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Semi-automated meningioma segmentation with bounding boxes 9th

Semi-automated meningioma segmentation with bounding boxes

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9th International Conference on Computer science and Computational Intelligence, ICCSCI 2024

作者： Heryanto, Nur Adhianti Isnan, Mahmud Henry, Matthew Martianus Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

Segmentation is manually performed by physicians, which takes considerable time and may be subject to observers. Automating this task can increase efficiency and consistency. Existing studies on meningioma segmentation used data from limited study centers, indicating the need for research on multi-center data to assess generalizability. In this work, two semi-automated methods with bounding box priors, LiteMedSAM and BBU-Net, are evaluated on the brain tumor segmentation (BraTS) 2023 meningioma dataset collected from five study-centers. Preprocessing included exclusion of small tumors, z-score normalization, and extraction of slices that contain tumors, generating 25,602 2D axial magnetic resonance imaging (MRI) scans. A fine-tuning strategy is adopted for LiteMedSAM while BBU-Net is trained from scratch. The models are evaluated using a five-fold cross-validation, with data split at the case level. Results show that while U-Net models can achieve performance close to LiteMedSAM, the foundation model has overall better performance, with more than 90% in all evaluation scores. © 2024 The Authors.

关键词： Magnetic resonance imaging

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Application of Predictive Analytics at Financial Institutions: A Systematic Literature Review 8

Application of Predictive Analytics at Financial Institution...

引用

8th IIAI International Congress on Advanced Applied Informatics, IIAI-AAI 2019

作者： Indriasari, Elisa Soeparno, Haryono Gaol, Ford Lumban Matsuo, Tokuro Doctor of Computer Science Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Advanced Institute of Industrial Technology Japan

ISBN: (纸本)9781728126272

The issues that relate with the automatics and intelligent tracing of the transaction and banking customer become the main issues nowadays. Whereas most of transaction that already moved to digital and online transaction that needed more intelligent features on the Predictive Analyst. The rise of predictive analytics (PA) is one of the biggest disruptions in financial services. In the last years, PA methods grew sharply to give the baseline of data driven decision-making process for forecasting future business situation. PA uses various algorithms to discover different patterns in the big data environment that might create more value for businesses including in financial institutions. The potential implementation of data science in financial industry is still to be explored. In this paper, we summarize work done on PA at financial industry. We also explore the potential application of PA and investigating how data science and big data is going to be used in financial institutions in the future. © 2019 IEEE.

关键词： Predictive analytics

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LDA Topic Modeling for bioinformatics Terms in arXiv Documents 9th

LDA Topic Modeling for Bioinformatics Terms in arXiv Documen...

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9th International Conference on Computer science and Computational Intelligence, ICCSCI 2024

作者： Karnyoto, Andrea Stevens Henry, Matthew Martianus Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

A wide variety of disciplines contribute to bioinformatics research, including computer science, biology, chemistry, mathematics, and physics. This study determines the number of research articles published on arXiv classified as bioinformatics topics and the most frequently used bioinformatics terms using topic modeling, Latent Dirichlet Allocation (LDA). An algorithm based on LDA is used to discover topics hidden within large collections of documents through the use of statistical analysis. Our research examined 226453 articles on arXiv between January 2023 and January 2024. As a result, there are more than 10521 articles categorized into bioinformatics topics. Most commonly, 6352 documents are in the "Mathematical Physics" category. The second most popular category is "Computer science," with 2950 documents. Accordingly, the terms 'RNA,' 'sequence,' 'tree,' and 'homology' are the three most commonly used terms in bioinformatics. The study of RNA plays a vital role in molecular biology;thus, the study of RNA is prevalent in bioinformatics. Sequential data refer to the order in which nucleotides or amino acids can be found in a DNA molecule or a protein. © 2024 The Authors.

关键词： arXiv bioinformatics Latent Dirichlet Allocation

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Evaluating the Effectiveness of Transformer Models for Molecular Property Prediction: A Review 9

Evaluating the Effectiveness of Transformer Models for Molec...

引用

9th International Conference on Information Technology and Digital Applications, ICITDA 2024

作者： Imani, Alyssa Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Binus Graduate Program Bina Nusantara University Computer Science Departement Jakarta11480 Indonesia

ISBN: (纸本)9798331510732

Transformer models, originally successful in natural language processing, are now being applied to chemical and biological studies, excelling in areas such as molecular property prediction, material science, and drug discovery. BERT, a Transformer-based model, has become foundational in cheminformatics, particularly for QSAR (Quantitative Structure-Activity Relationship) modeling and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) evaluations in drug discovery. However, achieving higher accuracy often requires designing more complex models, which can compromise their interpretability. This posing a challenge for researchers who need to understand the reasoning behind the predictions. The trade-off between accuracy and interpretability presents a critical challenge in applying black box models to real-world problems in cheminformatics. This work compares Transformer-based models with traditional machine learning and deep learning approaches, focusing on both interpretability and performance. The goal is to highlight the strengths and limitations of each method, offering insights into their optimal use in drug discovery and material science. © 2024 IEEE.

