Dionisios G. Vlachos

33 papers A 1Journal 31Unranked 1

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	A Python tool for parameter estimation of "black box" macro- and micro-kinetic models with Bayesian optimization - petBOA. Comput. Phys. Commun. Sashank Kasiraju, Yifan Wang, Saurabh Bhandari, Aayush R. Singh, Dionisios G. Vlachos
2025	J	`jnl`	Distance-Aware Molecular Property Prediction in Nonlinear Structure-Property Space. J. Chem. Inf. Model. Jae Young Kim, Dionisios G. Vlachos
2025	J	`jnl`	Rapid Adaptation of Chemical Named Entity Recognition Using Few-Shot Learning and LLM Distillation. J. Chem. Inf. Model. Yue Zhang, Dionisios G. Vlachos, Dongxia Liu, Hui Fang
2024	J	`jnl`	Process integration and systems optimization for the hydrodeoxygenation of 5-hydroxymethylfurfural to dimethylfuran. Comput. Chem. Eng. Zhaoxing Wang, Yuqing Luo, Prahalad Srinivasan, Yifan Wang, Tai-Ying Chen, Marianthi G. Ierapetritou, Dionisios G. Vlachos
2023	J	`jnl`	Automated descriptor selection, volcano curve generation, and active site determination using the DescMAP software. Comput. Phys. Commun. Xue Zong, Jonathan Lym, Dionisios G. Vlachos
2023	J	`jnl`	CKineticsDB─An Extensible and FAIR Data Management Framework and Datahub for Multiscale Modeling in Heterogeneous Catalysis. J. Chem. Inf. Model. Siddhant M. Lambor, Sashank Kasiraju, Dionisios G. Vlachos
2023	J	`jnl`	Machine Learning Validation via Rational Dataset Sampling with astartes. J. Open Source Softw. Jackson W. Burns, Kevin A. Spiekermann, Himaghna Bhattacharjee, Dionisios G. Vlachos, William H. Green Jr.
2023	J	`jnl`	OpenMKM: An Open-Source C++ Multiscale Modeling Simulator for Homogeneous and Heterogeneous Catalytic Reactions. J. Chem. Inf. Model. Bharat Medasani, Sashank Kasiraju, Dionisios G. Vlachos
2022	J	`jnl`	Exploring Structure-Sensitive Relations for Small Species Adsorption Using Machine Learning. J. Chem. Inf. Model. Xue Zong, Dionisios G. Vlachos
2022	J	`jnl`	LigninGraphs: lignin structure determination with multiscale graph modeling. J. Cheminformatics Yifan Wang, Jake Kalscheur, Elvis Ebikade, Qiang Li, Dionisios G. Vlachos
2022	J	`jnl`	Python Group Additivity (pGrAdd) software for estimating species thermochemical properties. Comput. Phys. Commun. Gerhard R. Wittreich, Dionisios G. Vlachos
2022	J	`jnl`	Unleashing the Power of Knowledge Extraction from Scientific Literature in Catalysis. J. Chem. Inf. Model. Yue Zhang, Cong Wang, Mya Soukaseum, Dionisios G. Vlachos, Hui Fang
2021	J	`jnl`	Chemical Kinetics Bayesian Inference Toolbox (CKBIT). Comput. Phys. Commun. Maximilian Cohen, Dionisios G. Vlachos
2021	J	`jnl`	Learning Chemistry of Complex Reaction Systems via a Python First-Principles Reaction Rule Stencil (pReSt) Generator. J. Chem. Inf. Model. Udit Gupta, Dionisios G. Vlachos
2021	J	`jnl`	NEXTorch: A Design and Bayesian Optimization Toolkit for Chemical Sciences and Engineering. J. Chem. Inf. Model. Yifan Wang, Tai-Ying Chen, Dionisios G. Vlachos
2020	J	`jnl`	A Python Multiscale Thermochemistry Toolbox (pMuTT) for thermochemical and kinetic parameter estimation. Comput. Phys. Commun. Jonathan Lym, Gerhard R. Wittreich, Dionisios G. Vlachos
