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TaxDiff: taxonomic-guided diffusion model for protein sequence generation

science China(Information sciences) 2025年第4期68卷 385-386页

作者： Zongying LIN Hao LI Liuzhenghao LV Yu WANG Bin LIN Junwu ZHANG Zijun CHEN Calvin Yu-Chian CHEN Li YUAN Yonghong TIAN School of Electronic and Computer Engineering Peking University AI for Science (AI4S)-Preferred Program Peking University Shenzhen Graduate School Peng Cheng Laboratory School of Chemical Biology and Biotechnology Peking University

Protein design aims to generate protein variants with targeted biological functions, which is significant in multiple biological areas, including enzyme reaction catalysis, vaccine design, and fluorescence intensity. Protein design contains two paradigms: sequence generation and structure generation. Recently, EvoDiff [1] proposed a universal designing paradigm, combining structure and sequence generation using the diffusion framework, which improves the protein design efficiency.

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Investigation of player emotion and instinct on racing video game using 6-11 framework (case study: split second (2010) single player modes) 9th

Investigation of player emotion and instinct on racing video...

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

作者： Pratama, Galih Dea Novika, Andien Dwi Ardiyanto, Elshad Ryan Game Application & Technology Program Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Binus Graduate Program Bina Nusantara University Jakarta11480 Indonesia

Racing is one of the most prominent genres in the modern video game industry, where the games within the genre enable players to use any vehicle of their choice and win through doing series of action within gameplay. Thus, it made the genre popular over the years, spawning many famous titles such as Split Second back in 2010. Like every other video game title, Split Second also invokes the player emotion and instinct during its gameplay session. To understand the emotion and instinct aspect present in players of the game, we will use 6-11 framework which focuses on the two aspects. As part of the conclusion, Split Second game involves instincts such as Competition, Collecting, and Survival, with emotions including Fear, Pride, Joy, and Excitement, which can be found from its vast single player game modes. © 2024 The Authors.

关键词： 6-11 framework game analysis racing video games video games

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Bridging Accuracy and Efficiency: The Role of PINNs in Immune Response Simulations

Bridging Accuracy and Efficiency: The Role of PINNs in Immun...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Fernandes, Thiago E. Dos Santos, Rodrigo W. Lobosco, Marcelo Federal University of Juiz de Fora Graduate Program on Computational Modelling Juiz de Fora Brazil Federal University of Juiz de Fora Institute of Exact Sciences Department of Computer Science Juiz de Fora Brazil

ISBN: (纸本)9798350386226

Myocarditis, characterized by inflammation of the heart muscle, has seen a notable 62.2% increase in incidence over the past three decades, leading to 324,490 deaths in 2019. Despite advancements in understanding its etiology, several critical questions remain unresolved, highlighting the need for improved patient treatment strategies. Computational methods play a crucial role in unraveling the complex interactions between pathogens and the immune system. This study explores the use of Physics-Informed Neural Networks (PINNs) to accelerate a newly developed model for myocardial edema formation in acute infectious myocarditis. The model describes the concentrations of pathogens and leukocytes using a nonlinear system of ordinary differential equations (ODEs). Our findings demonstrate a mean computational speedup of 5.93, while maintaining a Root Mean Squared Error of 0.0015. These results indicate that PINNs can accurately replicate the ODE system's solutions, offering substantial computational efficiency for this application. © 2024 IEEE.

关键词： Pathogens

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Flexible refractory castables based on the Al2O3-MgO-TiO2 system

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Ceramics International 2025年第15期51卷 20822-20829页

作者： Reitmann, B. Borges, O.H. Falsetti, L.O.Z. Pagliosa Neto, C. Pandolfelli, V.C. Federal University of São Carlos Graduate Program in Materials Science and Engineering São Carlos Brazil São Carlos Brazil RHI Magnesita Research and Development Center Contagem Brazil

Toughening by in-situ phase formation is highly desired for high-performance refractories, as it enhances their thermomechanical properties (e.g. thermal shock damage resistance). For this purpose, pseudobrookite and intermediary spinels are promising phases due to their thermal expansion mismatch, resulting in self-microcracking. Aiming to develop highly flexible refractory castables, compositions based on the Al2O3-MgO-TiO2 system were formulated with the aid of computational thermodynamics. Of the most promising compositions, five of them were experimentally produced and had their thermomechanical and physical properties assessed by X-ray diffraction, in-situ elastic modulus, thermal shock damage analysis (ΔT = 1000 °C) and scanning electron microscopy. Results pointed out that small titania contents led to a positive effect on microstructure densification, improving the mechanical performance of the refractories and generation of phases that induce microcracking upon cooling, enhancing the thermal shock damage resistance. Nevertheless, an excess of TiO2 led to extensive cracking and cohesion loss in the refractory matrix. © 2025

关键词： Microcracking

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Understanding the Definitions of Microcredentials in Higher Education: Systematic Literature Review

Understanding the Definitions of Microcredentials in Higher ...

