, this work explores the possibility of generating locomotion gaits by utilizing physical oscillations in a soft snake by means of a low-level spiking neural mechanism. To achieve this goal, we introduce the Double Threshold Spiking neuron model with adjustable thresholds to generate varied output patterns. This neuron model can excite the natural dynamics of soft robotic snakes, and it enables distinct movements, such as turning or moving forward, by simply altering the neural thresholds. Finally, we demonstrate that our approach, termed SpikingSoft, naturally pairs and integrates with reinforcement learning. The high-level agent only needs to adjust the two thresholds to generate complex movement patterns, thus strongly simplifying the learning of reactive locomotion. Simulation results demonstrate that the proposed architecture significantly enhances the performance of the soft snake robot, enabling it to achieve target objectives with a 21.6% increase in success rate, a 29% reduction in time to reach the target, and smoother movements compared to the vanilla reinforcement learning controllers or Central Pattern Generator controller acting in torque space. Copyright © 2025, The Authors. All rights reserved.

关键词： Neurons

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Explainable Supervised Method for Genetics Ancestry Estimation 1

Explainable Supervised Method for Genetics Ancestry Estimati...

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1st International Conference on computer science and Artificial Intelligence, ICCSAI 2021

作者： Budiarto, Arif Pardamean, Bens Bina Nusantara University School of Computer Science Computer Science Department Jakarta Indonesia Bina Nusantara University BINUS Graduate Program - Master of Computer Science Computer Science Department Jakarta Indonesia

ISBN: (纸本)9781728133331

Ancestry estimation is one crucial stage in genomic research. It generates scores that represent the admixed genetics profile as the result of human evolution. In the previous research, we implemented multiple unsupervised methods to estimate these scores from large genomics data obtained from the 1000 Genome Project. These methods were limited to only cluster the samples to the five global populations in the dataset. The main challenge arose when implementing these methods to cluster the samples into more specific subpopulations. In this paper, we proposed a supervised approach to answer this challenge. Two state-of-the-art supervised machine learning methods, XGBoost and Deep Neural Network (DNN), were applied to the same dataset. These methods were aimed to classify samples, both into five main populations and also into 26 sub-populations. In the first classification task, both methods achieved similar results to our previous unsupervised approach. Interestingly, for the second classification task, which posses a relatively higher difficulty, DNN yielded better performance in the train, validation, and test dataset, despite its overfitting problem. Furthermore, the feature importance scores from each model were calculated using Shapley Additive Explanations (SHAP) method. Finally, 11 overlapped SNPs from all models were evaluated based on the reported Minor Allele Frequency (MAF) from the 1000 Genome Project. Overall, only using these 11 SNPs, we could differentiate each population in regards to its average MAF. © 2021 IEEE.

关键词： Genome

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Prediction Tool on Fine Particle Pollutants and Air Quality for Environmental Engineering

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SN computer science 2022年第3期3卷 1-31页

作者： Varde, Aparna S. Pandey, Abidha Du, Xu Dept. of Computer Science Environmental Science and Management PhD Program Montclair State University Montclair NJ United States Visiting Researcher at Max Planck Institute for Informatics Saarbrücken Germany Department of Computer Science Montclair State University Montclair NJ United States Department of Earth and Environmental Science Environmental Science and Management PhD Montclair State University Montclair NJ United States

This article focuses on the research, design and implementation of a prediction tool for air quality to estimate pollutant concentrations, contributing to environmental engineering. It addresses prediction of fine particle air pollutants of diameter less than 2.5 µm (particulate matter 2.5), their concentration being substantially influenced by urban traffic. We collect worldwide multicity data from health-related public sources on which mining is performed using classical data mining/machine learning paradigms: association rules, clustering and classification. Challenges include adapting appropriate techniques based on data, and capturing subtle domain-specific aspects. The prediction tool is built using knowledge discovered by mining, leveraging health standards, catering to novice, intermediate and expert users. The prediction output is accurate, efficient, interpretable and useful as evident from our experiments. The tool is helpful for urban decision support. This work is beneficial in developing software systems such as intelligent tutors, mobile device apps and smart city tools. It contributes to smart environment, mobility and living, making a positive impact on smart cities and sustainability. In this work, we claim that classical computational paradigms in their fundamental form can be adapted to solve environmental engineering problems, with easy comprehension, as per the Occam’s razor principle that advocates simplicity. This article constitutes applied research: using computational techniques to solve domain-specific problems. Future work includes exploring models in deep learning such as CNN and Bi-LSTM, and considering different types of pollutants as well as other sources besides multicity traffic data, to conduct further studies. This would address additional challenges with enhancements. © 2022, The Author(s), under exclusive licence to Springer Nature Singapore Pte Ltd.

关键词： Applied research Decision support Environmental engineering Health informatics Machine learning Urban studies

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Gerald Edelman's Steps Toward a Conscious Artifact

Journal of Artificial Intelligence and Consciousness

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Journal of Artificial Intelligence and Consciousness 2021年第2期8卷 325-333页

作者： Krichmar, Jeffrey L. Department of Cognitive Sciences Department of Computer Science University of California Irvine Irvine 92697-5100 CA United States

In 2006, during a meeting of a working group of scientists in La Jolla, California at The Neurosciences Institute (NSI), Gerald Edelman described a roadmap towards the creation of a Conscious Artifact. As far as I know, this roadmap was not published. However, it did shape my thinking and that of many others in the years since that meeting. This short paper, which is based on my notes taken during the meeting, describes the key steps in this roadmap. I believe it is as groundbreaking today as it was more than 15 years ago. © 2021 World Scientific Publishing Company.

