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2024 IEEE International Conference on bioinformatics and Biomedicine, BIBM 2024

作者： Xiang, Jinhai Zhang, Yan Yu, JiaKun He, Xinwei Huazhong Agricultural University College of Informatics Wuhan430070 China Huazhong Agricultural University Agricultural Bioinformatics Key Laboratory of Hubei Province Wuhan430070 China Huazhong Agricultural University Key Laboratory of Smart Farming for Agricultural Animals Ministry of Agriculture Hubei Engineering Technology Research Center of Agricultural Big Data Wuhan430070 China

ISBN: (纸本)9798350386226

Semi-supervised semantic segmentation (SSS), which allows for learning a better model with a small fraction of labeled samples and a large amount of unlabeled ones, is valuable yet challenging in medical image analysis. Recent works (e.g., UniMatch) have found that weak-to-strong consistency via augmentation is especially conducive to SSS training. However, they inadvertently introduce cognitive biases for unlabeled images, making it difficult to segment accurately near the target's edge regions. In this paper we present a lightweight bias-correct module to self-correct these mistakes between the strong perturbations. Based on it, we design a new framework named BcMatch by plugging it into UniMatch to reduce such cognitive biases stemming from incorrect pseudo-labels for unlabeled images. Moreover, we also introduce a bias correction loss, which works in tandem with the consistency loss to guide the model learning, focusing more on the edge regions of the targets. Experiments on the representative semi-supervised segmentation dataset, ACDC, demonstrate our BcMatch surpasses UniMatch by a large margin, attaining new state-of-the-art performance. The code is at https://***/zhangyan498/BcMatch. © 2024 IEEE.

关键词： Semantic Segmentation

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LLM2Vec Sentence Embeddings Analysis in Sentiment Classification

LLM2Vec Sentence Embeddings Analysis in Sentiment Classifica...

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2024 IEEE International Conference on data and Software Engineering, ICoDSE 2024

作者： Henry, Matthew Martianus Heryanto, Nur Adhianti Isnan, Mahmud Kurnianingrum, Dian Ratnapuri, Chyntia Ika Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Entrepreneurship Department Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

ISBN: (纸本)9798331506407

Sentiment analysis is crucial method in business intelligence to extract insights, which typically begin with sentiment classification. One of the latest frameworks for generating sentence embeddings for sentiment classification is LLM2Vec, which allows Transformer decoder-based models to generate sentence embeddings for text representation. Its capability is deemed language-agnostic, which, in this study, the framework is leveraged for Tokopedia tweet sentiment analysis to prove the claim. The base decoder models used in the LLM2Vec framework were Llama 3 8B, Llama 2 7B, Sheared Llama 1.3B, and Mistral 7B. Two BERT-based models, which are the Indonesian SBERT model and IndoBERT trained with the SimCSE approach, were employed as a comparison. The generated embeddings were classified using logistic regression, SVM, and MLP Classifier. Classifiers using embedding generated by LLM2Vec with Llama 3 8B and Mistral 7B achieves on-par performance with classifiers that utilize IndoBERT SimCSE embeddings, while classifiers using embeddings generated by LLM2Vec with Llama 2 7B and Sheared Llama 1.3B achieves much lower performance. Classifiers with Indonesian SBERT embeddings achieve the highest F1 score performance. Despite slightly lower performance, this study has proven the language-agnostic capability of LLM2Vec, especially with Llama 3 8B and Mistral 7B in colloquial Bahasa Indonesia sentiment analysis, since none of the base decoders were ever trained using the Bahasa Indonesia corpus. © 2024 IEEE.

关键词： Decoding

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On the Measurement of the Inductive Bias Impact in Convolutional Neural Networks Training for Single Image Super-Resolution

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Procedia Computer Science 2023年 227卷 1086-1092页

作者： Aldrian Kwantawijaya Daniel Stephanus Najoan Tamimmanar Tjeng Wawan Cenggoro Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480

The performance of SISR models is currently growing at a rapid pace since the adoption of Convolutional Neural Networks (CNN) in the domain. Despite that, the understanding of the underlying factors of this rapid growth is still low. In this study, we proposed a study design to measure the impact of the inductive bias in CNN on its training performance, which is one of the factors of the excellent performance of CNN in SISR. With this study design, we observed that not all CNN has a supportive inductive bias to the training performance. This result can provide guidance to future research in choosing a suitable CNN architecture for optimal SISR performance.

