20 papers · ranked by Valyu relevance
María Andreína Francisco Rodríguez, Jordi Carreras Puigvert, Ola Spjuth
Microplates are indispensable in large-scale biomedical experiments but the physical location of samples and controls on the microplate can significantly affect the resulting data and quality metric values. We introduce a new method based on constraint programming for designing microplate layouts that reduces unwanted…
Christian Bessière, Luc De Raedt, Tias Guns, Lars Kotthoff + 6 more
'Mirco Nanni' 'Siegfried Nijssen' 'Barry O’Sullivan' 'Anastasia Paparrizou' 'Dino Pedreschi' 'Helmut Simonis'] Constraint programming is used for a variety of real-world optimisation problems, such as planning, scheduling and resource allocation problems. At the same time, one continuously gathers vast amounts of data…
Mikael Z. Lagerkvist, Magnus Rattfeldt
Propagators are central to the success of constraint programming, that is contracting functions removing values proven not to be in any solution of a given constraint. The literature contains numerous propagation algorithms, for many different constraints, and common to all these propagation algorithms is the notion of…
Fabio Tardivo
The focus of my PhD thesis is on exploring parallel approaches to efficiently solve problems modeled by constraints and presenting a new proposal. Current solvers are very advanced; they are carefully designed to effectively manage the high-level problems' description and include refined strategies to avoid useless…
Manjusha Nair, Jinesh Manchan Kannimoola, Bharat Jayaraman, Bipin Nair + 2 more
'Bipin Nair' 'Shyam Diwakar' 'Nicolas Rougier'] Background Several new programming languages and technologies have emerged in the past few decades in order to ease the task of modelling complex systems. Modelling the dynamics of complex systems requires various levels of abstractions and reductive measures in…
Max Ostrowski, Torsten Schaub
We present the hybrid ASP solver clingcon, combining the simple modeling language and the high performance Boolean solving capacities of Answer Set Programming (ASP) with techniques for using non-Boolean constraints from the area of Constraint Programming (CP). The new clingcon system features an extended syntax…
Rehan Aziz
Answer Set Programming (ASP) is a powerful modelling formalism that is very efficient in solving combinatorial problems. ASP solvers implement the stable model semantics that eliminates circular derivations between Boolean variables from the solutions of a logic program. Due to this, ASP solvers are better suited than…
Christophe Klopp, Valentin Durante, Thomas Schiex, Simon de Givry
Actual versions of hifiasm often produce unbalanced haplotype contigs for autopolyploid genome assemblies. Adding a contraint on the distribution of proteins among haplotypes improves haplotype sizes and busco scores balances. Four species were used to benchmark this approach against hifiasm raw results. The script can…
Martin Mann, Feras Nahar, Norah Schnorr, Rolf Backofen + 2 more
'Peter F Stadler' 'Christoph Flamm'] Chemical reactions are rearrangements of chemical bonds. Each atom in an educt molecule thus appears again in a specific position of one of the reaction products. This bijection between educt and product atoms is not reported by chemical reaction databases, however, so that the…
Yuliya Lierler
Constraint answer set programming or CASP, for short, is a hybrid approach in automated reasoning putting together the advances of distinct research areas such as answer set programming, constraint processing, and satisfiability modulo theories. Constraint answer set programming demonstrates promising results…
Abu Dayem Ullah, Kathleen Steinhöfel
Background The protein folding problem remains one of the most challenging open problems in computational biology. Simplified models in terms of lattice structure and energy function have been proposed to ease the computational hardness of this optimization problem. Heuristic search algorithms and constraint…
José Cano, David R. White, Alejandro Bordallo, Ciaran McCreesh + 3 more
'Anna Lito Michala' 'Jeremy Singer' 'Vijay Nagarajan'] We consider the problem of assigning software processes (or tasks) to hardware processors in distributed robotics environments. We introduce the notion of a task variant, which supports the adaptation of software to specific hardware configurations. Task variants…
Riley Hickman, Matteo Aldeghi, Alán Aspuru-Guzik
Model-based optimization strategies, such as Bayesian optimization (BO), have been deployed across the natural sciences in design and discovery campaigns due to their sample efficiency and flexibility. The combination of such strategies with automated laboratory equipment and/or high-performance computing in a…
Eric Hermes, Khachik Sargsyan, Habib Najm, Judit Zádor
We present a new algorithm for the optimization of molecular structures to saddle points on the potential energy surface using a redundant internal coordinate system. This algorithm automates the procedure of defining the internal coordinate system, including the handling of linear bending angles, e.g. through the…
Shengbing Ren, Weijia Zhou, Haiwei Zhou, Lei Xia + 1 more
Fault localization, a technique to fix and ensure the dependability of software, is rapidly becoming infeasible due to the increasing scale and complexity of multilingual programs. Compared to other fault localization techniques, slicing can directly narrow the range of the code which needed checking by abstracting a…
Brian Hie, Salvatore Candido, Zeming Lin, Ori Kabeli + 4 more
Combining a basic set of building blocks into more complex forms is a universal design principle. Most protein designs have proceeded from a manual bottom-up approach using parts created by nature, but top-down design of proteins is fundamentally hard due to biological complexity. We demonstrate how the modularity and…
Andre KY Low, Flore Mekki-Berrada, Aleksandr Ostudin, Jiaxun Xie + 7 more
The development of automated high-throughput experimental platforms has enabled fast sampling of high-dimensional decision spaces. To reach target properties efficiently, these platforms are increasingly paired with intelligent experimental design. When solving optimization problems, Bayesian-based optimizers are often…
Authors not listed
Automated chemistry platforms hold the potential to enable large-scale organic synthesis campaigns, such as producing a library of compounds for biological evaluation. The efficiency of such platforms will depend on the schedule according to which the synthesis operations are executed. In this work, we study the…
Rémi Segretain, Sergiu Ivanov, Laurent Trilling, Nicolas Glade
Formal interaction networks are well suited for representing complex biological systems and have been used to model signalling pathways, gene regulatory networks, interaction within ecosystems, etc. In this paper, we introduce Sign Boolean Networks (SBNs), which are a uniform variant of Threshold Boolean Networks…
Henri Schmidt, Benjamin J. Raphael
Reconstructing unobserved ancestral states of a phylogenetic tree provides insight into the history of evolving systems and is one of the fundamental problems in phylogenetics. For a fixed phylogenetic tree, the most parsimonious ancestral reconstruction – a solution to the small parsimony problem – can be efficiently…