Search · four archives
Search · four archives
10 papers · ranked by Valyu relevance
Hyun Dong Lee, Aditi Jha, Stephen E. Clarke, Michael P. Silvernagel + 2 more
Understanding neural dynamics is crucial for uncovering how the brain processes information and controls behavior. Linear dynamical systems (LDS) are widely used for modeling neural data due to their simplicity and effectiveness in capturing latent dynamics. However, LDS assumes a stable mapping from the latent states…
Peter J. Gawthrop, Michael Pan
The sensitivity of systems biology models to parameter variation can give insights into which parameters are most important for physiological function, and also direct efforts to estimate parameters. However, in general, kinetic models of biochemical systems do not remain thermodynamically consistent after perturbing…
Rodrigo Osuna-Orozco, Edward Castillo, Kameron Decker Harris, Samantha R. Santacruz
Large-scale recordings of neural activity over broad anatomical areas with high spatial and temporal resolution are increasingly common in modern experimental neuroscience. Recently, recurrent switching dynamical systems have been used to tackle the scale and complexity of these data. However, an important challenge…
Arturo Tozzi
A wide range of biological and evolutionary processes is determined not merely by the occurrence of specific events, but by the exact order in which those events unfold. Gene regulation, developmental pathways, metabolic cascades and genetic evolution often display non-commutative behaviour, in which reversing the…
Benjamin P. Kellman, Yujie Zhang, Emma Logomasini, Eric Meinhardt + 14 more
Systems glycobiology aims to provide models and analysis tools that account for the biosynthesis, regulation, and interactions with glycoconjugates. To facilitate these methods, there is a need for a clear glycan representation accessible to both computers and humans. Linear Code, a linearized and readily parsable…
Oluwateniayo O. Ogunsan, Daniel Lobo
Mathematical models formally and precisely represent biological mechanisms with complex dynamics. To understand the possible behaviors of such systems, phase portrait diagrams can be used to visualize their overall global dynamics across a domain. However, producing these phase portrait diagrams is a laborious process…
Ayush Pandey, Richard M. Murray
We present an automated model reduction algorithm that uses quasi-steady state approximation based reduction to minimize the error between the desired outputs. Additionally, the algorithm minimizes the sensitivity of the error with respect to parameters to ensure robust performance of the reduced model in the presence…
Jack Lindsey, Samuel A. Ocko, Surya Ganguli, Stephane Deny
The vertebrate visual system is hierarchically organized to process visual information in successive stages. Neural representations vary drastically across the first stages of visual processing: at the output of the retina, ganglion cell receptive fields (RFs) exhibit a clear antagonistic center-surround structure…
Ismaila Muhammed, Dimitris M. Manias, Dimitris A. Goussis, Haralampos Hatzikirou
Biomedical systems inherently exhibit multi-scale dynamics, making accurate system identification particularly challenging due to the complexity of capturing a wide time scale spectrum. Traditional methods capable of addressing this issue rely on explicit equations, limiting their applicability in cases where only…
Difei Tang, Natasa Miskov-Zivanov
In computational modeling, Bounded Linear Temporal Logic (BLTL) is a valuable formalism for describing and verifying the temporal behavior of biological systems. However, translating natural language (NL) descriptions of system behaviors into accurate BLTL properties remains a labor-intensive task, requiring deep…