Parametrizing using ML

This page was last updated on 2024-07-17 08:46:17 UTC

Manually curated articles on Parametrizing using ML

Abstract Title Authors Publication Date Journal/ Conference Citation count Highest h-index View recommendations
visibility_off Deep learning prediction of patient response time course from early data via neural-pharmacokinetic/pharmacodynamic modelling James Lu, B. Bender, Jin Y. Jin, Y. Guan 2020-10-22 Nature Machine Intelligence 35 38 open_in_new
visibility_off CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy. Bo Yuan, Ciyue Shen, Augustin Luna, Anil Korkut, D. Marks, John Ingraham, C. Sander 2020-12-21 Cell systems 71 153 open_in_new
visibility_off Efficient Amortised Bayesian Inference for Hierarchical and Nonlinear Dynamical Systems Geoffrey Roeder, Paul K. Grant, Andrew Phillips, Neil Dalchau, Edward Meeds 2019-05-24 International Conference on Machine Learning, ArXiv 21 28 open_in_new
Abstract Title Authors Publication Date Journal/ Conference Citation count Highest h-index View recommendations

Abstract Title Authors Publication Date Journal/Conference Citation count Highest h-index
visibility_off Bridging pharmacology and neural networks: A deep dive into neural ordinary differential equations. Idris Bachali Losada, N. Terranova 2024-07-11 CPT: pharmacometrics & systems pharmacology 0 12
visibility_off AI-driven multi-omics integration for multi-scale predictive modeling of causal genotype-environment-phenotype relationships You Wu, Lei Xie Ph.D. Program in Computer Science, The Graduate Center, The City College of New York, New York., Usa, Ph.D. Program in Biology, Biochemistry, Department of Computer Science, Hunter College, Helen, Robert Appel Alzheimers Disease Research Institute, Feil Family Brain, Mind Research Institute, Weill Cornell Medicine, Cornell University 2024-07-08 ArXiv 0 63
visibility_off Mechanism-based organization of neural networks to emulate systems biology and pharmacology models John Mann, Hamed Meshkin, Joel Zirkle, Xiaomei Han, Bradlee Thrasher, Anik Chaturbedi, Ghazal Arabidarrehdor, Zhihua Li 2024-05-27 Scientific Reports 0 10
visibility_off Predicting single-cell cellular responses to perturbations using cycle consistency learning. Wei Huang, Hui Liu 2024-06-28 Bioinformatics 0 0
visibility_off Biologically informed NeuralODEs for genome-wide regulatory dynamics Intekhab Hossain, Viola Fanfani, Jonas Fischer, John Quackenbush, R. Burkholz 2024-05-21 Genome Biology 0 13
visibility_off Prediction of cancer dynamics under treatment using Bayesian neural networks: A simulated study E. M. Myklebust, A. Frigessi, Fredrik Schjesvold, J. Foo, K. Leder, Alvaro Kohn-Luque 2024-05-23 ArXiv 0 1
visibility_off Transfer learning of condition-specific perturbation in gene interactions improves drug response prediction. D. Bang, Bonil Koo, Sun Kim 2024-06-28 Bioinformatics 0 3
visibility_off Data-Driven Discovery of Feedback Mechanisms in Acute Myeloid Leukaemia: Alternatives to classical models using Deep Nonlinear Mixed Effect modeling and Symbolic Regression Carl Julius Martensen, Niklas Korsbo, V. Ivaturi, Sebastian Sager 2024-06-19 bioRxiv 0 17
visibility_off Knowledge-Guided Learning of Temporal Dynamics and its Application to Gas Turbines Pawel Bielski, Aleksandr Eismont, Jakob Bach, Florian Leiser, D. Kottonau, Klemens Böhm 2024-05-31 Proceedings of the 15th ACM International Conference on Future and Sustainable Energy Systems 0 8
visibility_off DrugSK: A Stacked Ensemble Learning Framework for Predicting Drug Combinations of Multiple Diseases. Siqi Chen, Nana Gao, Chunzhi Li, Fei Zhai, Xiwei Jiang, Peng Zhang, Jibin Guan, Kefeng Li, Rongwu Xiang, Guixia Ling 2024-06-20 Journal of chemical information and modeling 0 5
visibility_off Adapting Physics-Informed Neural Networks To Optimize ODEs in Mosquito Population Dynamics D. V. Cuong, Branislava Lali'c, Mina Petri'c, Binh Nguyen, M. Roantree 2024-06-07 ArXiv 0 17
visibility_off Inferring dynamical models from time-series biological data using an interpretable machine learning method based on weighted expression trees Yu Zhou, Xiufen Zou 2024-07-09 Inverse Problems 0 0
visibility_off Perspectives on computational modeling of biological systems and the significance of the SysMod community B. L. Puniya, Meghna Verma, Chiara Damiani, Shaimaa Bakr, Andreas Dräger 2024-06-26 Bioinformatics Advances 0 11
visibility_off Multi-cell-line learning for the data-driven construction of mechanistic metabolic models. Yen-An Lu, Meghan G. McCann, Wei-Shou Hu, Qi Zhang 2024-06-03 Biotechnology and bioengineering 0 3
visibility_off Machine Learning for ALSFRS-R Score Prediction: Making Sense of the Sensor Data Ritesh Mehta, Aleksandar Pramov, Shashank Verma 2024-07-10 ArXiv 0 0
visibility_off Abstract PO-005: Mechanistic models of cancer heterogeneity explain and predict clinical outcomes of Large B-Cell Lymphoma (LBCL) treatment Amy E. Pomeroy, Adam C Palmer 2024-06-19 Blood Cancer Discovery 0 3
visibility_off Physiology-informed regularization enables training of universal differential equation systems for biological applications Max de Rooij, Balázs Erdős, N. V. van Riel, Shauna D. O’Donovan 2024-06-01 bioRxiv 0 5
visibility_off TarDis: Achieving Robust and Structured Disentanglement of Multiple Covariates Kemal Inecik, Aleyna Kara, Antony Rose, M. Haniffa, F. Theis 2024-06-25 bioRxiv 0 66
visibility_off Learning dynamical systems from data: An introduction to physics-guided deep learning Rose Yu, Rui Wang 2024-06-24 Proceedings of the National Academy of Sciences of the United States of America 1 1
visibility_off Predicting Survival in Patients with Advanced NSCLC Treated with Atezolizumab Using Pre- and on-Treatment Prognostic Biomarkers. Sébastien Benzekry, M. Karlsen, Célestin Bigarré, Abdessamad El Kaoutari, Bruno Gomes, Martin Stern, Ales Neubert, René Bruno, François Mercier, Suresh Vatakuti, P. Curle, C. Jamois 2024-07-12 Clinical pharmacology and therapeutics 0 12
visibility_off Reduced-Order Neural Operators: Learning Lagrangian Dynamics on Highly Sparse Graphs Hrishikesh Viswanath, Yue Chang, Julius Berner, Peter Yichen Chen, Aniket Bera 2024-07-04 ArXiv 0 28
visibility_off Drug safety assessment by machine learning models. Nan Miles Xi, D. Huang 2024-06-18 Journal of biopharmaceutical statistics 0 4
visibility_off Exploring the dynamics of monkeypox transmission with data-driven methods and a deterministic model Haridas K. Das 2024-05-22 Frontiers in Epidemiology 0 0
visibility_off Permutation invariant multi-output Gaussian Processes for drug combination prediction in cancer Leiv Rønneberg, V. Lalchand, Paul D. W. Kirk 2024-06-28 ArXiv 0 6
