Journal of Computational Biology最新文献

{"title":"Biogeography-Based Multi-Objective Discrete Optimization with Constraints.","authors":"Leyi Hu, Xuan Liu, Xiangyu Qu, Chenyan Wang, Bingmeng Hu, Jieyao Wei","doi":"10.1089/cmb.2024.0931","DOIUrl":"https://doi.org/10.1089/cmb.2024.0931","url":null,"abstract":"<p><p>Biogeography-based optimization (BBO) is an intelligent evolutionary algorithm based on biological populations, increasing the optimization search ability by adaptive migration operation. However, the original BBO is only feasible for continuous optimization with single-objective optimization, instead of more complex optimization problems, such as discrete and multi-objective optimization problems. Therefore, in this article, we propose the improved BBO algorithm to solve multi-objective discrete optimization problem with multiple constraints. We define the decision matrix, objective vector to fit variables and objective functions of the multi-objective discrete optimization problem, and define the ideal point and utility function so that different candidate solutions can be judged according to a metric. We propose similarity threshold, repeatability threshold, cost threshold, and stagnation threshold to make the proposed algorithm improve the diversity of search solutions and give consideration to convergence. Moreover, we conduct a case study on the NP-hard problem of composite functions, and the experimental results verify the effectiveness and efficiency of our approach.</p>","PeriodicalId":15526,"journal":{"name":"Journal of Computational Biology","volume":" ","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144302206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Counterfactual Debiased Co-Embedding Model for Enhanced Drug-Drug Interaction Prediction.","authors":"Xue Pan, Chunping Ouyang, Linlin Zhang, Yongbin Liu, Ying Yu","doi":"10.1089/cmb.2024.0882","DOIUrl":"https://doi.org/10.1089/cmb.2024.0882","url":null,"abstract":"<p><p>Predicting drug-drug interactions (DDIs) is critical to drug discovery and development because adverse interactions pose serious health risks. Most of the existing studies utilize the properties of drugs or network topology information of DDIs to predict unknown interactions between drugs. However, DDI networks are usually sparse with insufficient interaction information, and these approaches lack in-depth integration of these two types of information to effectively exploit potential associations between DDI network nodes and properties. In this work, we present a novel co-embedding model, counterfactual debiased co-embedding (CDCE), for counterfactual-based analyses. The model mitigates the effects of sparse networks and information embedding loss through counterfactual debiasing without losing the original information. In addition, we fuse two attribute information, Anatomical Therapeutic Chemical (ATC) code and Simplified Molecular Input Line Entry System (SMILES), from different perspectives. The implicit information obtained from the ATC code is embedded into the DDI network and then fused with SMILES through the variational graph autoencoder model. We validated CDCE on the benchmark dataset BioSNAP, with experimental results showing that it outperforms state-of-the-art methods.</p>","PeriodicalId":15526,"journal":{"name":"Journal of Computational Biology","volume":" ","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144289463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNAS-sgRNA: Recurrent Neural Architecture Search for Detection of On-Target Effects in Single Guide RNA.","authors":"Shehla Rafiq, Assif Assad","doi":"10.1089/cmb.2025.0031","DOIUrl":"https://doi.org/10.1089/cmb.2025.0031","url":null,"abstract":"<p><p>Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 is a leading genomic editing tool, but its effectiveness is limited by considerable heterogeneity in target efficiency among different single guide RNAs (sgRNA). This study presents RNAS-sgRNA, a hybrid model that integrates neural architecture search (NAS) with recurrent neural networks (RNN) to evaluate the on-target efficacy of CRISPR/Cas9 sgRNA. The RNAS-sgRNA model automates architectural discovery, improving sgRNA sequence categorization without considerable manual adjustment. The NAS component improves the RNN architecture, which analyzes sgRNA sequences represented as binary matrices and produces a classification score. Upon evaluation across several datasets, RNAS-sgRNA exhibits substantial performance enhancements with multiple cell lines, comparing its area under the receiver operating characteristic curve (AUROC) performance to the baseline