2020	J	`jnl`	Reaction Network Viewer (ReNView): An open-source framework for reaction path visualization of chemical reaction systems. SoftwareX Udit Gupta, Dionisios G. Vlachos
2020	J	`jnl`	Thermochemical Data Fusion Using Graph Representation Learning. J. Chem. Inf. Model. Himaghna Bhattacharjee, Dionisios G. Vlachos
2014	J	`jnl`	A robust and efficient triangulation-based optimization algorithm for stochastic black-box systems. Comput. Chem. Eng. Jacob A. McGill, Babatunde A. Ogunnaike, Dionisios G. Vlachos
2013	J	`jnl`	Parametric Sensitivity Analysis for Biochemical Reaction Networks based on Pathwise Information Theory CoRR Yannis Pantazis, Markos A. Katsoulakis, Dionisios G. Vlachos
2013	J	`jnl`	Parametric sensitivity analysis for biochemical reaction networks based on pathwise information theory. BMC Bioinform. Yannis Pantazis, Markos A. Katsoulakis, Dionisios G. Vlachos
2012	J	`jnl`	Efficient gradient estimation using finite differencing and likelihood ratios for kinetic Monte Carlo simulations. J. Comput. Phys. Jacob A. McGill, Babatunde A. Ogunnaike, Dionisios G. Vlachos
2012	J	`jnl`	Multilevel coarse graining and nano-pattern discovery in many particle stochastic systems. J. Comput. Phys. Evangelia Kalligiannaki, Markos A. Katsoulakis, Petr Plechác, Dionisios G. Vlachos
2011	J	`jnl`	Equivalence of on-lattice stochastic chemical kinetics with the well-mixed chemical master equation in the limit of fast diffusion. Comput. Chem. Eng. Michail Stamatakis, Dionisios G. Vlachos
2011	J	`jnl`	Long-time integration methods for mesoscopic models of pattern-forming systems. J. Comput. Phys. Nasser Mohieddin Abukhdeir, Dionisios G. Vlachos, Markos A. Katsoulakis, Michael Plexousakis
2010	J	`jnl`	Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes. BMC Bioinform. Stuart Collins, Michail Stamatakis, Dionisios G. Vlachos
2010	A	`conf`	Parallelization of tau-leap coarse-grained Monte Carlo simulations on GPUs. IPDPS Lifan Xu, Michela Taufer, Stuart Collins, Dionisios G. Vlachos
2007	J	`jnl`	A hybrid multiscale Monte Carlo algorithm (HyMSMC) to cope with disparity in time scales and species populations in intracellular networks. BMC Bioinform. Asawari Samant, Babatunde A. Ogunnaike, Dionisios G. Vlachos
2006	J	`jnl`	Hierarchical multiscale model-based design of experiments, catalysts, and reactors for fuel processing. Comput. Chem. Eng. Dionisios G. Vlachos, A. B. Mhadeshwar, Niket S. Kaisare
2005	J	`jnl`	Net-event kinetic Monte Carlo for overcoming stiffness in spatially homogeneous and distributed systems. Comput. Chem. Eng. M. A. Snyder, A. Chatterjee, Dionisios G. Vlachos
2005	J	`jnl`	Time accelerated Monte Carlo simulations of biological networks using the binomial r-leap method. Bioinform. Abhijit Chatterjee, Kapil Mayawala, Jeremy S. Edwards, Dionisios G. Vlachos
2001	—	`conf`	Stochastic kinetic analysis of transcriptional feedback models for circadian rhythms. CDC Daniel E. Zak, Francis J. Doyle III, Dionisios G. Vlachos, James S. Schwaber
1997	J	`jnl`	Growth of Nanophase Clusters and Potential Energy Minima: Hysteresis, Oscillations, and Phase Transitions. J. Glob. Optim. Dionisios G. Vlachos