visibility_off Integrating GNN and Neural ODEs for Estimating Two-Body Interactions in Mixed-Species Collective Motion Masahito Uwamichi, S. Schnyder, Tetsuya J. Kobayashi, Satoshi Sawai 2024-05-26 ArXiv 0 10
visibility_off From Fourier to Neural ODEs: Flow Matching for Modeling Complex Systems Xin Li, Jingdong Zhang, Qunxi Zhu, Chengli Zhao, Xue Zhang, Xiaojun Duan, Wei Lin 2024-05-19 ArXiv 0 12
visibility_off Integrating Shapley Values into Machine Learning Techniques for Enhanced Predictions of Hospital Admissions G. Feretzakis, A. Sakagianni, Athanasios Anastasiou, Ioanna Kapogianni, Εffrosyni Βazakidou, Petros Koufopoulos, Y. Koumpouros, C. Koufopoulou, Vasileios Kaldis, V. Verykios 2024-07-07 Applied Sciences 0 34
visibility_off Assessing the Role of Patient Generation Techniques in Virtual Clinical Trial Outcomes J. L. Gevertz, J. R. Wares 2024-06-12 None 0 0
visibility_off Multi-Task ADME/PK prediction at industrial scale: leveraging large and diverse experimentaldatasets. Moritz Walter, J. M. Borghardt, Lina Humbeck, Miha Škalič 2024-07-08 Molecular informatics 0 11
visibility_off On the generalization discrepancy of spatiotemporal dynamics-informed graph convolutional networks Yue Sun, Chao Chen, Yuesheng Xu, Sihong Xie, Rick S. Blum, Parv Venkitasubramaniam 2024-07-12 Frontiers in Mechanical Engineering 0 1
visibility_off Cell-Graph Compass: Modeling Single Cells with Graph Structure Foundation Model Chen Fang, Zhilong Hu, Shaole Chang, Qingqing Long, Wentao Cui, Wenhao Liu, Cong Li, Yana Liu, Pengfei Wang, Zhen Meng, Jia Pan, Yuanchun Zhou, Guihai Feng, Linghui Chen, Xin Li 2024-06-06 bioRxiv 0 3
visibility_off Variational and Explanatory Neural Networks for Encoding Cancer Profiles and Predicting Drug Responses Tianshu Feng, Rohan D Gnanaolivu, Abolfazl Safikhani, Yuanhang Liu, Jun Jiang, Nicholas Chia, A. Partin, Priyanka Vasanthakumari, Yitan Zhu, Chen Wang 2024-07-05 ArXiv 0 14
visibility_off Modeling, Inference, and Prediction in Mobility-Based Compartmental Models for Epidemiology Ning Jiang, Weiqi Chu, Yao Li 2024-06-17 ArXiv 1 0
visibility_off Agent-Based Modeling of Virtual Tumors Reveals the Critical Influence of Microenvironmental Complexity on Immunotherapy Efficacy Yixuan Wang, Daniel R. Bergman, Erica Trujillo, Anthony A. Fernald, Lie Li, Alexander T. Pearson, Randy F. Sweis, Trachette Jackson 2024-07-05 bioRxiv 0 5
visibility_off Inferring single-cell spatial gene expression with tissue morphology via explainable deep learning Yue Zhao, Elaheh Alizadeh, Yang Liu, Ming Xu, J. M. Mahoney, Sheng Li 2024-06-14 bioRxiv 0 8
visibility_off Deep learning-based approach for COVID-19 spread prediction S. Cumbane, Gyözö Gidófalvi 2024-06-10 International Journal of Data Science and Analytics 0 21
visibility_off A variational deep-learning approach to modeling memory T cell dynamics C. V. van Dorp, Joshua I. Gray, Daniel H. Paik, Donna L. Farber, Andrew J. Yates 2024-07-11 bioRxiv 0 10
visibility_off Increasing certainty in systems biology models using Bayesian multimodel inference Nathaniel Linden-Santangeli, Jin Zhang, Boris Kramer, P. Rangamani 2024-06-17 bioRxiv 0 4
visibility_off QSARtuna: An Automated QSAR Modeling Platform for Molecular Property Prediction in Drug Design. Lewis Mervin, Alexey Voronov, Mikhail Kabeshov, O. Engkvist 2024-07-01 Journal of chemical information and modeling 0 4
visibility_off Injecting Hierarchical Biological Priors into Graph Neural Networks for Flow Cytometry Prediction Fatemeh Nassajian Mojarrad, Lorenzo Bini, Thomas Matthes, Stéphane Marchand-Maillet 2024-05-28 ArXiv 0 1
visibility_off Data-driven learning of structure augments quantitative prediction of biological responses Yuanchi Ha, Helena R. Ma, Feilun Wu, Andrea Weiss, Katherine Duncker, Helen Xu, Jia Lu, Max Golovsky, Daniel Reker, Lingchong You 2024-06-01 PLOS Computational Biology 0 8
visibility_off Learning Molecular Representation in a Cell Gang Liu, Srijit Seal, John Arevalo, Zhenwen Liang, A. Carpenter, Meng Jiang, Shantanu Singh 2024-06-17 ArXiv 0 7
visibility_off Coupling quantitative systems pharmacology modelling to machine learning and artificial intelligence for drug development: its pAIns and gAIns Núria Folguera-Blasco, Florencia A. T. Boshier, Aydar Uatay, C. Pichardo-Almarza, Massimo Lai, Jacopo Biasetti, Richard Dearden, Megan Gibbs, Holly Kimko 2024-07-12 Frontiers in Systems Biology 0 13
visibility_off Prediction of Human Liver Microsome Clearance with Chirality-Focused Graph Neural Networks. Chengtao Pu, Lingxi Gu, Yuxuan Hu, Weijie Han, Xiaohe Xu, Haichun Liu, Yadong Chen, Yanmin Zhang 2024-07-08 Journal of chemical information and modeling 0 18
visibility_off Perspectives on benchmarking foundation models for network biology Christina V. Theodoris 2024-07-11 Quantitative Biology 1 0
visibility_off Benchmark on Drug Target Interaction Modeling from a Structure Perspective Xinnan Zhang, Jialin Wu, Junyi Xie, Tianlong Chen, Kaixiong Zhou 2024-07-04 ArXiv 0 1
visibility_off KAN-ODEs: Kolmogorov-Arnold Network Ordinary Differential Equations for Learning Dynamical Systems and Hidden Physics Benjamin C. Koenig, Suyong Kim, Sili Deng 2024-07-05 ArXiv 0 2
visibility_off Opportunities in deep learning methods development for computational biology Alex J. Lee, Reza Abbasi-Asl 2024-06-12 ArXiv 0 1
visibility_off A comprehensive review of computational cell cycle models in guiding cancer treatment strategies Chenhui Ma, Evren Gurkan-Cavusoglu 2024-07-05 NPJ Systems Biology and Applications 0 3
visibility_off Physics-constrained learning for PDE systems with uncertainty quantified port-Hamiltonian models Kaiyuan Tan, Peilun Li, Thomas Beckers 2024-06-17 DBLP, ArXiv 0 1
visibility_off Data-Driven Computing Methods for Nonlinear Physics Systems with Geometric Constraints Yunjin Tong 2024-06-20 ArXiv 0 0
visibility_off DeepGRNCS: deep learning-based framework for jointly inferring gene regulatory networks across cell subpopulations Yahui Lei, Xiao-Tai Huang, Xingli Guo, Kei Hang Katie Chan, Lin Gao 2024-05-23 Briefings in Bioinformatics 0 0
visibility_off Predicting the physiological effects of multiple drugs using electronic health record Junhyeok Jeon, Eujin Hong, Jong-Yeup Kim, Suehyun Lee, Hyun Uk Kim 2024-07-02 bioRxiv 0 9
visibility_off CellFM: a large-scale foundation model pre-trained on transcriptomics of 100 million human cells Yuansong Zeng, Jiancong Xie, Zhuoyi Wei, Yun Su, Ningyuan Shangguan, Shuangyu Yang, Chengyang Zhang, Wenbing Li, Jinbo Zhang, Nan Fang, Hongyu Zhang, Huiying Zhao, Yutong Lu, Jue Fan, Weijiang Yu, Yuedong Yang 2024-06-06 bioRxiv 0 5