CRISPRpred(SEQ) and DeepCRISPR models. RNAS-sgRNA demonstrated substantial improvements in AUROC performance in several cell lines compared with existing models. Notable improvements include enhancements of 8.62% for HCT116, 121.57% for HEK293T, 13.40% for HeLa, and 20.78% for HL60 cell lines, resulting in an overall improvement of 13.46%. Compared with DeepCRISPR, the model achieved additional AUROC gains in all cell lines tested, with an average improvement of 14.74%. The study also highlighted the ability of the model to deliver superior performance on smaller datasets through transfer learning, underscoring its potential applications in personalized medicine and genetic research. RNAS-sgRNA introduces a novel integration of NAS with RNN to evaluate the efficacy of CRISPR/Cas9 sgRNA. Unlike traditional methods that require significant manual adjustments, this model automates architectural discovery, optimizing the RNN structure for sgRNA sequence analysis. Furthermore, the application of transfer learning to fine-tune the pretrained model on small cell-line datasets represents a pioneering approach in the domain. The model's demonstrated ability to significantly outperform existing algorithms, including CRISPRpred(SEQ) and DeepCRISPR, across multiple cell lines highlights its innovative contribution to genomic editing research and personalized medicine.</p>","PeriodicalId":15526,"journal":{"name":"Journal of Computational Biology","volume":" ","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144275029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Spatial-Correlated Multitask Linear Mixed-Effects Model for Imaging Genetics.","authors":"Zhibin Pu, Shufei Ge","doi":"10.1089/cmb.2024.0721","DOIUrl":"https://doi.org/10.1089/cmb.2024.0721","url":null,"abstract":"<p><p>Imaging genetics aims to uncover the hidden relationship between imaging quantitative traits (QTs) and genetic markers [e.g., single nucleotide polymorphism (SNP)] and brings valuable insights into the pathogenesis of complex diseases, such as cancers and cognitive disorders (e.g., Alzheimer's disease). However, most linear models in imaging genetics did not explicitly model the inner relationship among QTs, which might miss some potential efficiency gains from information borrowing across brain regions. In this work, we developed a novel Bayesian regression framework for identifying significant associations between QTs and genetic markers while explicitly modeling spatial dependency between QTs, with the main contributions as follows. First, we developed a spatial-correlated multitask linear mixed-effects model to account for dependencies between QTs. We incorporated a population-level mixed-effects term into the model, taking full advantage of the dependent structure of brain imaging-derived QTs. Second, we implemented the model in the Bayesian framework and derived a Markov chain Monte Carlo (MCMC) algorithm to achieve the model inference. Further, we incorporated the MCMC samples with the Cauchy combination test to examine the association between SNPs and QTs, which avoided computationally intractable multitest issues. The simulation studies indicated improved power of our proposed model compared with classical models where inner dependencies of QTs were not modeled. We also applied the new spatial model to an imaging dataset obtained from the Alzheimer's Disease Neuroimaging Initiative database (https://adni.loni.usc.edu). The implementation of our method is available at https://github.com/ZhibinPU/spatialmultitasklmm.git.</p>","PeriodicalId":15526,"journal":{"name":"Journal of Computational Biology","volume":" ","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using Partition Information Entropy to Computationally Rank Order Critical Subreactions in a Petri Net Model of a Biochemical Signaling Network.","authors":"Janet B Jones-Oliveira, Hans-Joseph B Oliveira, Joseph S Oliveira, David A Dixon","doi":"10.1089/cmb.2024.0849","DOIUrl":"https://doi.org/10.1089/cmb.2024.0849","url":null,"abstract":"<p><p>Improved computational methods to analyze the mathematical structure and function of biochemical networks are needed when the biomolecular connectivity is known but when a complete set of the equilibrium and rate constants may not be available. We use Petri nets, which are equivalently bipartite digraphs, to analyze the rule-based flow of information through the network. We present several computational improvements to Petri net modeling as an aid to improve this approach, previously limited by the combinatorics of network size and complexity. The generation of Petri nets using equations for three elemental stencils (molecular reaction, synthesis complex formation, and decomposition complex formation) has been automated. A set of finite probability measures is defined in terms of a partition information entropy, where the complete listing of unique minimal cycles (UMCs) of the Petri net provides the natural partitioning. This enables the ranking of the UMC listing that covers all possible information flows in the reaction network; the information entropy measure enables the identification of which UMCs are more significant than others. In terms of the information entropy, forward cycles are less surprising and carry less information entropy, whereas backward cycles carry more information entropy and serve as regulators by providing feedback to control the network. As the systems analyzed increase in size and complexity, the automatic rank ordering of the UMCs provides a mechanism to highlight the globally most important information without the need to make local simplifying modeling choices. The information entropy metric is also used to compute source-to-sink information costs and is related to knockout analyses. The hybrid Petri net approach shows the most important species and where it is easiest to disrupt or otherwise affect the network. As exemplar, the enhanced methodology is applied to a model of the initial subnetwork in the EGFR network.</p>","PeriodicalId":15526,"journal":{"name":"Journal of Computational Biology","volume":" ","pages":""},"PeriodicalIF":1.4,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144248128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FedOpenHAR: Federated Multitask Transfer Learning for Sensor-Based Human Activity Recognition.","authors":"Egemen İşgÜder, Özlem Durmaz İncel","doi":"10.1089/cmb.2024.0631","DOIUrl":"10.1089/cmb.2024.0631","url":null,"abstract":"<p><p>Wearable and mobile devices equipped with motion sensors offer important insights into user behavior. Machine learning and, more recently, deep learning techniques have been applied to analyze sensor data. Typically, the focus is on a single task, such as human activity recognition (HAR), and the data is processed centrally on a server or in the cloud. However, the same sensor data can be leveraged for multiple tasks, and distributed machine learning methods can be employed without the need for transmitting data to a central location. In this study, we introduce the FedOpenHAR framework, which explores federated transfer learning in a multitask setting for both sensor-based HAR and device position identification tasks. This approach utilizes transfer learning by training task-specific and personalized layers in a federated manner. The OpenHAR framework, which includes ten smaller datasets, is used for training the models. The main challenge is developing robust models that are applicable to both tasks across different datasets, which may contain only a subset of label types. Multiple experiments are conducted in the Flower federated learning environment using the DeepConvLSTM architecture. Results are presented for both federated and centralized training under various parameters and constraints. By employing transfer learning and training task-specific and personalized federated models, we achieve a higher accuracy (72.4%) compared to a fully centralized training approach (64.5%), and similar accuracy to a scenario where each client performs individual training in isolation (72.6%). However, the advantage of FedOpenHAR over individual training is that, when a new client joins with a new label type (representing a new task), it can begin training from the already existing common layer. Furthermore, if a new client wants to classify a new class in one of the existing tasks, FedOpenHAR allows training to begin directly from the task-specific layers.</p>","PeriodicalId":15526,"journal":{"name":"Journal of Computational Biology","volume":" ","pages":"558-572"},"PeriodicalIF":1.4,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143972829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The 2nd International Workshop on Pattern Recognition in Healthcare Analytics 2023 Preface.","authors":"Inci M Baytas","doi":"10.1089/cmb.2025.0117","DOIUrl":"10.1089/cmb.2025.0117","url":null,"abstract":"","PeriodicalId":15526,"journal":{"name":"Journal of Computational Biology","volume":" ","pages":"557"},"PeriodicalIF":1.4,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143985486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generating Heterogeneous Data on Gene Trees.","authors":"Martí Cortada Garcia, Adrià Diéguez Moscardó, Marta Casanellas","doi":"10.1089/cmb.2024.0843","DOIUrl":"10.1089/cmb.2024.0843","url":null,"abstract":"<p><p>We introduce GenPhylo, a Python module that simulates nucleotide sequence data along a phylogeny avoiding the restriction of continuous-time Markov processes. GenPhylo uses directly a general Markov model and therefore naturally incorporates heterogeneity across lineages. We solve the challenge of generating transition matrices with a pre-given expected number of substitutions (the branch length information) by providing an algorithm that can be incorporated in other simulation software.