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2024 International Conference on TVET Excellence and Development, ICTeD 2024

作者： Wihendro Warnars, Harco Leslie Hendric Spits Prabowo, Harjanto Sfenrianto Bina Nusantara University BINUS Graduate Program- Computer Science Information Systems Department Jakarta Indonesia Bina Nusantara University BINUS Graduate Program- Computer Science Computer Science Department Jakarta Indonesia Bina Nusantara University BINUS Business School Undergraduate Program Management Department Jakarta Indonesia Bina Nusantara University BINUS Graduate Program-Master of Information Systems Management Information Systems Management Department Jakarta Indonesia

ISBN: (纸本)9798331516413

The growing focus on microcredentials emphasizes the urgent need for precise and widely accepted definitions, as existing uncertainties hinder their effective implementation. This research aims to investigate the comprehension of microcredentials definitions in the context of higher education by conducting a systematic literature review. The goal is to identify current definitions of microcredentials to facilitate standardization initiatives. Following The Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) methodology to systematically search in Scopus database within 2019-2024 resulting 940 articles, by removing the duplicates, 280 articles were initially reviewed, with 29 selected for detailed thematic analysis based on specific inclusion and exclusion criteria. By adapting the six phases of thematic analysis, selected articles were identified analyzed, organized, described, and themes found the data set were reported. Key findings reveal that, while a universally accepted definition is lacking, common themes emerge: microcredentials are competency-based, modular, portable, stackable, and often include quality assurance. These attributes highlight microcredentials as valuable for upskilling and reskilling in a flexible manner. The study concludes that establishing standard definitions can increase the recognition and utility of microcredentials across educational and professional sectors and recommends further research to strengthen core elements for consistency. © 2024 IEEE.

关键词： Competency-based Higher Education Microcredentials Modular Reskilling Upskilling

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Optimization of Node Reduction Using BRKGA for GNN-Based Traffic Speed Forecasting 13

Optimization of Node Reduction Using BRKGA for GNN-Based Tra...

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13th IEEE Congress on Evolutionary Computation, CEC 2024

作者： Inokuchi, Yuto González, Pedro Henrique Mendonça, Israel Aritsugi, Masayoshi Graduate School of Science and Technology Kumamoto University Kumamoto Japan Federal University of Rio de Janeiro System Engineering and Computer Science Program Rio de Janeiro Brazil Kumamoto University Faculty of Advanced Science and Technology Kumamoto Japan

ISBN: (纸本)9798350308365

While Spatio-Temporal Graph Convolutional Networks (STGCNs) are an effective method for traffic speed fore-casting, their training and inference tend to be time-consuming. In this paper, we aim to refine these networks by strategically reducing their number of nodes, thereby boosting computational efficiency. The nodes in these graphs represent data observed for road segments, and by analyzing the interconnections and layout of the graph, we can identify nodes with minimal contribution to overall performance. Removing these nodes can potentially decrease computation time while maintaining the prediction accuracy. We employ the Biased Random-Key Genetic Algorithm (BRKGA) to identify a good set of nodes for removal, based on a predefined percentage reduction of the original graph size (e.g., retaining 95 % of the original graph). We evaluate different graph size configurations, ranging from 95 % to 70 % node retention, to determine the least impactful node set performance. Our experiments on three real-world datasets reveal that reducing nodes can decrease computation time by up to 29%, and as a byproduct of removing noise, even improve the prediction accuracy. © 2024 IEEE.

关键词： Genetic algorithms

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Efficient Hyperparameter Optimization Using Deep Q-Network and BRKGA 13

Efficient Hyperparameter Optimization Using Deep Q-Network a...

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13th IEEE Congress on Evolutionary Computation, CEC 2024

作者： Kobayashi, Kosei Aritsugi, Masayoshi González, Pedro Henrique Mendonça, Israel Graduate School of Science and Technology Kumamoto University Kumamoto Japan Faculty of Advanced Science and Technology Kumamoto University Kumamoto Japan System Engineering and Computer Science Program Federal University of Rio de Janeiro Rio de Janeiro Brazil

ISBN: (纸本)9798350308365

Hyperparameter optimization (HPO) is paragon to maximize performance when designing machine learning models. Among different HPO methods, Genetic Algorithm (GA) based optimization is considered effective because it allows a wide and diverse range of solutions to be explored. However, GA's exploratory nature makes this type of algorithm to evaluate many solutions that do not improve the overall performance. This is specially costly when the objective function to be evaluated is time-consuming, like in the HPO field. In this paper, we propose an efficient hybrid algorithm that is able to reduce computational cost by combining deep reinforcement learning with the Biased Random Key Genetic Algorithm (BRKGA), a variant of genetic algorithms. Our reinforcement learning agent has a decision-making role during the population's fitness calculation, in which it filters out chromosomes that would not improve the overall fitness of the population. The agent uses small amounts of pre-trained data to identify trends in potentially good solutions, and carry out its decision process. We conduct experiments on eight different datasets to assess the effectiveness of the proposed method, and the results show that the proposed method can significantly reduce the computation time of hyperparameter search using BRKGA (up to 44% reduction in computational time) without compromising the quality of the solution (no statistically difference in results). © 2024 IEEE.