visibility_off DeepFusionCDR: Employing Multi-Omics Integration and Molecule-Specific Transformers for Enhanced Prediction of Cancer Drug Responses. Xiaowen Hu, Pan Zhang, Jiaxuan Zhang, Lei Deng 2024-06-27 IEEE journal of biomedical and health informatics 0 1
visibility_off Lung Adenocarcinoma Systems Biomarker and Drug Candidates Identified by Machine Learning, Gene Expression Data, and Integrative Bioinformatics Pipeline. Semra Melis Soyer, Pemra Ozbek, Ceyda Kasavi 2024-07-09 Omics : a journal of integrative biology 0 8
visibility_off Improvement of the ANN-Based Prediction Technology for Extremely Small Biomedical Data Analysis I. Izonin, R.O. Tkachenko, O. Berezsky, Iurii Krak, Michal Kováč, M. Fedorchuk 2024-07-12 Technologies 0 23
visibility_off Prediction of therapeutic response and cancer outcomes in solid tumours via in silico clinical trials. Uzma Asghar, M. Griffiths, Amanzhol Kubeyev, Jordan Laurie, Andrea Giorni, Luiz A Zillmann da Silva, Prabu Sivasubramaniam, Matthew Foster, Andrew Biankin 2024-06-01 Journal of Clinical Oncology 0 1
visibility_off Early ctDNA kinetics as a dynamic biomarker of cancer treatment response Aaron Li, Emil Lou, K. Leder, Jasmine Foo 2024-07-03 bioRxiv 0 1
visibility_off Deep learning methods for protein function prediction. Frimpong Boadu, Ahhyun Lee, Jianlin Cheng 2024-07-12 Proteomics 0 5
visibility_off CAVACHON: a hierarchical variational autoencoder to integrate multi-modal single-cell data Ping-Han Hsieh, Ru-Xiu Hsiao, Katalin Ferenc, Anthony Mathelier, R. Burkholz, Chien-Yu Chen, G. K. Sandve, T. Belova, M. Kuijjer 2024-05-28 ArXiv 0 31
visibility_off Learning nonlinear operators in latent spaces for real-time predictions of complex dynamics in physical systems Katiana Kontolati, S. Goswami, G. Em Karniadakis, Michael D Shields 2024-06-14 Nature Communications 0 19
visibility_off Advancing cancer drug development with mechanistic mathematical modeling: bridging the gap between theory and practice. Alexander Kulesza, C. Couty, Paul Lemarre, Craig J Thalhauser, Yanguang Cao 2024-06-21 Journal of pharmacokinetics and pharmacodynamics 0 1
visibility_off A Data-Driven Pandemic Simulator with Reinforcement Learning Yuting Zhang, Biyang Ma, Langcai Cao, Yanyu Liu 2024-06-27 Electronics 0 4
visibility_off KG-LIME: predicting individualized risk of adverse drug events for multiple sclerosis disease-modifying therapy. Jason Patterson, Nicholas Tatonetti 2024-07-04 Journal of the American Medical Informatics Association : JAMIA 0 0
visibility_off Combinatorial Complex Score-based Diffusion Modelling through Stochastic Differential Equations Adrien Carrel 2024-06-07 ArXiv 0 0
visibility_off EpiLearn: A Python Library for Machine Learning in Epidemic Modeling Zewen Liu, Yunxiao Li, Mingyang Wei, Guancheng Wan, Max S. Y. Lau, Wei Jin 2024-06-10 ArXiv 0 1
visibility_off Foundation Model for Chemical Process Modeling: Meta-Learning with Physics-Informed Adaptation Zihao Wang, Zhen Wu 2024-05-20 ArXiv 0 1
visibility_off LSTM-COX Model: A Concise and Efficient Deep Learning Approach for Handling Recurrent Events Runquan Huang, Xiaoping Shi 2024-05-28 ArXiv 0 0
visibility_off Multicell-Fold: geometric learning in folding multicellular life Haiqian Yang, , Dapeng Bi, Markus J. Buehler, Ming Guo 2024-07-09 ArXiv 0 6
visibility_off Bond Graphs for multi-physics informed Neural Networks for multi-variate time series Alexis-Raja Brachet, Pierre-Yves Richard, C'eline Hudelot 2024-05-22 ArXiv 0 1
visibility_off Exploring Machine Learning Methods for Developing a Predictive System for Parkinson's Disease Sumit Das, Tanusree Saha, Ira Nath, Dipansu Mondal 2024-07-01 Biosciences Biotechnology Research Asia 0 2
visibility_off New Horizons of Model Informed Drug Development in Rare Diseases Drug Development. Amitava Mitra, Nessy Tania, Mariam A Ahmed, Noha Rayad, Rajesh Krishna, Salwa Albusaysi, Rana B Bakhaidar, Elizabeth Shang, Maria Burian, Michelle Martin-Pozo, Islam R Younis 2024-07-11 Clinical pharmacology and therapeutics 0 3
visibility_off Machine learning and deep learning approaches for enhanced prediction of hERG blockade: a comprehensive QSAR modeling study. Jie Liu, Md Kamrul Hasan Khan, Wenjing Guo, Fan Dong, W. Ge, Chaoyang Zhang, Ping Gong, T. Patterson, Huixiao Hong 2024-07-05 Expert opinion on drug metabolism & toxicology 0 31
visibility_off Low-dimensional representations of genome-scale metabolism Samuel Cain, C. Merzbacher, D. Oyarzún 2024-06-03 bioRxiv 0 19
visibility_off LogicGep: Boolean networks inference using symbolic regression from time-series transcriptomic profiling data Dezhen Zhang, Shuhua Gao, Zhiping Liu, Rui Gao 2024-05-23 Briefings in Bioinformatics 0 4
visibility_off CVGAE: A Self-Supervised Generative Method for Gene Regulatory Network Inference Using Single-Cell RNA Sequencing Data. Wei Liu, Zhijie Teng, Zejun Li, Jing Chen 2024-05-23 Interdisciplinary sciences, computational life sciences 0 0
visibility_off Big data and deep learning for RNA biology. Hyeonseo Hwang, Hyeonseong Jeon, Nagyeong Yeo, Daehyun Baek 2024-06-14 Experimental & molecular medicine 1 6
visibility_off Simulation-based Benchmarking for Causal Structure Learning in Gene Perturbation Experiments Luka Kovavcevi'c, Izzy Newsham, Sach Mukherjee, John Whittaker 2024-07-08 ArXiv 0 1
visibility_off Data hazards in synthetic biology Natalie R Zelenka, Nina Di Cara, Kieren Sharma, Seeralan Sarvaharman, Jasdeep S. Ghataora, Fabio Parmeggiani, Jeff Nivala, Z. Abdallah, Lucia Marucci, T. Gorochowski 2024-06-21 Synthetic Biology 0 27
visibility_off Pi-fusion: Physics-informed diffusion model for learning fluid dynamics Jing Qiu, Jiancheng Huang, Xiangdong Zhang, Zeng Lin, Minglei Pan, Zengding Liu, F. Miao 2024-06-06 ArXiv 1 20
visibility_off Long short-term memory model for COVID-19 forecasting Pengfei Lou 2024-05-28 Theoretical and Natural Science 0 0
visibility_off Pharmaceutical Synthesis and Discloser Approach Using Naïve Bayesian Method in Machine Learning a. 2024-06-13 INTERANTIONAL JOURNAL OF SCIENTIFIC RESEARCH IN ENGINEERING AND MANAGEMENT 0 0
visibility_off PhyGICS – A Physics-informed Graph Neural Network-based Intelligent HVAC Controller for Open-plan Spaces S. Nagarathinam, Arunchandar Vasan 2024-05-31 Proceedings of the 15th ACM International Conference on Future and Sustainable Energy Systems 0 15
visibility_off Prediction of pair interactions in mixtures by matrix completion. Marco Hoffmann, N. Hayer, M. Kohns, F. Jirasek, Hans Hasse 2024-07-08 Physical chemistry chemical physics : PCCP 0 11