关键词： Single-Image Super Resolution Inductive Bias Convolutional Neural Networks Deep Learning

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Fine-tuning protein language models to understand the functional impact of missense variants

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Computational and Structural Biotechnology Journal 2025年 27卷 2199-2207页

作者： Ali Saadat Jacques Fellay School of Life Sciences Ecole Polytechnique Fédérale de Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland Precision Medicine Unit Biomedical Data Science Center Lausanne University Hospital and University of Lausanne Lausanne Switzerland

Elucidating the functional effects of missense variants is crucial yet challenging. To investigate their impact, we fine-tuned protein language models, including ESM2 and ProtT5, to classify 20 protein features at amino acid resolution. In addition, we trained a fully connected neural network classifier on frozen embeddings and compared its performance to fine-tuning in order to quantify the added value of task-specific adaptation. We then used the fine-tuned models to: 1) identify protein features enriched in either pathogenic or benign missense variants, and 2) compare the predicted feature profiles of proteins with reference and alternate alleles to understand how missense variants affect protein functionality. We show that our models can be used to reclassify variants of uncertain significance and provide mechanistic insights into the functional consequences of missense mutations.

关键词： Missense variant Mechanistic interpretation Protein language models Fine-tuning Token classification

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Systematic Literature Review on Machine Learning Predictive Models for Indoor Climate in Smart Solar Dryer Dome 4

Systematic Literature Review on Machine Learning Predictive ...

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4th International Conference on Cybernetics and Intelligent System, ICORIS 2022

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

ISBN: (纸本)9781665453950

Precise predictions of indoor climate conditions are required in the implementation of Smart Solar Dryer Dome (SDD). Trend development of prediction models is discussed in this review from 15 selected research papers (2018-2022) on indoor climate prediction which was obtained from research paper databases The output shows that the most used model for predicting indoor climate is Artificial Neural Network (ANN), especially Recurrent Neural Network (RNN) such as LSTM and GRU. However, there are some potential methods such as Transformer, Combined Support Vector Machines (SVM)-Deep Learning, and sequence-to-sequence which could outperform other commonly used models. Based on findings various opportunities exist to improve the precision of indoor climate prediction, which can bring power consumption efficiency and others benefit to Smart SDD users. Such studies may further be explored to produce more accurate machine learning models. © 2022 IEEE.

关键词： Domes

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Time-series Analysis of Correlation between Climatic Parameters and Dengue Fever in Indonesia 4

Time-series Analysis of Correlation between Climatic Paramet...

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4th International Conference on Informatics, Multimedia, Cyber and Information System, ICIMCIS 2022

作者： Nirwantono, Rudi Trinugroho, Joko Pebrianto Sudigyo, Digdo Hidayat, Alam Ahmad Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Bina Nusantara University Binus Graduate Program Master of Computer Science Program Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665473279

Dengue fever is mainly caused by female mosquitoes from the genus Aedes. It predominantly occurs in equatorial to sub-tropical regions. The weather factors play a significant role in the mosquito life cycle, so a study on the impact of climate parameters on dengue incidence is required. This study aimed to understand the statistical association between the annual fluctuation of dengue cases with climate factors in Indonesia. Climatic data, annual rainfall, and annual mean ambient temperature of Indonesia were obtained from *** from 2010 to 2020, while the data on the annual incidence of dengue fever in Indonesia were collected from the Indonesian Health Profile by the Ministry of Health of Indonesia from 2010 to 2020. The association between climatic factors with dengue cases was calculated with Spearman statistical test after the data was indicated as not normally distributed. In addition, we performed Poisson regression analysis to examine how the changes in climatic parameters affect the dengue cases. The rain precipitation was insignificantly correlated with the dengue incidence in Indonesia during the study time. In contrast, the ambient temperature statistically showed a strong association with the dengue cases. The association between climatic factors and the number of dengue cases suggests that the model would likely be prospectively applied to the dengue early warning system as a nationwide intervention to reduce the epidemic impact in Indonesia. © 2022 IEEE.

关键词： data mining

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Prediction of Kinase-Substrate Associations Using The Functional Landscape of Kinases and Phosphorylation Sites 28

Prediction of Kinase-Substrate Associations Using The Functi...

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28th Pacific Symposium on Biocomputing, PSB 2023

作者： Ayati, Marzieh Yilmaz, Serhan Blasco Tavares Pereira Lopes, Filipa Chance, Mark Koyuturk, Mehmet Department Of Computer Science University Of Texas Rio Grande Valley EdinburgTX United States Department Of Computer And Data Sciences ClevelandOH United States Department Of Nutrition ClevelandOH United States Center For Proteomics And Bioinformatics ClevelandOH United States Case Comprehensive Cancer Center Case Western Reserve University ClevelandOH United States