关键词： Genetic algorithms

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Challenges and Recommendations for Improving Logistic Skills Through Simulation-Based Learning Technology

Challenges and Recommendations for Improving Logistic Skills...

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2025 International Conference on Advancement in Data science, E-learning and Information System, ICADEIS 2025

作者： Sirait, Tamsir Hasudungan Meyliana Arifin, Yulyani Yulianto, Budi Bina Nusantara University Binus Graduate Program Jakarta Indonesia Bina Nusantara University Computer Science Department Jakarta Indonesia

ISBN: (纸本)9798331513320

Simulation-based learning is one of the most powerful tools to support the educational process. This learning offers an opportunity to learn based on experiences that are very similar to real-world environments. In the context of logistics, which can be considered a complex system, significant efforts are required to enhance students' understanding and practical skills. For that reason, simulations are used so that benefits such as skills and knowledge in the field of logistics can be achieved. However, there are currently several challenges in developing simulation-based learning in higher education. These challenges include the need for simulations that are appropriate for the current learning context, where the students are generally from Generation Z, and how to improve their learning quality in the era of Industry 4.0. To address these challenges, more suitable simulations need to be developed, and higher education institutions must carefully examine how to develop them, including identifying the essential components in the development of simulations for logistics learning. In this research, a systematic literature review using the PRISMA method and also creating a conceptual model of simulation that better meets the current needs of logistics education will be proposed. The results of this research can be used as a basis for developing updated simulations to better prepare students for the challenges of Industry 4.0. © 2025 IEEE.

关键词： industry 4.0 logistics simulation development simulation learning simulation learning component

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Indonesian Hoax News Classification with Multilingual Transformer Model and BERTopic

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Informatica (Slovenia) 2022年第8期46卷 81-90页

作者： Hutama, Leonnardo B. 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

Technology and information growth enable internet users to play a role in disseminating information, including hoax news. One way that to avoid hoax news is to look for sources of information, but valid news is not always perceived as 'true' by individuals because human judgments can lead to bias. Several studies on automatic hoax news classification have been carried out using various deep learning approaches such as the pre-trained multilingual transformer model. This study focuses on classifying Indonesian hoax news using the pre-trained transformer multilingual model (XLM-R and mBERT) combined with a BERTopic model as a topic distribution model. The result shows that the proposed method outperforms the baseline model in classifying fake news in the low-resource language (Indonesian) with accuracy, precision, recall, and F1 results of 0.9051, 0.9515, 0.8233, and 0.8828 respectively. © 2022 Slovene Society Informatika. All rights reserved.

关键词： Deep learning

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Efficient Node Reduction Heuristic for GNN-Based Traffic Speed Forecasting 11

Efficient Node Reduction Heuristic for GNN-Based Traffic Spe...

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11th IEEE/ACM International Conference on Big Data Computing, Applications and Technologies, BDCAT 2024

作者： Inokuchi, Yuto Gonzalez, Pedro Henrique Aritsugi, Masayoshi Mendonca, Israel Kumamoto University Graduate School of Science and Technology Kumamoto Japan Federal University of Rio de Janeiro System Engineering and Computer Science Program Rio de Janeiro Brazil Kumamoto University Faculty of Advanced Science and Technology Kumamoto Japan

ISBN: (纸本)9798350367300

In this paper, we aim to reduce the number of nodes from Graph Neural Networks (GNNs), thereby simplifying models and reducing computational costs. GNNs are highly effective for various tasks, such as prediction, classification, and clustering, due to their ability to learn node and edge attributes and relationships, and they have been utilized for intelligent transportation systems recently by converting sensor networks into graph structures. Deep spatio-temporal neural networks, including Spatio-Temporal Graph Convolutional Networks (STGCNs), capture spatial and temporal dependencies, making them suitable for traffic speed forecasting, traffic demand prediction, and travel time estimation. Despite their success, GNNs face challenges in industrial applications due to significant memory usage and time consumption. In this paper, we propose a new approach to node reduction that outperforms existing methods in computational efficiency. Our experiments on two real-world traffic datasets demonstrate that using the heuristic and edge information to reduce nodes can cut computation time of optimization up to 95% and, by eliminating noise, can even enhance prediction accuracy. © 2024 IEEE.

关键词： Graph neural networks

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