visibility_off CODI: Enhancing machine learning-based molecular profiling through contextual out-of-distribution integration Tarek Eissa, Marinus Huber, Barbara Obermayer-Pietsch, Birgit Linkohr, A. Peters, Frank Fleischmann, M. Žigman 2024-06-17 bioRxiv 0 10
visibility_off Predicting Future Kinetic States of Physicochemical Systems Using Generative Pre-trained Transformer Palash Bera, Jagannath Mondal 2024-06-19 bioRxiv 0 4
visibility_off Simulating realistic patient profiles from pharmacokinetic models by a machine learning postprocessing correction of residual variability. Christos Kaikousidis, Robert R Bies, A. Dokoumetzidis 2024-06-14 CPT: pharmacometrics & systems pharmacology 0 24
visibility_off Tree-based variational inference for Poisson log-normal models Alexandre Chaussard, Anna Bonnet, Elisabeth Gassiat, S. Corff 2024-06-25 ArXiv 0 9
visibility_off In Silico Chemical Experiments in the Age of AI: From Quantum Chemistry to Machine Learning and Back. Abdulrahman Aldossary, J. A. Campos-Gonzalez-Angulo, Sergio Pablo-García, Shi Xuan Leong, Ella Miray Rajaonson, Luca Thiede, Gary Tom, Andrew Wang, Davide Avagliano, Alán Aspuru-Guzik 2024-05-25 Advanced materials 0 3
visibility_off Predicting Progression Events in Multiple Myeloma from Routine Blood Work Maximilian Ferle, N. Grieb, Markus Kreuz, U. Platzbecker, Thomas Neumuth, Kristin Reiche, Alexander Oeser, M. Merz 2024-05-28 ArXiv 0 4
visibility_off Toward a semi-supervised learning approach to phylogenetic estimation. Daniele Silvestro, Thibault Latrille, N. Salamin 2024-06-25 Systematic biology 0 3
visibility_off Towards detailed and interpretable hybrid modeling of continental-scale bird migration Fiona Lippert, Bart Kranstauber, Patrick Forr'e, E. E. V. Loon 2024-07-14 ArXiv 0 5
visibility_off Assessment of Uncertainty Quantification in Universal Differential Equations Nina Schmid, David Fernandes del Pozo, Willem Waegeman, Jan Hasenauer 2024-06-13 ArXiv 0 0
visibility_off Stochastic Modeling of Biophysical Responses to Perturbation T. Chari, Gennady Gorin, L. Pachter 2024-07-05 bioRxiv 0 75
visibility_off tauX: A Gene Expression Ratio Strategy to Improve Machine Learning Applications in Precision Medicine Jacob Pfeil, Liqian Ma, Hin Ching Lo, Tolga Turan, R. T. McLaughlin, Xu Shi, Severiano Villarruel, Stephen Wilson, Xi Zhao, Josue Samayoa, Kyle Halliwill 2024-07-04 bioRxiv 0 1
visibility_off Uncovering hidden and complex relations of pandemic dynamics using an AI driven system Umit Demirbaga, Navneet Kaur, G. Aujla 2024-07-04 Scientific Reports 0 36
visibility_off Computational model predicts patient outcomes in Luminal B breast cancer treated with endocrine therapy and CDK4/6 inhibition. Leonard Schmiester, F. Brasó-Maristany, B. González-Farré, T. Pascual, J. Gavilá, Xavier Tekpli, Jürgen Geisler, Vessela N Kristensen, A. Frigessi, A. Prat, A. Köhn-Luque 2024-06-26 Clinical cancer research : an official journal of the American Association for Cancer Research 0 26
visibility_off Benchmarking Deep Jansen-Rit Parameter Inference: An in Silico Study Deepa Tilwani, Christian O'Reilly 2024-06-07 ArXiv 0 2
visibility_off Gradient matching accelerates mixed-effects inference for biochemical networks Yulan B van Oppen, Andreas Milias-Argeitis 2024-06-12 bioRxiv 0 15
visibility_off Computational single-cell methods for predicting cancer risk. Andrew E Teschendorff 2024-06-10 Biochemical Society transactions 0 2
visibility_off Graph Structure Learning with Interpretable Bayesian Neural Networks Max Wasserman, Gonzalo Mateos 2024-06-20 ArXiv 0 3
visibility_off GRACE: Unveiling Gene Regulatory Networks With Causal Mechanistic Graph Neural Networks in Single-Cell RNA-Sequencing Data. Jiacheng Wang, Yao-Jia Chen, Quan Zou 2024-06-19 IEEE transactions on neural networks and learning systems 0 1
visibility_off The development of drug resistance in metastatic tumours under chemotherapy: an evolutionary perspective Federica Padovano, Chiara Villa 2024-05-30 ArXiv 0 0
visibility_off How more data can hurt: Instability and regularization in next-generation reservoir computing Yuanzhao Zhang, Sean P. Cornelius 2024-07-11 ArXiv 0 1
visibility_off MIST: an interpretable and flexible deep learning framework for single-T cell transcriptome and receptor analysis Wenpu Lai, Yangqiu Li, Oscar Junhong Luo 2024-07-13 bioRxiv 0 7
visibility_off TCKIN: A Novel Integrated Network Model for Predicting Mortality Risk in Sepsis Patients Fanglin Dong 2024-07-09 ArXiv 0 0
visibility_off The expression patterns of different cell types and their interactions in the tumor microenvironment are predictive of breast cancer patient response to neoadjuvant chemotherapy S. R. Dhruba, S. Sahni, Binbin Wang, Di Wu, P. Rajagopal, Yael Schmidt, E. Shulman, Sanju Sinha, Stephen-John Sammut, Carlos Caldas, Kun Wang, E. Ruppin 2024-06-14 bioRxiv 0 15
visibility_off An Ensemble Cascade Forest‐Based Framework for Multi‐Omics Drug Response and Synergy Prediction Ruijiang Li, Binsheng Sui, Dongjing Leng, Song He, Kunhong Liu, Xiaochen Bo 2024-06-09 Advanced Intelligent Systems 0 11
visibility_off Representing mutations for predicting cancer drug response. Patrick Wall, T. Ideker 2024-06-28 Bioinformatics 0 80
visibility_off Enhancing generalizability and performance in drug–target interaction identification by integrating pharmacophore and pre-trained models Zuolong Zhang, Xin He, Dazhi Long, Gang Luo, Shengbo Chen 2024-06-28 Bioinformatics 0 1
visibility_off Machine learning identifies prognostic subtypes of the tumor microenvironment of NSCLC Duo Yu, M. Kane, Eugene J. Koay, I. Wistuba, Brian,P. Hobbs 2024-07-01 Scientific Reports 0 5
visibility_off Spatial Deconvolution of Cell Types and Cell States at Scale Utilizing TACIT Jinze Liu, Khoa Huynh, Katarzyna Tyc, B. Matuck, Quinn T. Easter, Aditya Pratapa, Nikhil V. Kumar, Paola Pérez, Rachel Kulchar, T. Pranzatelli, Deiziane Souza, Theresa Weaver, Xufeng Qu, Luiz Soares Junior, Marisa Dolhnokoff, David E. Kleiner, Stephen Hewitt, Luiz Fernando Ferraz da Silva, V. Rocha, B.M. Warner, K. Byrd 2024-06-27 Research Square 0 8
visibility_off Deep learning models for predicting the survival of patients with medulloblastoma based on a surveillance, epidemiology, and end results analysis Meng Sun, Jikui Sun, M. Li 2024-06-24 Scientific Reports 0 1
visibility_off A hypercubic Mk model framework for capturing reversibility in disease, cancer, and evolutionary accumulation modelling Iain G. Johnston, Ramon Diaz-Uriarte 2024-07-01 bioRxiv 0 1