ISBN: (纸本)9789811270604

Protein phosphorylation is a key post-translational modification that plays a central role in many cellular processes. With recent advances in biotechnology, thousands of phosphorylated sites can be identified and quantified in a given sample, enabling proteome-wide screening of cellular signaling. However, for most (> 90%) of the phosphorylation sites that are identified in these experiments, the kinase(s) that target these sites are unknown. To broadly utilize available structural, functional, evolutionary, and contextual information in predicting kinase-substrate associations (KSAs), we develop a network-based machine learning framework. Our framework integrates a multitude of data sources to characterize the landscape of functional relationships and associations among phosphosites and kinases. To construct a phosphosite-phosphosite association network, we use sequence similarity, shared biological pathways, co-evolution, co-occurrence, and co-phosphorylation of phosphosites across different biological states. To construct a kinase-kinase association network, we integrate protein-protein interactions, shared biological pathways, and membership in common kinase families. We use node embeddings computed from these heterogeneous networks to train machine learning models for predicting kinase-substrate associations. Our systematic computational experiments using the PhosphositePLUS database shows that the resulting algorithm, NetKSA, outperforms two state-of-the-art algorithms, including KinomeXplorer and LinkPhinder, in overall KSA prediction. By stratifying the ranking of kinases, NetKSA also enables annotation of phosphosites that are targeted by relatively less-studied kinases. Availability: The code and data are available at ***/NetKSA/. © 2022 The Authors.

关键词： Association reactions

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bioinformatics tools and resources for cancer and application

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Chinese Medical Journal 2024年第17期137卷 2052-2064页

作者： Jin Huang Lingzi Mao Qian Lei An-Yuan Guo Department of Thoracic Surgery West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengduSichuan 610041China Hubei Bioinformatics&Molecular Imaging Key Laboratory College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei 430074China

Tumor bioinformatics plays an important role in cancer research and precision *** primary focus of traditional cancer research has been molecular and clinical studies of a number of fundamental pathways and *** recent years,driven by breakthroughs in high-throughput technologies,large-scale cancer omics data have accumulated *** to effectively utilize and share these data is particularly *** address this crucial task,many computational tools and databases have been developed over the past few *** help researchers quickly learn and understand the functions of these tools,in this review,we summarize publicly available bioinformatics tools and resources for pan-cancer multi-omics analysis,regulatory analysis of tumorigenesis,tumor treatment and prognosis,immune infiltration analysis,immune repertoire analysis,cancer driver gene and driver mutation analysis,and cancer single-cell analysis,which may further help researchers find more suitable tools for their research.

关键词： Tumor bioinformatics Cancer research Tools databases

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Systematic Literature Review on Statistics and Machine Learning Predictive Models for Rice Phenotypes 8

Systematic Literature Review on Statistics and Machine Learn...

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8th International Conference on Computer Science and Computational Intelligence, ICCSCI 2023

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

Predicting the best-quality of rice phenotypes is the priority among agricultural researchers to fulfill worldwide food security. Trend development of predictive models from statistics to machine learning is the subject of this review. Gathered from the Google Scholar database, 14 appropriate papers (2016-2020) related to the rice phenotypes prediction were selected through title and abstract content filtering. The outputs show that Support Vector Machine, Multi-layer Perceptron, and regression are the most used models, while yield is the priority prediction point besides tiller, panicle, and 1000-grain weight of rice. However, finding the accurate predictor is invariably challenging due to distinct rice varieties in the world and high confounding factors. Thus, developing an advanced deep learning model that accommodates these needs is worth considering further. © 2023 The Authors. Published by Elsevier B.V.

关键词： machine learning rice phenotypes prediction statistics

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Indonesian Agricultural-crops Classification Using Transfer Learning Model 8

Indonesian Agricultural-crops Classification Using Transfer ...

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8th International Conference on Computer Science and Computational Intelligence, ICCSCI 2023

作者： Isnan, Mahmud Hidayat, Alam Ahmad Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Department of Mathematics School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia

Classification of Indonesian crops is a critical task in developing farming and getting more understanding of agriculture. However, there is no clear task in classifying types of crops in Indonesia. Transfer learning has been used successfully in a variety of image classification applications. Thus, in this paper, we collected images of Indonesian crops from the internet randomly and proposed a classification by using transfer learning of deep learning with four pre-trained models: EffficientNetB0, ResNet18, VGG19, and AlexNet. In the experiment, augmentation techniques such as random horizontal flip, random vertical flip, and random affine were utilized to prevent the network from overfitting. The result found that EfficientNet-B0 outperformed other models with an accuracy of 82.55. Then, the model struggled to distinguish between crops in the same family. According to the results, although transfer learning can work well to classify images of Indonesian agricultural crops, some improvements are still required to address existing issues. © 2023 The Authors. Published by Elsevier B.V.

关键词： Agriculture Classification Crop Deep Learning Transfer learning

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