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29th International Conference on Research in Computational Molecular Biology, RECOMB 2025

作者： Lee, Wei-Hao Li, Lechuan Dannenfelser, Ruth Yao, Vicky Systems Synthetic and Physical Biology Graduate Program Rice University Houston United States Department of Computer Science Rice University Houston United States Ken Kennedy Institute Rice University Houston United States Rice Synthetic Biology Institute Rice University Houston United States

ISBN: (纸本)9783031902512

Advancements in sequencing technology have expanded data availability, capturing diverse phenotypic traits and biological perturbations. However, increased resolution also raises complexity, as studies now examine multiple dimensions, including donor phenotypes, anatomical regions, cell types, and time points. Integrating datasets across studies promises insights into health and disease beyond the scope of individual experiments, but this requires methods that can separate technical artifacts from meaningful biological signals while providing interpretable insights into condition-related genetic factors. Existing approaches tend to focus on either integration or interpretability, rarely addressing both simultaneously. To overcome these challenges, we introduce ALPINE, a joint supervised-unsupervised non-negative matrix factorization framework that disentangles technical and biological variation while directly identifying condition-associated genes. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2025.

关键词： Matrix factorization

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GranatumX:A Community-engaging, Modularized, and Flexible Webtool for Single-cell Data Analysis

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Genomics, Proteomics & Bioinformatics 2021年第3期19卷 452-460页

作者： David G.Garmire Xun Zhu Aravind Mantravadi Qianhui Huang Breck Yunits Yu Liu Thomas Wolfgruber Olivier Poirion Tianying Zhao Cédric Arisdakessian Stefan Stanojevic Lana X.Garmire Department of Electrical Engineering&Computer Science University of MichiganAnn ArborMI 48109USA Epidemiology Program University of Hawaii Cancer CenterHonoluluHI 96813USA Department of Biostatistics University of MichiganAnn ArborMI 48109USA Department of Computational Medicine and Bioinformatics University of MichiganAnn ArborMI 48105USA Molecular Biosciences and Bioengineering Graduate Program University of Hawaii at ManoaHonoluluHI 96822USA

We present GranatumX,a next-generation software environment for single-cell RNA sequencing(scRNA-seq)data *** is inspired by the interactive webtool *** enables biologists to access the latest scRNA-seq bioinformatics methods in a web-based graphical *** also offers software developers the opportunity to rapidly promote their own tools with others in customizable *** architecture of GranatumX allows for easy inclusion of plugin modules,named Gboxes,which wrap around bioinformatics tools written in various programming languages and on various *** can be run on the cloud or private servers and generate reproducible *** is a community-engaging,flexible,and evolving software ecosystem for scRNA-seq analysis,connecting developers with bench *** is freely accessible at http://***/granatumx/app.

关键词： Single-cell RNA sequencing Analysis Pipeline Webtool Module

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Measurement of airline service sentiment analysis using vector space model

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AIP Conference Proceedings 2024年第1期3132卷

作者： Aries Maesya Harco Leslie Hendric Spits Warnars Ford Lumban Gaol Benfano Soewito Department of Computer Science BINUS Graduate Program Bina Nusantara University Jakarta Indonesia

Airlines are an organization that provides flight services for passengers or goods in Indonesia. There are many airlines available at this time giving passengers the option to choose the airline they want to use. Online reviews are one factor that is quite important in influencing consumer trust and interest in choosing an airline. On the Tripadvisor site, few or many reviews are given by consumers will have an influence on other potential customers but monitoring and organizing reviews from other consumers is not easy. There are too many reviews published from online review sites if they are processed manually. Therefore, it is necessary to use a sentiment analysis application to classify positive, negative, and neutral reviews from consumers so that it speeds up and makes it easier to review the shortcomings of each airline. Method Vector Space Model is used because it is relevant and effective in searching and categorizing text documents by using Cosine Similarity to look for similarities between the query vector and the document vector. The evaluation method used is Confusion Matrix which will calculate the accuracy precision and recall of the resulting test value. The results of the evaluation and validation carried out by this study resulted in an accuracy value of 76,42% with a value of precision of 83% and a recall of 87%.

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Hypersaline Tidal Flats Detection Using Deep Learning Over 37 Years of Landsat Data

Hypersaline Tidal Flats Detection Using Deep Learning Over 3...