visibility_off Advancing precision prognostication in neuro-oncology: Machine learning models for data-driven personalized survival predictions in IDH-wildtype glioblastoma Mert Karabacak, Pemla Jagtiani, L. Di, Ashish H Shah, Ricardo J Komotar, Konstantinos Margetis 2024-06-11 Neuro-Oncology Advances 0 12
visibility_off GeneBag: training a cell foundation model for broad-spectrum cancer diagnosis and prognosis with bulk RNA-seq data Yu-ping Liang, Dan Li, Aguix Guohua Xu, Yan Shao, Kun Tang 2024-07-02 bioRxiv 0 1
visibility_off Bayesian Networks and Machine Learning for COVID-19 Severity Explanation and Demographic Symptom Classification O. Ajayi, Yu Cheng 2024-06-16 ArXiv 0 4
visibility_off Graph Neural Reaction Diffusion Models Moshe Eliasof, Eldad Haber, Eran Treister 2024-06-16 ArXiv 1 15
visibility_off Editorial: Artificial intelligence in predicting, determining and controlling cell phenotype or tissue function in inflammatory diseases Melanie L. Hart, Ryuji Kato, Bernd Rolauffs 2024-06-18 Frontiers in Immunology 0 2
visibility_off Designing Machine Learning Tools to Characterize Multistationarity of Fully Open Reaction Networks Shenghao Yao, AmirHosein Sadeghimanesh, Matthew England 2024-07-01 ArXiv 0 4
visibility_off Sparsity regularization via tree-structured environments for disentangled representations Elliot Layne, Dhanya Sridhar, Jason S. Hartford, M. Blanchette 2024-05-30 ArXiv 0 50
visibility_off Impact of Hyperparameter Optimization to Enhance Machine Learning Performance: A Case Study on Breast Cancer Recurrence Prediction Lorena González-Castro, Marcela Chávez, Patrick Duflot, Valérie Bleret, G. Del Fiol, M. López-Nores 2024-07-06 Applied Sciences 0 19
visibility_off Optimization Under Uncertainty Using Physics-Based Label-Free Machine Learning Xiaoping Du 2024-05-23 2024 International Congress on Human-Computer Interaction, Optimization and Robotic Applications (HORA) 0 0
visibility_off Simulation-based Inference on Virtual Brain Models of Disorders Meysam Hashemi, Abolfazl Ziaeemehr, M. Woodman, Jan Fousek, S. Petkoski, V. Jirsa 2024-07-11 Machine Learning: Science and Technology 0 17
visibility_off Reducing phenotype-structured PDE models of cancer evolution to systems of ODEs: a generalised moment dynamics approach Chiara Villa, P. K. Maini, Alexander P Browning, A. Jenner, Sara Hamis, Tyler Cassidy 2024-06-03 ArXiv 0 26
visibility_off Protein pathways as a catalyst to directed evolution of the topology of artificial neural networks Oscar Lao, Konstantinos Zacharopoulos, A. Fournaris, Rossano Schifanella, Ioannis Arapakis 2024-06-07 ArXiv 0 27
visibility_off Do Deep Learning Models for Co-Folding Learn the Physics of Protein-Ligand Interactions? Matthew Masters, Amr H. Mahmoud, Markus A. Lill 2024-06-04 bioRxiv 0 9
visibility_off Challenges with the application and adoption of artificial intelligence for drug discovery G. Ghislat, Saiveth Hernández-Hernández, Chayanit Piwajanusorn, Pedro J. Ballester 2024-07-06 ArXiv 0 14
visibility_off Hybrid metapopulation agent-based epidemiological models for efficient insight on the individual scale: a contribution to green computing Julia Bicker, Ren´e Schmieding, Martin J. Kuhn 2024-06-06 ArXiv 0 1
visibility_off Flexible inference in heterogeneous and attributed multilayer networks Martina Contisciani, Marius Hobbhahn, Eleanor A. Power, Philipp Hennig, C. D. Bacco 2024-05-31 ArXiv 0 12
visibility_off Stochastic Machine Learning Models for Mutation Rate Analysis of Malignant Cancer Cells in Patients with Acute Lymphoblastic Leukemia Martsenyuk Vasyl, Abubakar Umar Sadiq, Sverstiuk Andriy, Dimitrov Georgi, Gancarczyk Tomasz 2024-07-05 International Journal of Circuits, Systems and Signal Processing 0 0
visibility_off Deep learning of SARS-CoV-2 outbreak phylodynamics with contact tracing data Ruopeng Xie, D. Adam, Shu Hu, Benjamin J. Cowling, Olivier Gascuel, Anna Zhukova, V. Dhanasekaran, Kong S.A.R 2024-06-11 None 0 15
visibility_off A Large Language Model Pipeline for Breast Cancer Oncology Tristen Pool, Dennis Trujillo 2024-06-10 ArXiv 0 0
visibility_off A Cyclical Route Linking Fundamental Mechanism and AI Algorithm: An Example from Poisson's Ratio in Amorphous Networks Changliang Zhu, Chenchao Fang, Zhipeng Jin, Baowen Li, Xiangying Shen, Lei Xu 2023-12-06 ArXiv 0 4
visibility_off Bayesian calibration of stochastic agent based model via random forest Connor Robertson, C. Safta, Nicholson T. Collier, J. Ozik, Jaideep Ray 2024-06-27 ArXiv 0 21
visibility_off Improving Molecular Dynamics Simulations for Solid-Liquid Interface with Machine Learning Interatomic Potentials. Pengfei Hou, Yumiao Tian, Xing Meng 2024-06-14 Chemistry 0 1
visibility_off Evolving reservoir computers reveals bidirectional coupling between predictive power and emergent dynamics Hanna M. Tolle, A. Luppi, Anil K. Seth, P. Mediano 2024-06-27 ArXiv 0 25
visibility_off Leveraging Machine Learning and Patient Reviews for Developing a Drug Recommendation System to Reduce Medical Errors K. P. Swain, S.K. Mohapatra, Vinayakumar Ravi, S. R. Nayak, Tahani Jaser Alahmadi, Prabhishek Singh, M. Diwakar 2024-06-25 The Open Bioinformatics Journal 0 22
visibility_off node2vec2rank: Large Scale and Stable Graph Differential Analysis via Multi-Layer Node Embeddings and Ranking Panagiotis Mandros, Ian Gallagher, Viola Fanfani, Chen Chen, Jonas Fischer, Anis Ismail, Lauren Hsu, Enakshi Saha, Derrick K. DeConti, John Quackenbush 2024-06-17 bioRxiv 0 8
visibility_off Physics-informed neural networks for parameter learning of wildfire spreading K. Vogiatzoglou, C. Papadimitriou, V. Bontozoglou, Konstantinos Ampountolas 2024-06-20 ArXiv 0 45
visibility_off ALPHAGMUT: A Rationale-Guided Alpha Shape Graph Neural Network to Evaluate Mutation Effects Boshen Wang, Bowei Ye, Lin Xu, Jie Liang 2024-06-13 ArXiv 0 3
visibility_off Learning dynamical models from stochastic trajectories Pierre Ronceray 2024-06-04 ArXiv 0 0
visibility_off DDN3.0: determining significant rewiring of biological network structure with differential dependency networks Yi Fu, Yingzhou Lu, Yizhi Wang, Bai Zhang, Zhen Zhang, Guoqiang Yu, Chunyu Liu, Robert Clarke, David M. Herrington, Yue Wang 2024-06-01 Bioinformatics 1 19
visibility_off Probabilistic pathway-based multimodal factor analysis. Alexander Immer, Stefan G. Stark, Francis Jacob, Ximena Bonilla, Tinu Thomas, A. Kahles, Sandra Goetze, Emanuela S Milani, Bernd Wollscheid, Gunnar Rätsch, K. Lehmann 2024-06-28 Bioinformatics 0 31
visibility_off Particle uptake in cancer cells can predict malignancy and drug resistance using machine learning. Yoel Goldstein, Ora T. Cohen, Ori Wald, Danny Bavli, Tommy Kaplan, Ofra Benny 2024-05-31 Science advances 0 26