</p>","PeriodicalId":15526,"journal":{"name":"Journal of Computational Biology","volume":" ","pages":"626-630"},"PeriodicalIF":1.4,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143972956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generative Adversarial Networks for Neuroimage Translation.","authors":"Cassandra Czobit, Reza Samavi","doi":"10.1089/cmb.2024.0635","DOIUrl":"10.1089/cmb.2024.0635","url":null,"abstract":"<p><p>Image-to-image translation has gained popularity in the medical field to transform images from one domain to another. Medical image synthesis via domain transformation is advantageous in its ability to augment an image dataset where images for a given class are limited. From the learning perspective, this process contributes to the data-oriented robustness of the model by inherently broadening the model's exposure to more diverse visual data and enabling it to learn more generalized features. In the case of generating additional neuroimages, it is advantageous to obtain unidentifiable medical data and augment smaller annotated datasets. This study proposes the development of a cycle-consistent generative adversarial network (CycleGAN) model for translating neuroimages from one field strength to another (e.g., 3 Tesla [T] to 1.5 T). This model was compared with a model based on a deep convolutional GAN model architecture. CycleGAN was able to generate the synthetic and reconstructed images with reasonable accuracy. The mapping function from the source (3 T) to the target domain (1.5 T) performed optimally with an average peak signal-to-noise ratio value of 25.69 ± 2.49 dB and a mean absolute error value of 2106.27 ± 1218.37. The codes for this study have been made publicly available in the following GitHub repository.^a.</p>","PeriodicalId":15526,"journal":{"name":"Journal of Computational Biology","volume":" ","pages":"573-583"},"PeriodicalIF":1.4,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effective Integration of Single-Cell Multi-Omics Data Using Improved Network-Based Integrative Clustering with Multigraph Regularization.","authors":"Shunqin Zhang, Wei Kong, Shuaiqun Wang, Kai Wei, Kun Liu, Gen Wen, Yaling Yu","doi":"10.1089/cmb.2023.0460","DOIUrl":"10.1089/cmb.2023.0460","url":null,"abstract":"<p><p>The purpose of integrating different omics data is to study cellular heterogeneity at the level of transcriptional regulation from different gene levels, which can effectively identify cell types and reveal the pathogenesis of Alzheimer's disease (AD) from two perspectives. However, implementing such algorithms faces challenges such as high data noise levels, increased dimensionality, and computational complexity. In this study, multigraph regularization constraints were introduced in the network-based integrative clustering algorithm (MGR-NIC) to remove redundant features and keep the geometry structures underlying the data by fusing two types of data (snRNA-seq and snATAC-seq) of glial cells from AD samples. The effectiveness of the MGR-NIC algorithm was validated using both simulation datasets and real datasets derived from various tissues. The MGR-NIC algorithm can improve clustering accuracy by selecting features that better represent the dataset's structure. The clustering results obtained with the MGR-NIC algorithm show strong consistency with the clustering results inherent to the published DLPFC dataset, while the classification results generated using the NIC algorithm often lead to cluster overlap when applied to the DLPFC dataset. We will use the same state-of-the-art algorithms for a comprehensive evaluation with our proposed MGR-NIC algorithm, including NIC, scAI, Multi-Omics Factor Analysis v2, and JSNMF. MGR-NIC is the most stable and reliable method, implying its robustness across different datasets and its reliability in yielding consistent and accurate results.</p>","PeriodicalId":15526,"journal":{"name":"Journal of Computational Biology","volume":" ","pages":"601-614"},"PeriodicalIF":1.4,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144119822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}