关键词： Prediction models

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Knowledge Graph-Enhanced Semantic Cache for Low-Latency and Cost-Effective Inference in Large Language Models 9

Knowledge Graph-Enhanced Semantic Cache for Low-Latency and ...

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9th International Conference on Information Management and Technology, ICIMTech 2024

作者： Dominic, Nicholas Pardamean, Bens Bina Nusantara University Bioinformatics & Data Science Research Center Jakarta11480 Indonesia BINUS Graduate Program - Master of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798350390025

In organizational knowledge management, Large Language Model (LLM) caches act as a semantic repository gathered from previous LLM responses. Due to intensive calls from multiple users, LLM may suffer from high inference latency. While there are many prior available approaches to solve this problem, most of them are inherently complex. This paper introduced a Knowledge Graph-enhanced Semantic Cache mechanism as an alternative, lightweight technique to boost retrieval for similar prompts. The latest state-of-the-art open-source LLM, named Google's Gemma-2B-it, was used to generate sample prompts and responses as a draft, while a knowledge graph (KG) was built from Wikipedia sentences. To create embeddings of prompts and KG, all-MiniLM-L6-v2 from SentenceTransformer was used. This new cache system resulted in up to 28% improvement over a standard model. In particular, reinforcement with KG cache embeddings yielded more than 85% semantic cache accuracy. To map the next trajectory of this pilot study, an overview of the extended framework for LLM knowledge management was also presented in this paper. The framework includes the new KG- enhanced cache system equipped with scalable security and fallback mechanisms that can promote green technology through substantial improvements in latency, throughput, and overall LLM costs. © 2024 IEEE.

关键词： Knowledge graph

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Variational quantum neural network with optimized ansatz for predicting malignant ventricular arrhythmias 9th

Variational quantum neural network with optimized ansatz for...

引用

9th International Conference on Computer science and Computational Intelligence, ICCSCI 2024

作者： Dominic, Nicholas Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Computer Science Program Bina Nusantara University Jakarta11480 Indonesia

Preventive strategies should be the utmost priority when dealing with diverse patients suffering from malignant ventricular arrhythmia (MVA) that can lead to sudden cardiac death (SCD). Electrocardiogram (ECG) data is commonly used as a predictor for MVA predictive models. In this study, all ECG signals from MIT-BIH databases were fragmented into five-minute durations with a frequency sampling of 128 Hz. To solve the absence of hybrid optimizations in Machine Learning (ML) models, a novel Variational Quantum Neural Network (VQNN) was invented. Empowered by deep learning capabilities and optimized quantum circuits design, VQNN achieved remarkable performances designated by an accuracy of up to 95.1%, a perfect 100% recall, and a 95.2% score of the area under the Receiver Operating Characteristic curve (AUC ROC) with Conjugate Gradient as an optimizer and EfficientSU2 as a quantum ansatz. Despite the susceptibility to quantum noise, this research settles a new trajectory of utilizing quantum variational algorithms to predict and expand its applicability for MVA cases. © 2024 The Authors.

关键词： Quantum computers

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database Design for Indonesian Scholarship Recommender Systems 7

Database Design for Indonesian Scholarship Recommender Syste...

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7th International Conference on Information Management and Technology, ICIMTech 2022

作者： Elwirehardja, Gregorius Natanael Jason Dominic, Nicholas Pardamean, Bens BINUS Graduate Program - Master of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia

ISBN: (数字)9781665450904

ISBN: (纸本)9781665450904

Following the evolution of technology, researchers have conducted several studies to propose reliable scholarship recommender systems. However, few have explored the data storage systems, which are highly beneficial to collect huge volumes of real data in training the recommender systems. In this paper, a database design for collecting such data was proposed, equipped with integer encodings for categorical variables and a method to normalize variables with varying ranges. Using Connoly and Begg's database design method, the final design consisted of a normalized Entity Relationship Diagram (ERD) and data dictionaries. The design was also constructed to support usages of various data for determining scholarship recipients, including education history, achievements, and organizational experiences. The proposed design can be implemented on information systems to allow easier information access for scholarships in Indonesia. © 2022 IEEE.

