15 papers · ranked by Valyu relevance
Eva Brombacher, Clemens Kreutz, Pier Luigi Martelli
Ordinary differential equation (ODE) models are currently the method of choice in systems biology for mathematically modelling the dynamics of signalling pathways within cells. However, ODEs have limitations, including the lack of analytical solutions and the need for large, complex models that require extensive…
Tim Litwin, Jens Timmer, Clemens Kreutz
Dynamic behavior of biological systems is commonly represented by non-linear models such as ordinary differential equations. A frequently encountered task in such systems is the estimation of model parameters based on measurement of biochemical compounds. Non-linear models require special techniques to estimate the…
Dilan Pathirana, Frank T. Bergmann, Domagoj Doresic, Polina Lakrisenko + 8 more
A central question in mathematical modeling of biological systems is determining which processes are relevant and how they can be described. There are often competing hypotheses, which yield different models. Model comparison requires parameter optimization and sampling methods. Yet, standards for the specification of…
Eric D. Sun, Rong Ma, James Zou
Dimensionality reduction (DR) is commonly used to project highdimensional data into lower dimensions for visualization, which could then generate new insights and hypotheses. However, DR algorithms necessarily introduce distortions in the visualization and cannot faithfully represent all relations in the data. As such…
Somayeh Dodge, Mert Toka, Crystal J. Bae
Background This paper introduces DynamoVis version 1.0, an open-source software developed to design, record and export custom animations and multivariate visualizations from movement data, enabling visual exploration and communication of patterns capturing the associations between animals’ movement and its affecting…
Danial Yazdani, Juergen Branke, Mohammad Sadegh Khorshidi, Mohammad Nabi Omidvar + 3 more
Generation With Heterogeneous Changes Authors: ['Danial Yazdani' 'Juergen Branke' 'Mohammad Sadegh Khorshidi' 'Mohammad Nabi Omidvar' 'Xiaodong Li' 'Amir H. Gandomi' 'Xin Yao'] XIN YAO, Research Institute of Trustworthy Autonomous Systems (RITAS), and Guangdong Provincial Key Laboratory of Brain inspired Intelligent…
Lijia Jia, Yue Shi, Jing Yang, Shangzhe Li + 14 more
The explosive growth of digital data is overwhelming conventional storage media, creating an urgent need for more efficient solutions. DNA offers immense potential for digital data storage, yet most systems remain static and archival. Here, we present a modular DNA storage architecture based on dynamic DNA bytes…
Pavel S Novichkov, John-Marc Chandonia, Adam P Arkin
Dynamic data types are most often used for data related to the core types, such as measurements taken on core objects. Dynamic types are defined by combining a limited number of simple, mathematical data structures (e.g., matrices, trees, graphs) with contextons that provide critical context to the data, in order to…
Jun-Feng Yao, Yong Yang, Xue-Cheng Wang, Xiao-Peng Zhang
As one of the most important applications of digitalization, intelligence, and service, the digital twin (DT) breaks through the constraints of time, space, cost, and security on physical entities, expands and optimizes the relevant functions of physical entities, and enhances their application value. This phenomenon…
Anna Quaglieri, Joseph Bloom, Aaron Triantafyllidis, Bradley Green + 4 more
Data processing is essential to reliably generate knowledge from proteomics studies. The complexity of the proteomics data, as well as the ability of research teams to adopt complex analysis pipelines, have proven to be an obstacle to effective collaboration and more efficient biological insight generation. Here, we…
Authors not listed
Real-world datasets in chemical engineering and bioengineering processes--such as those from catalytic reactors, multiphase flows, polymerization reactors, bioreactors, and clinical trials--can often be unlabelled or disorganized, rendering the training of existing supervised learning models ineffective at learning the…
Authors not listed
The persistent failure to drug mutant forms of key oncogenes—such as TP53, KRAS, and MYC—is largely due to their lack of stable, visible binding pockets in crystal structures. These proteins are frequently labeled “undruggable,” not because they cannot be modulated, but because their ligandable sites are hidden…
Harley Edwards, Joseph Zavorskas, Walker Huso, Alexander G. Doan + 4 more
Derivative profiling (DP) is a novel approach to identify differential signals from dynamic omics data sets. This approach applies variable step-size differentiation to time dynamic omics data. This work assumes that there is a general omics derivative that is a useful and descriptive feature of dynamic omics…
Heribert Pascual, Xavi Masip Bruin, Albert Alonso, Judit Cerdà
— Human Digital Twins (HDTs) are digital replicas of humans that either mirror a complete human body, some parts of it –as can be organs, flows, cells–, or even human behaviors. An HDT is a human specific replica application inferred from the digital twin (DT) manufacturing concept, defined as a technique that creates…
Kristin Wulff, Hanne Finnestrand
Because of the increase in data and the possibilities created by machine learning, organizations are now looking to become more data-driven. In sociotechnical systems design there has been a focus on designing information for action to support decentralized organizations. The purpose of this article, published in…