关键词： Artificial Intelligence Consciousness Machine Consciousness Robotics

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A Hybrid CNN-SVM Approach for Malaria in Blood Cell Detection

A Hybrid CNN-SVM Approach for Malaria in Blood Cell Detectio...

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Software Engineering and Information Technology (ICoSEIT), International Conference on

作者： Andrea Stevens Karnyoto Mahmud Isnan Bens Pardamean 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

There is still a severe malaria problem worldwide, particularly in regions with limited access to diagnostic tools. It is crucial to develop a system for detecting malaria in blood cells. This paper presents a hybrid Convolutional Neural Network (CNN), and as a classifier, we use a Support Vector Machine (SVM) framework for the automated detection of malaria parasites in blood cell images. The proposed system leverages the strengths of CNNs in feature extraction and representation learning from images, combined with the discriminative power of SVMs for classification. Initially, CNN extracts intricate features from blood cell images, capturing essential patterns indicative of malaria infection. Subsequently, the extracted features are used to train an SVM classifier, enabling accurate discrimination between parasitized and uninfected blood cells. Experimental dataset evaluations were obtained from the Lister Hill National Center for Biomedical Communications website of the National Library of Medicine. The proposed model achieves a better f1-score, outperforming individual CNN or SVM models, around 0.015 compared to individual CNN models and 0.27 compared to individual SVM models. This hybrid CNN-SVM methodology offers a promising solution for accurately and efficiently detecting malaria parasites in blood cell images.

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Long short-term memory for hate speech and abusive language detection on Indonesian YouTube comment section 11

Long short-term memory for hate speech and abusive language ...

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2021 11th International Workshop on computer science and Engineering, WCSE 2021

作者： Salim, Calvin Erico Rudy Suhartono, Derwin Computer Science Department BINUS Graduate Program Master of Computer Science Bina Nusantara University Jakarta Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (纸本)9789811817915

Hate speech is one of the most challenging problem internet is facing today. With increasing numbers of users online, hate speech also rise and takes time to be classified manually particularly in languages other than English. This research examines hate speech detection problem in form of Bahasa Indonesia. Millions of comments and text posts are added to various social media and discussion platforms. Manual classification in all of the internet as hate speech and offensive language is a near impossible and time-consuming task. This research uses Long Short-Term Memory (LSTM) and Bidirectional Long Short Term Memory (Bi-LSTM) for the method of classifying hate speech and abusive language. The final accuracy is 88,44% by using 200 neurons with Bi-LSTM method. Most common challenges are different languages, out of vocabulary words, long range dependencies, and sarcasm. © 2021 11th International Workshop on computer science and Engineering, WCSE 2021. All Rights Reserved.

关键词： Long short-term memory

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Speed Bump Detection Through Inertial Sensors and Deep Learning in a Multi-contextual Analysis

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SN computer science 2023年第1期4卷 1-20页

作者： Menegazzo, Jeferson von Wangenheim, Aldo Graduate Program in Computer Science (PPGCC) Image Processing and Computer Graphics Lab (LAPIX) Brazilian National Institute for Digital Convergence (INCoD) Department of Informatics and Statistics (INE) Federal University of Santa Catarina (UFSC)-Florianópolis Santa Catarina Brazil

Speed bumps are vertical raisings of the road pavement used to force drivers to slow down to ensure greater safety in traffic. However, these obstacles have disadvantages in terms of efficiency and safety, where the presence of speed bumps can affect travel time and fuel consumption, cause traffic jams, delay emergency vehicles, and cause vehicle damage or accidents when not properly signaled. Due to these factors, the availability of geolocation information for these obstacles can benefit several applications in Intelligent Transportation System (ITS), such as Advanced Driver Assistance Systems (ADAS) and autonomous vehicles, allowing to trace more efficient routes or alert the driver of the presence of the obstacle ahead. Speed bump detection applications described in the literature employ cameras or inertial sensors, represented by accelerometers and gyroscopes. While camera-based solutions are mature with evaluation in different contextual conditions, those based on inertial sensors do not offer multi-contextual analyses, being mostly simple applications of proof of concept, not applicable in real-world scenarios. For this reason, in this work, we propose the development of a reliable speed bump detection model based on inertial sensors, capable of operating reliably in contextual variations: different vehicles, driving styles, and environments in which vehicles can travel to. For the model development and validation, we collect nine datasets with contextual variations, using three different vehicles, with three different drivers, in three different environments, in which there are three different surface types, in addition to variations in conservation state and the presence of obstacles and anomalies. The speed bumps are present in two different pavement types, asphalt and cobblestone. We use the collected data in experiments to evaluate aspects such as the influence of the placement of the sensors for vehicle data collection and the data window size. Afterwar

关键词： Autonomous vehicles Deep learning Inertial sensors Intelligent transport systems Road conditions Speed bump

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