关键词： Recommender systems

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Exploring Recurrent Neural Network Models for Depression Detection Through Facial Expressions: A Systematic Literature Review 6

Exploring Recurrent Neural Network Models for Depression Det...

引用

6th International Conference on Computer and Informatics Engineering, IC2IE 2023

作者： Rumahorbo, Brilyan Nathanael Pardamean, Bens Elwirehardja, Gregorius Natanael Bina Nusantara University Binus Graduate Program - Master of Computer Science Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia

ISBN: (纸本)9798350345162

Major Depressive Disorder (MDD) is a prevalent mental disorder, affecting a significant number of individuals, with estimates reaching 300 million cases worldwide. Currently, the diagnosis of this condition relies heavily on subjective assessments based on the experience of medical professionals. Therefore, researchers have turned to deep learning models to explore the detection of depression. The objective of this review is to gather information on detecting depression based on facial expressions in videos using deep learning techniques. Overall, this research found that RNN models achieved 7.22 MAE for AVEC2014. LSTM models produced 4.83 MAE for DAIC-WOZ, while GRU models achieved an accuracy of 89.77% for DAIC-WOZ. Features like Facial Action Units (FAU), eye gaze, and landmarks show great potential and need to be further analyzed to improve results. Analysis can include applying feature engineering techniques. Aggregation methods, such as mean calculation, are recommended as effective approaches for data processing. This Systematic Literature Review found that facial expressions do have relevant patterns related to MDD. © 2023 IEEE.

关键词： deep learning facial expression GRU LSTM major depressive disorder

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Sequence to Sequence Deep Learning Architecture for Forecasting Temperature and Humidity inside Closed Space 10

Sequence to Sequence Deep Learning Architecture for Forecast...

引用

10th International Conference on Cyber and IT Service Management, CITSM 2022

作者： Setiawan, Karli Eka Elwirehardja, Gregorius Natanael Pardamean, Bens Bina Nusantara University Binus Graduate Program Computer Science Program Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia

ISBN: (数字)9781665460743

ISBN: (纸本)9781665460743

Solar Dryer Dome (SDD), an agricultural facility for drying and preserving agricultural products, needs a smart ability to predict the future indoor climate accurately, including indoor temperature and indoor humidity, in order to optimize electricity usage. To overcome these challenges, deep learning has been a widely adopted method. This research aims to forecast the future indoor climate using time series data by implementing a sequence-to-sequence (seq2seq) architecture, which is mostly used in Natural Language Processing (NLP) tasks. The two proposed seq2seq models, Long Short-Term Memory (LSTM) seq2seq and Gated Recurrent Unit (GRU) seq2seq, have proven to be superior to the adapted LSTM and GRU. The results show that the seq2seq GRU model outperforms the adapted GRU baseline model by an average difference of 0.03013 in MAE and the seq2seq LSTM model outperforms the adapted LSTM baseline model by an average difference of 0.00941 in MAE. To the best of our knowledge, this is the first implementation of seq2seq models for indoor climate forecasting on the Room Climate dataset. © 2022 IEEE.

关键词： Long short-term memory

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Web Information System Design for Fast Protein Post-Translational Modification Site Prediction 7

Web Information System Design for Fast Protein Post-Translat...

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7th International Conference on Information Management and Technology, ICIMTech 2022

作者： Elwirehardja, Gregorius Natanael Dominic, Nicholas Pardamean, Bens BINUS Graduate Program - Master of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Research Center Bina Nusantara University Bioinformatics and Data Science Jakarta11480 Indonesia

ISBN: (数字)9781665450904

ISBN: (纸本)9781665450904

In the field of bioinformatics, the protein Post-Translational Modification (PTM) site prediction has been widely studied and Web Information Systems (WIS) has been deployed by researchers for this task. Through a literature review and benchmarking process, we identified the requirements which included quick predictions, efficient memory usage, and input validations. However, no detailed designs have been proposed so far, which may have contributed to some requirements not being implemented in some of the websites. Therefore, we propose a detailed WIS conceptual design, which can be used for predicting the sites of multiple PTM types, equipped with a validation algorithm and compared the usage of various string searching algorithms as well as file storage formats. Experiment results showed that the linear search algorithm is the fastest for this task and storing the protein data in npz format when performing multi-PTMs site prediction can assist in reducing memory usage. The proposed design can be implemented into user-friendly web tools that are both efficient in speed and memory usage in future studies. © 2022 IEEE.

关键词： Forecasting

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