visibility_off Robust and highly scalable estimation of directional couplings from time-shifted signals Luca Ambrogioni, Louis Rouillard, Demian Wassermann 2024-06-04 ArXiv 0 2
visibility_off Conditional Similarity Triplets Enable Covariate-Informed Representations of Single-Cell Data Chi-Jane Chen, Haidong Yi, Natalie Stanley 2024-06-12 ArXiv 0 0
visibility_off Explainable chemical artificial intelligence from accurate machine learning of real-space chemical descriptors. Miguel Gallegos, Valentin Vassilev-Galindo, I. Poltavsky, Á. Martín Pendás, Alexandre Tkatchenko 2024-05-21 Nature communications 1 16
visibility_off Gene regulatory network structure informs the distribution of perturbation effects Matthew Aguirre, J. Spence, Guy Sella, Jonathan K. Pritchard 2024-07-05 bioRxiv 0 17
visibility_off PINNs-MPF: A Physics-Informed Neural Network Framework for Multi-Phase-Field Simulation of Interface Dynamics Seifallah Elfetni, R. D. Kamachali 2024-07-02 ArXiv 0 14
visibility_off Prediction of the Change Rate of Tumor Cells, Healthy Host Cells, and Effector Immune Cells in a Three-Dimensional Cancer Model using Extended Kalman Filter Nina Fitriyati, Salma Abidah Faizah, Taufik Edy Sutanto 2024-06-27 Jambura Journal of Biomathematics (JJBM) 0 0
visibility_off Empirical Networks are Sparse: Enhancing Multi-Edge Models with Zero-Inflation Giona Casiraghi, George Andres 2024-06-13 ArXiv 0 9
visibility_off Nutmeg and SPICE: Models and Data for Biomolecular Machine Learning Peter K. Eastman, Benjamin P. Pritchard, J. Chodera, T. Markland 2024-06-18 ArXiv 0 57
visibility_off Bayesian inference of covariate-parameter relationships for population modelling Han Cheng Lie 2024-07-12 ArXiv 0 0
visibility_off Robust CATE Estimation Using Novel Ensemble Methods Oshri Machluf, Tzviel Frostig, Gal Shoham, Tomer Milo, Elad Berkman, Raviv Pryluk 2024-07-04 ArXiv 0 4
visibility_off Comparing AI versus Optimization Workflows for Simulation-Based Inference of Spatial-Stochastic Systems Michael A. Ramirez-Sierra, T. Sokolowski 2024-07-15 ArXiv 0 7
visibility_off Exploring the Potential of Radiomic Features in Predictive Murine Tumor Growth Modeling Assia Hamitou, A. Rifi, I. Dufait, Camille Raets, M. De Ridder, Kurt Barbé 2024-05-20 2024 IEEE International Instrumentation and Measurement Technology Conference (I2MTC) 0 15
visibility_off Dynamic undirected graphical models for time-varying clinical symptom and neuroimaging networks. Erin I. McDonnell, Shanghong Xie, Karen Marder, Fanyu Cui, Yuanjia Wang 2024-07-15 Statistics in medicine 0 2
visibility_off A modeling framework for detecting and leveraging node-level information in Bayesian network inference. Xiaoyue Xi, H. Ruffieux 2024-06-25 Biostatistics 0 10
visibility_off Expressive Symbolic Regression for Interpretable Models of Discrete-Time Dynamical Systems Adarsh Iyer, N. Boddupalli, Jeff Moehlis 2024-06-05 ArXiv 0 5
visibility_off Mixed effect estimation in deep compartment models: Variational methods outperform first-order approximations. A. Janssen, Frank C Bennis, M. Cnossen, R. Mathôt 2024-07-04 Journal of pharmacokinetics and pharmacodynamics 0 30
visibility_off Guided Trajectory Generation with Diffusion Models for Offline Model-based Optimization Taeyoung Yun, Sujin Yun, Jaewoo Lee, Jinkyoo Park 2024-06-29 ArXiv 0 3
visibility_off Establishment of a predictive model for antidepressant efficacy based on machine learning Yiyao Liu, Huitong Ni, Teng Zhi, Ziqi Zhao, Xiaoxi Zeng, Ming Hu, Zhiang Wu 2024-07-12 Health Decision 0 0
visibility_off Machine Learning of Reactive Potentials. Yinuo Yang, Shuhao Zhang, Kavindri D. Ranasinghe, O. Isayev, A. Roitberg 2024-06-01 Annual review of physical chemistry 0 57
visibility_off Unveiling Clonal Cell Fate and Differentiation Dynamics: A Hybrid NeuralODE-Gillespie Approach Mingze Gao, Melania Barile, Shirom Chabra, M. Haltalli, Emily F. Calderbank, Yiming Chao, E. Laurenti, B. Gottgens, Yuanhua Huang 2024-07-11 bioRxiv 0 34
visibility_off Bayesian Deep Generative Models for Replicated Networks with Multiscale Overlapping Clusters Yuren Zhou, Yuqi Gu, D. Dunson 2024-05-31 ArXiv 0 2
visibility_off Combining the Strengths of the Explainable Boosting Machine and Metabolomics Approaches for Biomarker Discovery in Acute Myocardial Infarction A. Arslan, F. Yağın, Abdulmohsen Algarni, F. Al-Hashem, L. P. Ardigò 2024-06-26 Diagnostics 0 17
visibility_off Gaussian process regression + deep neural network autoencoder for probabilistic surrogate modeling in nonlinear mechanics of solids Saurabh Deshpande, Hussein Rappel, Mark Hobbs, Stéphane P. A. Bordas, Jakub Lengiewicz 2024-07-15 ArXiv 0 4
visibility_off Balancing Molecular Information and Empirical Data in the Prediction of Physico-Chemical Properties Johannes Zenn, Dominik Gond, F. Jirasek, Robert Bamler 2024-06-12 ArXiv 0 14
visibility_off Predicting Tumor Dynamics Post-Staged GKRS: Machine Learning Models in Brain Metastases Prognosis A. Trofin, C. Buzea, Razvan-Cristian Buga, M. Agop, L. Ochiuz, D. Iancu, Lucian Eva 2024-06-01 Diagnostics 0 25
visibility_off Physics-Informed Neural Networks for Dynamic Process Operations with Limited Physical Knowledge and Data M. Velioglu, Song Zhai, Sophia Rupprecht, Alexander Mitsos, Andreas Jupke, M. Dahmen 2024-06-03 ArXiv 0 13
visibility_off Advanced methods for gene network identification and noise decomposition from single-cell data Zhou Fang, Ankit Gupta, Sant Kumar, Mustafa Khammash 2024-06-08 Nature Communications 0 16
visibility_off Bridging the gap between two-stage and joint models: The case of tumor growth inhibition and overall survival models. Danilo Alvares, F. Mercier 2024-06-03 Statistics in medicine 1 13
visibility_off Inferring stochastic low-rank recurrent neural networks from neural data Matthijs Pals, A. E. Saugtekin, Felix Pei, Manuel Gloeckler, J. H. Macke 2024-06-24 ArXiv 0 3
visibility_off Learning Dynamic Bayesian Networks from Data: Foundations, First Principles and Numerical Comparisons Vyacheslav Kungurtsev, Petr Rysavy, Fadwa Idlahcen, Pavel Rytir, Ales Wodecki 2024-06-25 ArXiv 0 2
visibility_off Information transfer pathways: signal propagation in complex global topologies Qitong Hu, Xiao-Dong Zhang 2024-05-20 Physica Scripta 0 1
visibility_off Predicting therapeutic clinical trial enrollment for underrepresented patients in neuro-oncology using supervised machine learning. Mulki Mehari, G. Warrier, Abraham Dada, Aymen Kabir, U. Chukwueke, Alyx B Porter, Shawn L. Hervey-Jumper 2024-06-01 Journal of Clinical Oncology 0 19
visibility_off Building multiscale models with PhysiBoSS, an agent-based modeling tool Marco Ruscone, Andrea Checcoli, Randy W. Heiland, Emmanuel Barillot, P. Macklin, Laurence Calzone, Vincent Noël 2024-06-26 ArXiv 0 30
