22 papers · ranked by Valyu relevance
Eric Mitchell, Charles P. Lin, Antoine Bosselut, Chelsea Finn + 1 more
'Christopher D. Manning'] While large pre-trained models have enabled impressive results on a variety of downstream tasks, the largest existing models still make errors, and even accurate predictions may become outdated over time. Because detecting all such failures at training time is impossible, enabling both…
Alida Palmisano, Stefan Hoops, Layne T Watson, Thomas C Jones Jr + 2 more
'John J Tyson' 'Clifford A Shaffer'] Background Building models of molecular regulatory networks is challenging not just because of the intrinsic difficulty of describing complex biological processes. Writing a model is a creative effort that calls for more flexibility and interactive support than offered by many of…
Susanne Göbel, Ralf Lämmel
Graphical model editing is shifting from desktop applications to web-based tools. We analyze the characteristics of existing frameworks and, based on this analysis, we derive a set of design principles that imply low-effort generation, extensive customization possibilities, and straightforward deployment of the…
Damiano Di Vincenzo, Juri Di Rocco, Davide Di Ruscio, Alfonso Pierantonio
'Alfonso Pierantonio'] Abstract—Domain-specific modelling helps tame the complexity of today's application domains by formalizing concepts and their relationships in modelling languages. While meta-editors are widely-used frameworks for implementing graphical editors for such modelling languages, they are best suitable…
Brenno Lemos Melquiades dos Santos, Diego Augusto Silva Castro, Sávio Francisco Cirino da Paz, Davi Jannotti Coelho Pinheiro + 4 more
'Sávio Francisco Cirino da Paz' 'Davi Jannotti Coelho Pinheiro' 'Bárbara de Melo Quintela' 'Marcelo Lobosco' 'Alexandre Bittencourt Pigozzo' 'Teddy Lazebnik'] Mathematical and computational modeling are transforming biological research by enabling detailed exploration of complex systems. However, building computational…
Ionut Predoaia, James Harbin, Simos Gerasimou, Christina Vasiliou + 2 more
Study of Testing Specifications Authors: ['Ionut Predoaia' 'James Harbin' 'Simos Gerasimou' 'Christina Vasiliou' 'Dimitrios S. Kolovos' 'Antonio García‐Domínguez'] Tree-based model editors and hybrid graphical-textual model editors have advantages and limitations when editing domain models. Data is displayed…
Randy Heiland, Daniel Bergman, Blair Lyons, Grant Waldow + 5 more
'Julie Cass' 'Heber Lima da Rocha' 'Marco Ruscone' 'Vincent Noël' 'Paul Macklin'] Defining a multicellular model can be challenging. There may be hundreds of parameters that specify the attributes and behaviors of objects. In the best case, the model will be defined using some format specification - a markup language -…
Mohammad Nurullah Patwary, Ana Jovanovic, Allison Sullivan
Alloy is well known a declarative modeling language. A key strength of Alloy is its scenario finding toolset, the Analyzer, which allows users to explore all valid scenarios that adhere to the model's constraints up to a user-provided scope. Despite the Analyzer, Alloy is still difficult for novice users to learn and…
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…
Mercedes Huertas-Migueláñez, Daniel Mora, Isaac Cano, Dieter Maier + 3 more
'David Gomez-Cabrero' 'Magí Lluch-Ariet' 'Felip Miralles'] Background Today, many different tools are developed to execute and visualize physiological models that represent the human physiology. Most of these tools run models written in very specific programming languages which in turn simplify the communication among…
Katie Willis, Austin Burt
Effective control of pest populations remains a major challenge for agriculture, public health, and conservation. While genetic control strategies such as the release of sterile males or individuals carrying dominant lethal alleles have achieved some success, they typically require repeated, large-scale releases due to…
Lorenzo Adreani, Pierfrancesco Bellini, Stefano Bilotta, Daniele Bologna + 4 more
Due to increasing urbanization, nowadays, cities are facing challenges spanning multiple domains such as mobility, energy, environment, etc. For example, to reduce traffic congestion, energy consumption, and excessive pollution, big data gathered from legacy systems (e.g., sensors not conformant with modern standards)…
Michelle L. Johnson, Bruce A. Hay, Maciej Maselko
Population-scale genome editing can be used to alter the composition or fate of wild populations. One approach to achieving these aims utilizes a synthetic gene drive element—a multi-gene cassette—to bring about an increase in the frequency of an existing allele. However, the use of gene drives is complicated by the…
Alexander L.R. Lubbock, Carlos F. Lopez
Computational modeling has become an established technique to encode mathematical representations of cellular processes and gain mechanistic insights that drive testable predictions. These models are often constructed using graphical user interfaces or domain-specific languages, with SBML used for interchange. Models…
Kirti Prasad, Nivedhitha Devaraju, Anila George, Nithin Sam Ravi + 15 more
β-thalassemia and HbE result from mutations in the β-globin locus that impedes the production of functional β-hemoglobin and represents one of the most common genetic disorders worldwide. Recent advances in genome engineering have opened up new therapeutic opportunities to directly correct these pathogenic mutations…
Authors not listed
While virtual libraries of synthetically accessible compounds have exploded in size to many billions, our capacity to extract valuable drug leads from these vast databases remains limited by computational resources. To overcome this, we developed SLICE SMARTS and Logic In ChEmistry), a powerful new tool designed for…
Naruki Yoshikawa, Ryuichi Kubo, Kazuki Yamamoto
Social media activity on a research article is considered to be an altmetric, a new measure to estimate research impact. Demonstrating software on Twitter is a powerful way to attract attention from a larger audience. SNS integration of software can also lower the barriers to trying the tools and make it easier to save…
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…
E. Adrian Henle, Nickolas Gantzler, Praveen K. Thallapally, Xiaoli Z. Fern + 1 more
PoreMatMod.jl is a free, open-source, user-friendly, and documented Julia package for modifying crystal structure models of porous materials such as metal-organic frameworks (MOFs). PoreMatMod.jl functions as a find-and-replace algorithm on crystal structures by leveraging (i) Ullmann's algorithm to search for…
Authors not listed
Digital twins are virtual companions for the design, scale-up, and control of chemical processes. Equipping digital twins with mechanistic models of their mirrored unit operation expands their range of applicability compared to pure data-driven models. As constructing mechanistic models requires time, effort, and…
Authors not listed
Large Language Models and Agentic Artificial Intelligence stand poised to completely overhaul our collective approach to science. Within chemical property prediction in particular, natural language-based workflows for modeling are already making serious inroads. To further this aim, in this white paper we introduce…
Muffy Calder, Claire Craig, Dave Culley, Richard de Cani + 15 more
'Christl A. Donnelly' 'Rowan Douglas' 'Bruce Edmonds' 'Jonathon Gascoigne' 'Nigel Gilbert' 'Caroline Hargrove' 'Derwen Hinds' 'David C. Lane' 'Dervilla Mitchell' 'Giles Pavey' 'David Robertson' 'Bridget Rosewell' 'Spencer Sherwin' 'Mark Walport' 'Alan Wilson'] In order to deal with an increasingly complex world, we…