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IEEE International Symposium on Geoscience and Remote Sensing (IGARSS)

作者： Maria Luize Pinheiro Luiz Cortinhas Cesar Diniz Raian V Maretto Mateus Grellert Graduate Program in Computer Science Federal University of Santa Catarina (UFSC) Brazil Solved - Solutions in Geoinformation Brazil Faculty of Geo-Information Science and Earth Observation (ITC) University of Twente The Netherlands Federal University of Rio Grande do Sul (UFRGS) Informatics Institute Brazil

Hypersaline tidal flats are plane areas usually related to mangrove forests, acting as guard and buffer against rising sea levels, and as maintainer of regional biodiversity. Such areas are primarily impacted by anthropogenic and natural activities, such as sea-salt extraction and pollution, so identifying and monitoring them is an important and challenging task. The present work uses a U-shaped Convolutional Neural Network architecture to systematically classify such formations over Landsat imagery. A large dataset containing data from 1985 to 2021 of the Brazilian Coastal Zone is used to train and evaluate our model. Experimental results show that the total area increased by 58.6 km 2 from 1985 to 2001, and decreased by approximately 92 km 2 from 2001 to 2021, representing a total reduction of ≈ 33.34 km 2 for the entire period. We also show that our model outperforms a related solution trained with the same dataset, achieving 70% and 86% for 1985 and 2020 respectively, against 69% and 82%.

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Ant Colony Optimization based Medical Image Preservation and Segmentation 2

Ant Colony Optimization based Medical Image Preservation and...

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2nd IEEE International Conference on Advanced Technologies in Intelligent Control, Environment, Computing and Communication Engineering, ICATIECE 2022

作者： Nandihal, Priya Pareek, Piyush Kumar De Albuquerque, Victor Hugo Costa Madhumala, R.B. Khanna, Ashish Sunil Kumar, V. Dayananda Sagar Academy of Technology and Management Dept of Computer Science and Design Bangalore India Graduate Program in Telecommunication Engineering Federal Institute of Education Science and Technology of Ceara Fortaleza Brazil Federal University of Ceara Department of Teleinformatics Engineering Brazil Maharaja Agrasen Institute of Technology GGSIPU CSE Dept India Nitte Meenakshi Institute of Technology Department of Artificial Intelligence & Machine Learning Bengaluru India

ISBN: (纸本)9781665493963

Image segmentation is an essential component in many different types of computer vision systems. Image segmentation is used in order to identify objects and boundaries within pictures. It is important to note that the success of recognition algorithms is heavily dependent on the quality of the picture segmentation, and there is yet no technique that can universally segment images. Boundary detection has a long history of being recognised as one of the most difficult challenges in the fields of image processing and pattern analysis, in particular, when it comes to applications in medical imaging. The clarity of the picture is being muddled by more information, which is the source of the problem's complexity. The creation of segmentation algorithms for medical pictures is an active field of study, and segmentation algorithms are meant to account for a variety of factors, including noise, intensity inhomogeneity, poor contrast between the lesion and the surrounding skin, and so on. There is currently no active contour model that combines the locally statistical property of being more noise-resistant, in which the intensities in the transformed domain have less overlapping in the statistics, and the locally image fitting property of extracting the local image information in order to be able to segment images with intensity inhomogeneity. This is because there is no such model. So the proposed work includes Ant colony optimization based double threshold segmentation in medical images. Performance of the proposed algorithm is more efficient, reliable and accurate than the existing algorithm. Performance parameters such as segmentation accuracy, error rate, and Dice co-efficient are used in order to conduct the evaluation of the proposed work. © 2022 IEEE.

关键词： Impulse noise

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LaPE: Layer-adaptive Position Embedding for Vision Transformers with Independent Layer Normalization

LaPE: Layer-adaptive Position Embedding for Vision Transform...

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International Conference on computer Vision (ICCV)

作者： Runyi Yu Zhennan Wang Yinhuai Wang Kehan Li Chang Liu Haoyi Duan Xiangyang Ji Jie Chen School of Electronic and Computer Engineering Peking University Shenzhen China AI for Science (AI4S)-Preferred Program Peking University Shenzhen Graduate School China Peng Cheng Laboratory Shenzhen China Department of Automation and BNRist Tsinghua University Beijing China School of Computer Science and Technology Zhejiang University Zhejiang China

Position information is critical for Vision Transformers (VTs) due to the permutation-invariance of self-attention operations. A typical way to introduce position information is adding the absolute Position Embedding (PE) to patch embedding before entering VTs. However, this approach operates the same Layer Normalization (LN) to token embedding and PE, and delivers the same PE to each layer. This results in restricted and monotonic PE across layers, as the shared LN affine parameters are not dedicated to PE, and the PE cannot be adjusted on a per-layer basis. To overcome these limitations, we propose using two independent LNs for token embeddings and PE in each layer, and progressively delivering PE across layers. By implementing this approach, VTs will receive layer-adaptive and hierarchical PE. We name our method as Layer-adaptive Position Embedding, abbreviated as LaPE, which is simple, effective, and robust. Extensive experiments on image classification, object detection, and semantic segmentation demonstrate that LaPE significantly outperforms the default PE method. For example, LaPE improves +1.06% for CCT on CIFAR100, +1.57% for DeiT-Ti on ImageNet-1K, +0.7 box AP and +0.5 mask AP for ViT-Adapter-Ti on COCO, and +1.37 mIoU for tiny Segmenter on ADE20K. This is remarkable considering LaPE only increases negligible parameters, memory, and computational cost.