visibility_off Modeling and validation of drug release kinetics using hybrid method for prediction of drug efficiency and novel formulations Saad M. Alshahrani, H. F. Alotaibi, Mohammed A Alqarni 2024-06-21 Frontiers in Chemistry 0 9
visibility_off Robust Optimization in Protein Fitness Landscapes Using Reinforcement Learning in Latent Space Minji Lee, L. Vecchietti, Hyunkyu Jung, Hyun Joo Ro, Meeyoung Cha, Ho Min Kim 2024-05-29 ArXiv 0 7
visibility_off Neural Operator-Based Proxy for Reservoir Simulations Considering Varying Well Settings, Locations, and Permeability Fields Daniel Badawi, Eduardo Gildin 2024-07-13 ArXiv 0 1
visibility_off Quantifying uncertainty in Bayesian Networks structural learning Vitor O. Barth, H. O. Caetano, C. Maciel, Marco Aiello 2024-05-23 2024 IEEE International Conference on Evolving and Adaptive Intelligent Systems (EAIS) 0 3
visibility_off Two-part predictive modeling for COVID-19 cases and deaths in the U.S. Teresa-Thuong Le, Xiyue Liao 2024-06-06 PLOS ONE 0 0
visibility_off Explainable Bayesian Recurrent Neural Smoother to Capture Global State Evolutionary Correlations Shi Yan, Yan Liang, Huayu Zhang, Le Zheng, Difan Zou, Binglu Wang 2024-06-17 ArXiv 0 3
visibility_off Detection of Bias in Machine Learning Models for Predicting Deaths Caused by COVID-19 Fatimatus Zachra, Setio Basuki 2024-06-30 Jurnal ELTIKOM 0 0
visibility_off A Bayesian joint model of multiple nonlinear longitudinal and competing risks outcomes for dynamic prediction in multiple myeloma: joint estimation and corrected two-stage approaches Danilo Alvares, Jessica K. Barrett, Franccois Mercier, S. Roumpanis, Sean Yiu, Felipe Castro, Jochen Schulze, Yajing Zhu 2024-05-30 ArXiv 0 2
visibility_off Evaluating the forecasting performance of ensemble sub-epidemic frameworks and other time series models for the 2022–2023 mpox epidemic A. Bleichrodt, R. Luo, A. Kirpich, Gerardo Chowell 2024-07-01 Royal Society Open Science 0 13
visibility_off Joint identification of spatially variable genes via a network-assisted Bayesian regularization approach Mingcong Wu, Yang Li, Shuangge Ma, Mengyun Wu 2024-07-07 ArXiv 0 1
visibility_off Anomaly detection for high-content image-based phenotypic cell profiling Alon Shpigler, Naor Kolet, Shahar Golan, Erin Weisbart, A. Zaritsky 2024-06-03 bioRxiv 0 17
visibility_off Biologically meaningful genome interpretation models to address data underdetermination for the leaf and seed ionome prediction in Arabidopsis thaliana Daniele Raimondi, Antoine Passemiers, N. Verplaetse, Massimiliano Corso, Ángel Ferrero-Serrano, Nelson Nazzicari, Filippo Biscarini, Piero Fariselli, Yves Moreau 2024-06-08 Scientific Reports 0 9
visibility_off Deep representation learning of chemical-induced transcriptional profile for phenotype-based drug discovery X. Tong, Ning Qu, Xiangtai Kong, Shengkun Ni, Jingyi Zhou, Kun Wang, Lehan Zhang, Yiming Wen, Jiangshan Shi, Sulin Zhang, Xutong Li, Mingyue Zheng 2024-06-25 Nature Communications 0 12
visibility_off Metadata-guided Feature Disentanglement for Functional Genomics Alexander Rakowski, Remo Monti, Viktoriia Huryn, Marta Lemanczyk, Uwe Ohler, Christoph Lippert 2024-05-29 ArXiv 0 7
visibility_off Building a small brain with a simple stochastic generative model Oren Richter, Elad Schneidman 2024-07-04 bioRxiv 0 29
visibility_off Reducing Uncertainty Through Mutual Information in Structural and Systems Biology Vincent D. Zaballa, Elliot E. Hui 2024-07-11 ArXiv 0 1
visibility_off Evaluation of normalization methods for predicting quantitative phenotypes in metagenomic data analysis Beibei Wang, Yihui Luan 2024-06-05 Frontiers in Genetics 0 1
visibility_off iResNetDM: interpretable and comprehensive deep learning model for 4 types of DNA modifications prediction Zerui Yang, Wei Shao, Yudai Matsuda, Linqi Song 2024-05-21 bioRxiv 0 1
visibility_off Cellular Dynamics Upon Immune Checkpoint Inhibition Zhongyang Lin, Eketerina Petrenko, Mitalee Chandra, Nalini Srinivas, Selma Ugurel, Jürgen C. Becker, Dvir Aran 2024-07-02 bioRxiv 0 7
visibility_off Contrastive learning of T cell receptor representations Yuta Nagano, Andrew Pyo, Martina Milighetti, James Henderson, John Shawe-Taylor, Benjamin Chain, Andreas Tiffeau-Mayer 2024-06-10 ArXiv 0 4
visibility_off Optimal Recurrent Network Topologies for Dynamical Systems Reconstruction Christoph Jurgen Hemmer, Manuel Brenner, Florian Hess, Daniel Durstewitz 2024-06-07 ArXiv 0 3
visibility_off Seventy Years of Dose-response Models: From the Target Theory to the Use of Big Databases Involving Cell Survival and DNA Repair. L. Bodgi, Laurent Pujo-Menjouet, Audrey Bouchet, Michel Bourguignon, N. Foray 2024-05-28 Radiation research 0 37
visibility_off Vaccine design and development: Exploring the interface with computational biology and AI. Ananya, Darshan C Panchariya, Anandakrishnan Karthic, S. P. Singh, Ashutosh Mani, A. Chawade, Sandeep Kushwaha 2024-07-10 International reviews of immunology 0 25
visibility_off Data-driven modeling of E. coli transcriptional regulation Christopher Dalldorf, Griffith Hughes, Gaoyuan Li, Bernhard O. Palsson, Daniel C. Zielinski 2024-06-03 bioRxiv 0 20
visibility_off DeepMol: An Automated Machine and Deep Learning Framework for Computational Chemistry João Correia, João Capela, M. Rocha 2024-06-01 bioRxiv 0 4
visibility_off Linearization Turns Neural Operators into Function-Valued Gaussian Processes Emilia Magnani, Marvin Pförtner, Tobias Weber, Philipp Hennig 2024-06-07 ArXiv 0 3
visibility_off Mapping Network-Coordinated Stacked Gated Recurrent Units for Turbulence Prediction Zhiming Zhang, Shangce Gao, Mengchu Zhou, Mengtao Yan, Shuyang Cao 2024-06-01 IEEE/CAA Journal of Automatica Sinica 0 14
visibility_off An overview about neural networks potentials in molecular dynamics simulation R. Martin‐Barrios, E. Navas‐Conyedo, Xuyi Zhang, Yunwei Chen, J. Gulín‐González 2024-05-21 International Journal of Quantum Chemistry 0 9
visibility_off Nonlinear compartmental modeling to monitor ovarian follicle population dynamics on the whole lifespan. Guillaume Ballif, Frédérique Clément, Romain Yvinec 2024-06-06 Journal of mathematical biology 0 1
visibility_off Predicting the Predicted: A Comparison of Machine Learning-Based Collision Cross-Section Prediction Models for Small Molecules Sara M de Cripan, Trisha Arora, Adrià Olomí, N. Canela, Gary Siuzdak, Xavier Domingo-Almenara 2024-05-24 Analytical Chemistry 0 24
