13 papers · ranked by Valyu relevance
Justin Eilertsen, Valery G. Romanovski, Santiago Schnell, Sebastian Walcher
We investigate linear lumping for parameter-dependent mass action reaction networks, distinguishing between generic and critical parameter regimes. For generic parameters -- those ranging in some non-empty open subset of parameter space -- we prove that exact linear lumping yields only "obvious" reductions: elimination…
Shan Pan, Stephen B. Duffull
Physiologically based pharmacokinetic (PBPK) models are an important type of systems model used commonly in drug development before commencement of first-in-human studies. Due to structural complexity, these models are not easily utilised for future data-driven population pharmacokinetic (PK) analyses that require…
Hanlin Gu, Wei Wang, Siqin Cao, Ilona Christy Unarta + 3 more
Markov State Model (MSM) is a powerful tool for modeling the long timescale dynamics based on numerous short molecular dynamics (MD) simulation trajectories, which makes it a useful tool for elucidating the conformational changes of biological macromolecules. By partitioning the phase space into discretized states and…
Lea Seep, Zahra Razaghi-Moghadam, Zoran Nikoloski
Thermodynamic metabolic flux analysis (TMFA) can narrow down the space of steady-state flux distributions, but requires knowledge of the standard Gibbs free energy for the modelled reactions. The latter are often not available due to unknown Gibbs free energy change of formation $,{\Delta}_{f}G^{0}$, of metabolites. To…
Brent D. Fegley, Vetle I. Torvik, Marco Tomassini
The assumption that a name uniquely identifies an entity introduces two types of errors: splitting treats one entity as two or more (because of name variants); lumping treats multiple entities as if they were one (because of shared names). Here we investigate the extent to which splitting and lumping affect…
Bernhard C. Geiger, Christoph Temmel
A lumping of a Markov chain is a coordinate-wise projection of the chain. We characterise the entropy rate preservation of a lumping of an aperiodic and irreducible Markov chain on a finite state space by the random growth rate of the cardinality of the realisable preimage of a finite-length trajectory of the lumped…
Alexander Rivkind, Hallel Schreier, Naama Brenner, Omri Barak
Biological networks are often heterogeneous in their connectivity pattern, with degree distributions featuring a heavy tail of highly connected hubs. The implications of this heterogeneity on dynamical properties are a topic of much interest. Here we introduce a novel approach to analyze such networks the lumped hub…
Timothy Disher, Chris Cameron, Brian Hutton
Network meta-analysis (NMA) synthesizes evidence for multiple treatments, but decisions on node formation can have important statistical implications including bias or inflated uncertainty. Existing data-driven methods often lack flexibility or fail to fully account for node uncertainty and adjust for between-trial…
Dalila Ressi, Riccardo Romanello, Sabina Rossi, Carla Piazza
The increasing size of recently proposed Neural Networks makes it hard to implement them on embedded devices, where memory, battery and computational power are a non-trivial bottleneck. For this reason during the last years network compression literature has been thriving and a large number of solutions has been been…
Kai Röth, Shuai Shao, Julijana Gjorgjieva
Sensory organs transmit information to downstream brain circuits using a neural code comprised of spikes from multiple neurons. According to the prominent efficient coding framework, the properties of sensory populations have evolved to encode maximum information about stimuli given biophysical constraints. How…
Hyo-jeong Ryu, Won-ho Kang, Taeheon Kim, Jae Kyoung Kim + 3 more
'Kwang-Hee Shin' 'Jung-woo Chae' 'Hwi-yeol Yun'] Pharmacokinetic (PK) modeling is a useful method for investigating drug absorption, distribution, metabolism, and excretion. The most commonly used mathematical models in PK modeling are the compartment model and physiologically based pharmacokinetic (PBPK) model.…
Juliana Stropp, Andreza S. S. Pereira, Thaise Emilio, Leila Meyer + 4 more
Although taxonomy is an evolving discipline, taxonomic change is rarely accounted for in macroecological studies. By tracking the history of species descriptions and synonymizations of more than 800 names of Amazonian palms, we reveal shifts in species counts across space and time, the factors associated with taxonomic…
Michał Łepek
In a process of aggregation, a finite number of particles merge irreversibly to create growing clusters. In this work, impact of particular initial conditions: monodisperse, power–law, exponential, and inspired by condensation nuclei was tested against several aggregation processes: constant, additive, product…