21 papers · ranked by Valyu relevance
Maxwell L. Neal, Michael T. Cooling, Lucian P. Smith, Christopher T. Thompson + 5 more
Biological researchers increasingly rely on computational models to integrate biological systems knowledge, test hypotheses, and forecast system behavior. The expanding size of these models requires solutions for managing their complexity. Modularity, a time-tested design principle for managing complexity, can be…
Michael Pan, Peter J. Gawthrop, Joseph Cursons, Edmund J. Crampin
It is widely acknowledged that the construction of large-scale dynamic models in systems biology requires complex modelling problems to be broken up into more manageable pieces. To this end, both modelling and software frameworks are required to enable modular modelling. While there has been consistent progress in the…
Brenden K Petersen, Glen EP Ropella, C Anthony Hunt
Background Currently, most biomedical models exist in isolation. It is often difficult to reuse or integrate models or their components, in part because they are not modular. Modular components allow the modeler to think more deeply about the role of the model and to more completely address a modeling project’s…
Samiyuru Menik, Lakshmish Ramaswamy
Machine learning technologies have demonstrated immense capabilities in various domains. They play a key role in the success of modern businesses. However, adoption of machine learning technologies has a lot of untouched potential. Cost of developing custom machine learning solutions that solve unique business problems…
Christopher Schölzel, Valeria Blesius, Gernot Ernst, Andreas Dominik
Reproducible, understandable models that can be reused and combined to true multi-scale systems are required to solve the present and future challenges of systems biology. However, many mathematical models are still built for a single purpose and reusing them in a different context can be challenging due to an…
Xianni Zhong, Jihui Zhao, Liping Sun
A whole-cell model represents certain aspects of the cell structure and/or function. Due to the high complexity of the cell, an integrative modeling approach is often taken to utilize all available information including experimental data, prior knowledge and prior models. In this review, we summarize an emerging…
Ryan Bernstein
Probabilistic programming makes it easy to represent a probabilistic model as a program. Building an individual model, however, is only one step of probabilistic modeling. The broader challenge of probabilistic modeling is in understanding and navigating spaces of alternative models. There is currently no good way to…
Authors not listed
Modeling of chemical reactions is essential for understanding kinetic mechanisms and predicting possible outcomes of reacting systems. Quantum mechanical calculations are accurate but often prohibitively expensive. Deep learning has emerged as a faster alternative, but progress is slowed by a fragmented software…
Authors not listed
Deriving versatile and robust mechanistic models from experimental data is a key challenge in engineering and natural sciences. This is especially true in chemical reaction engineering, where reactor manufacturers and operators increasingly pursue the development and maintenance of digital twins that rely on frequent…
Anubhav Dogra, Sakshay Mahna, Srikant Sekhar Padhee, Ekta Singla
Customization of manipulator configurations using modularity and reconfigurability aspects is receiving much attention. Modules presented so far in literature deals with the conventional and standard configurations. This paper presents the 3D printable, light-weight and unconventional modules: MOIRs' Mark-2, to develop…
Filip Milisav, Andrea I. Luppi, Laura E. Suárez, Guillaume Lajoie + 1 more
Modularity is a fundamental principle of brain organization, reflected in the presence of segregated sub-networks that enable specialized information processing. These small, densely connected modules are often nested within larger, higher-order modules, giving rise to a hierarchical modular architecture. This…
Niloofar Shahidi, Michael Pan, Soroush Safaei, Kenneth Tran + 2 more
Simulating complex biological and physiological systems and predicting their behaviours under different conditions remains challenging. Breaking systems into smaller and more manageable modules can address this challenge, assisting both model development and simulation. Nevertheless, existing computational models in…
Liliang Ren, Yang Liu, Shuohang Wang, Xu Yi‐chong + 2 more
'ChengXiang Zhai'] Recent hybrid models combining Linear State Space Models (SSMs) with selfattention mechanisms have demonstrated impressive results across a range of sequence modeling tasks. However, current approaches apply attention modules statically and uniformly to all elements in the input sequences, leading to…
Noah Kleinschmidt, Thomas Lemmin
In recent years computational methods for molecular modeling have become a prime focus of computational biology and cheminformatics. Many dedicated systems exist for modeling specific classes of molecules such as proteins or small drug-like ligands. These are often heavily tailored toward the automated gen- eration of…
Authors not listed
Rapid and robust simulation of chemical processes is critical to conduct process design, optimization, techno-economic analysis, and sustainability analysis. Yet, efficiently solving simulation models remains a challenge due to the highly coupled and nonlinear nature of the underlying algebraic equations that capture…
Luna Xingyu Li, Boris Aguilar, John H Gennari, Guangrong Qin
Gene regulatory network (GRN) models provide mechanistic understanding of genetic interactions that regulate gene expression and, consequently, influence cellular behavior. Dysregulated gene expression plays a critical role in disease progression and treatment response, making GRN models a promising tool for precision…
J. Crossa, J. Sun, A. Montesinos‐López, P. Pérez‐Rodríguez + 4 more
The rapid expansion of genomic, environmental, phenomic, and other high-dimensional data sources has transformed genomic prediction in plant breeding. However, the terms multimodal, interaction modeling, and multimodule architecture are often used inconsistently, generating ambiguity regarding whether they refer to…
Maja Rudolph, Stefan Kurz, Barbara Rakitsch
Design patterns provide a systematic way to convey solutions to recurring modeling challenges. This paper introduces design patterns for hybrid modeling, an approach that combines modeling based on first principles with data-driven modeling techniques. While both approaches have complementary advantages there are often…
Niloofar Shahidi, Michael Pan, Kenneth Tran, Edmund J. Crampin + 1 more
Hierarchical modelling is essential to achieving complex, large-scale models. However, not all modelling schemes support hierarchical composition, and correctly mapping points of connection between models requires comprehensive knowledge of each model’s components and assumptions. To address these challenges in…
Mojeeb Al-Rhman Al-Khiaty, Moataz Ahmed
— Software reuse allows the software industry to simultaneously reduce development cost and improve product quality. Reuse of early-stage artifacts has been acknowledged to be more beneficial than reuse of later-stage artifacts. In this regard, early-stage reference models have been considered as good tools to allow…
Peter Sagmeister, Lukas Melnizky, Jason Williams, C. Oliver Kappe
In modern pharmaceutical research, the demand for expeditious development of synthetic routes to active pharmaceutical ingredients (APIs) has led to a paradigm shift towards data-rich process development. Conventional methodologies en-compass prolonged timelines for reaction and analytical model developments. Both…