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Economics of Semantic Communication in Metaverse: An Auction Approach

Economics of Semantic Communication in Metaverse: An Auction...

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Consumer Communications and Networking Conference, CCNC IEEE

作者： Zi Qin Liew Hongyang Du Wei Yang Bryan Lim Zehui Xiong Dusit Niyato Han Yu Alibaba-NTU Singapore Joint Research Institute Nanyang Technological Univerity Singapore School of Computer Science and Engineering Energy Research Institute @ NTU Interdisciplinary Graduate Program Nanyang Technological University Singapore Pillar of Information Systems Technology and Design Singapore University of Technology and Design Singapore School of Computer Science and Engineering Nanyang Technological University Singapore

Metaverse provides embodied artificial-reality experience to the users in the virtual spaces. Many innovative and creative services such as virtual conference and tourism have been realized in the digital twins maintained by the virtual service providers (VSP) in Metaverse. Digital twins are digital copies of the physical world constructed virtually by the VSPs using real-world data. For a realistic experience, VSPs need to collect data that is up-to-date and relevant to their services. In this paper, we propose an incentive design framework to support the data trading between VSPs and edge devices. In the auction model, we model the valuation of data by considering data relatedness and data freshness. In our model, the semantic communication model is used to filter the relevant data, and the age of information (AoI) metric is used to assess the data freshness. Results show that by considering the data freshness, our mechanism helps to increase the average update frequency so that the VSPs obtain fresh data for construction of digital twins. Our model ensures the desired properties of individual rationality, incentive compatibility, and budget balance.

关键词： Measurement Metaverse Data integrity Semantics Streaming media Information filters Data models

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A Convolutional Neural Network-based Ancient Sundanese Character Classifier with Data Augmentation

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Procedia computer science 2021年 179卷 195-201页

作者： Alam Ahmad Hidayat Kartika Purwandari Tjeng Wawan Cenggoro Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

With an increasing interest in the digitization effort of ancient manuscripts, ancient character recognition becomes one of the most important areas in the automated document image analysis. In this regard, we propose a Convolutional Neural Network (CNN)-based classifier to recognize the ancient Sundanese characters obtained from a digital collection of Southeast Asian palm leaf manuscripts. In this work, we utilize two different preprocessing techniques for the dataset. The first technique involves the use of geometric transformations, noise background addition, and brightness adjustment to augment the imbalanced samples to be fed into the classifier. The second technique makes use of the Otsu’s threshold method to binarize the characters and only uses the usual geometric transformations for the data augmentation. The proposed network with different data augmentation processes is trained on the training set and tested on the testing set. Image binarization from the second technique can outperform the performance of the CNN-based classifier upon the first technique by achieving a testing accuracy of 97.74%.

关键词： ancient sundanese characters convolutional neural network data augmentation document image analysis Otsu’s threshold method

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Systematic Evaluation of Cross Population Polygenic Risk Score on Colorectal Cancer

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Procedia computer science 2021年 179卷 344-351页

作者： Bharuno Mahesworo Arif Budiarto Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

The number of findings in cancer genomics research has grown rapidly in the last decade due to the decline in the cost of human sequencing and genotyping. However, the majority of the reported significant marker associated with cancer traits are based on European and East Asian population. Large population such as South Asian and South-East Asian population are under-represented in genomics research. In this study, we explored the possibility of computing a Polygenic Risk Score (PRS) of colorectal cancer on our test sample based on reported significant Single Nucleotide Polymorphism (SNP). The SNPs used to compute the risk score were collected from GWAS Central and GWAS Catalog. Significant SNPs from IC3 study were used as a benchmark. The result shows that calculating colorectal cancer risk score using reported significant marker from different population group is possible. The p-value of our statistic model shows significant differences between case and control group risk score.

关键词： Polygenic Risk Score Cross Population Colorectal Cancer

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Convolutional Neural Networks for Scops Owl Sound Classification

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Procedia computer science 2021年 179卷 81-87页

作者： Alam Ahmad Hidayat Tjeng Wawan Cenggoro Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Adopting a deep learning model into bird sound classification tasks becomes a common practice in order to construct a robust automated bird sound detection system. In this paper, we employ a four-layer Convolutional Neural Network (CNN) formulated to classify different species of Indonesia scops owls based on their vocal sounds. Two widely used representations of an acoustic signal: log-scaled mel-spectrogram and Mel Frequency Cepstral Coefficient (MFCC) are extracted from each sound file and fed into the network separately to compare the model performance with different inputs. A more complex CNN that can simultaneously process the two extracted acoustic representations is proposed to provide a direct comparison with the baseline model. The dual-input network is the well-performing model in our experiment that achieves 97.55% Mean Average Precision (MAP). Meanwhile, the baseline model achieves a MAP score of 94.36% for the mel-spectrogram input and 96.08% for the MFCC input.

关键词： acoustic features bird sound classification convolutional neural network mean average precision scops owl

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