visibility_off Token-Mol 1.0: Tokenized drug design with large language model Jike Wang, Rui Qin, Mingyang Wang, Meijing Fang, Yangyang Zhang, Yuchen Zhu, Qun Su, Qiaolin Gou, Chao Shen, Odin Zhang, Zhenxing Wu, Dejun Jiang, Xujun Zhang, Huifeng Zhao, Xiaozhe Wan, Zhourui Wu, Liwei Liu, Yu Kang, Chang-Yu Hsieh, Tingjun Hou 2024-07-10 ArXiv 0 13
visibility_off Application of Transformers in Cheminformatics Kha-Dinh Luong, Ambuj Singh 2024-05-30 Journal of Chemical Information and Modeling 0 1
visibility_off Generative deep learning for data generation in natural hazard analysis: motivations, advances, challenges, and opportunities Zhengjing Ma, Gang Mei, N. Xu 2024-05-30 Artif. Intell. Rev. 0 17
visibility_off MMIL: A novel algorithm for disease associated cell type discovery. Erin Craig, Timothy Keyes, J. Sarno, Maxim E. Zaslavsky, Garry Nolan, Kara Davis, Trevor Hastie, R. Tibshirani 2024-06-12 ArXiv 0 154
visibility_off Self-supervised machine learning methods for protein design improve sampling, but not the identification of high-fitness variants Moritz Ertelt, Rocco Moretti, Jens Meiler, Clara T. Schoeder 2024-06-24 bioRxiv 0 14
visibility_off CPMI: comprehensive neighborhood-based perturbed mutual information for identifying critical states of complex biological processes Jing Ren, Peiluan Li, Jinling Yan 2024-06-15 BMC Bioinformatics 0 1
visibility_off Likelihood-based inference, identifiability and prediction using count data from lattice-based random walk models Yihan Liu, D. Warne, Matthew J. Simpson 2024-06-24 ArXiv 0 12
visibility_off Modeling and control of COVID-19 disease using deep reinforcement learning method. Nazanin Ghazizadeh, S. Taghvaei, S. Haghpanah 2024-06-28 Medical & biological engineering & computing 0 9
visibility_off Predictive Model for Extended-Spectrum β-Lactamase-Producing Bacterial Infections Using Natural Language Processing Technique and Open Data in Intensive Care Unit Environment: Retrospective Observational Study. Genta Ito, Shuntaro Yada, Shoko Wakamiya, E. Aramaki 2024-07-10 JMIR formative research 0 20
visibility_off Unveiling gene regulatory networks during cellular state transitions without linkage across time points Ruosi Wan, Yuhao Zhang, Yongli Peng, Feng Tian, Ge Gao, Fuchou Tang, Jinzhu Jia, Hao Ge 2024-05-29 Scientific Reports 0 2
visibility_off Tackling Data Scarcity Challenge through Active Learning in Materials Processing with Electrospray Fanjin Wang, A. Harker, Mohan Edirisinghe, M. Parhizkar 2024-05-23 Advanced Intelligent Systems 0 17
visibility_off An Optimal Transport Approach for Network Regression Alex G. Zalles, Kai M. Hung, Ann E. Finneran, L. Beaudrot, C'esar A. Uribe 2024-06-18 ArXiv 0 22
visibility_off Gene regulatory network inference from single-cell data using optimal transport François Lamoline, Isabel Haasler, Johan Karlsson, Jorge Gonçalves, A. Aalto 2024-05-30 bioRxiv 0 11
visibility_off Learning Patterns from Biological Networks: A Compounded Burr Probability Model Tanujit Chakraborty, Shraddha M. Naik, Swarup Chattopadhyay, Suchismita Das 2024-07-05 ArXiv 0 18
visibility_off Deep Cell-Type Deconvolution from Bulk Gene Expression Data Using DECODE Eran Hermush, R. Sharan 2024-06-18 Digital Medicine and Healthcare Technology 0 1
visibility_off A guided network estimation approach using multi-omic information G. Bartzis, C. Peeters, W. Ligterink, Fred A. van Eeuwijk 2024-05-30 BMC Bioinformatics 0 34
visibility_off Application of a variational autoencoder for clustering and analyzing in situ articular cartilage cellular response to mechanical stimuli Jingyang Zheng, Han Kheng Teoh, M. Delco, L. Bonassar, I. Cohen 2024-05-20 PLOS ONE 0 68
visibility_off Advection Augmented Convolutional Neural Networks N. Zakariaei, Siddharth Rout, Eldad Haber, Moshe Eliasof 2024-06-27 ArXiv 0 6
visibility_off A Study on the Robustness and Stability of Explainable Deep Learning in an Imbalanced Setting: The Exploration of the Conformational Space of G Protein-Coupled Receptors M. A. Gutierrez-Mondragon, Alfredo Vellido, Caroline König 2024-06-01 International Journal of Molecular Sciences 0 2
visibility_off Zebrafish Avatar-test forecasts clinical response to chemotherapy in patients with colorectal cancer Bruna Costa, Marta F Estrada, António Gomes, Laura M. Fernández, José M Azevedo, Vanda Póvoa, Márcia Fontes, António Alves, António Galzerano, Mireia Castillo-Martin, Ignacio Herrando, Shermann Brandão, Carla Carneiro, Vítor Nunes, Carlos Carvalho, Amjad Parvaiz, Ana Marreiros, R. Fior 2024-06-05 Nature Communications 0 14
visibility_off Network-based Neighborhood regression Yaoming Zhen, Jin-Hong Du 2024-07-04 ArXiv 0 0
visibility_off PyMulSim: a method for computing node similarities between multilayer networks via graph isomorphism networks Pietro Cinaglia 2024-06-13 BMC Bioinformatics 0 9
visibility_off Deconvolving Complex Neuronal Networks into Interpretable Task-Specific Connectomes Yifan Wang, V. Ravindra, A. Grama 2024-06-28 ArXiv 0 46
visibility_off Development of a machine learning model to predict overall survival results from randomized clinical trials of patients with metastatic prostate cancer. A. Sabbagh, David A Quigley, Nicholas Lillis, Li Zhang, I. Friesner, A. Bailey, Rahul R Aggarwal, Meera Reddy Chappidi, Hari Singhal, Ke Zhang, J. Greshock, Jinhui Li, Margaret K. Yu, Eric J. Small, Julian C. Hong 2024-06-01 Journal of Clinical Oncology 0 3
visibility_off Bayesian Occam’s Razor to Optimize Models for Complex Systems Chenxi Wang, Jihui Zhao, Jingjing Zheng, Barak Raveh, Xuming He, Liping Sun 2024-06-02 bioRxiv 0 9
visibility_off Clinical Validation of Mathematically Derived Early Tumor Dynamics for Solid Tumors in Response to Durvalumab. Qin Li, Vittorio Cristini, Ashok Gupta, I. Achour, J. C. Barrett, Eugene J Koay 2024-07-01 JCO clinical cancer informatics 0 17
visibility_off Learning Diffusion at Lightspeed Antonio Terpin, Nicolas Lanzetti, Florian Dörfler 2024-06-18 ArXiv 0 10
visibility_off emle-engine: A Flexible Electrostatic Machine Learning Embedding Package for Multiscale Molecular Dynamics Simulations Kirill Zinovjev, Lester Hedges, Rubén Montagud Andreu, Christopher Woods, I. Tuñón, M. W. van der Kamp 2024-05-28 Journal of Chemical Theory and Computation 1 42
visibility_off Bayesian Entropy Neural Networks for Physics-Aware Prediction R. Rathnakumar, Jiayu Huang, Hao Yan, Yongming Liu 2024-07-01 ArXiv 0 3
visibility_off Functional Control of Network Dynamical Systems: An Information Theoretic Approach Moirangthem Sailash Singh, R. Pasumarthy, Umesh Vaidya, Steffen Leonhardt 2024-06-17 bioRxiv 0 14
Abstract Title Authors Publication Date Journal/Conference Citation count Highest h-index