24 papers · ranked by Valyu relevance
Yuzhen Ye, Thomas G. Doak, Christos A. Ouzounis
A common biological pathway reconstruction approach-as implemented by many automatic biological pathway services (such as the KAAS and RAST servers) and the functional annotation of metagenomic sequences-starts with the identification of protein functions or families (e.g., KO families for the KEGG database and the FIG…
Leonard Dăuş, Marilena Jianu
The concept of network reliability can be traced back to 1956, when Von Neumann [10], and Moore and Shannon [7], respectively, published two prescient papers. The original purpose of Moore and Shannon was to understand the reliability of electrical circuits/networks having unreliable individual components. In order to…
Pablo Carbonell, Davide Fichera, Shashi B Pandit, Jean-Loup Faulon
Background We consider the possibility of engineering metabolic pathways in a chassis organism in order to synthesize novel target compounds that are heterologous to the chassis. For this purpose, we model metabolic networks through hypergraphs where reactions are represented by hyperarcs. Each hyperarc represents an…
Authors not listed
The identification of kinetically feasible reaction pathways that connect a reactant to its product, including numerous intermediates and transition states, is crucial for predicting chemical reactions and elucidating reaction mechanisms. However, as molecular systems become increasingly complex or larger, the number…
Jordi Palacín, Elena Rubies, Ricard Bitriá, Eduard Clotet + 3 more
'Ankit A. Ravankar' 'Jose Victorio Salazar Luces' 'Abhijeet Ravankar'] Planning the path of a mobile robot that must transport and deliver small packages inside a multi-story building is a problem that requires a combination of spatial and operational information, such as the location of origin and destination points…
Fernando H. C. Dias, Alexandru I. Tomescu
Minimum flow decomposition (MFD) is a common problem across various fields of Computer Science, where a flow is decomposed into a minimum set of weighted paths. However, in Bioinformatics applications, such as RNA transcript or quasi-species assembly, the flow is erroneous, since is obtained from noisy read coverages.…
Olena Doroshenko
Pathfinding in complex topographies poses a challenge with applications extending from urban planning to autonomous navigation. While numerous algorithms offer potential solutions, their comparative efficiency and reliability when confronted with nonlinear terrains remain to be systematically evaluated. This study…
Anil Maheshwari, Arash Nouri, Jörg-Rüdiger Sack
The determination of time-dependent collision-free shortest paths has received a fair amount of attention. Here, we study the problem of computing a time-dependent shortest path among growing discs which has been previously studied for the instance where the departure times are fixed. We address a more general setting…
Tunç Başar Köse, Jiarong Li, Anna Ritz
A major challenge in molecular systems biology is to understand how proteins work to transmit external signals to changes in gene expression. Computationally reconstructing these signaling pathways from protein interaction networks can help understand what is missing from existing pathway databases. We formulate a new…
Fotis E. Psomopoulos, Jacques van Helden, Claudine Médigue, Anastasia Chasapi + 1 more
As genome sequencing efforts are unveiling the genetic diversity of the biosphere with an unprecedented speed, there is a need to accurately describe the structural and functional properties of groups of extant species whose genomes have been sequenced, as well as their inferred ancestors, at any given taxonomic level…
Oren Salzman, Brian Hou, Siddhartha S Srinivasa
We consider the motion-planning problem of planning a collision-free path of a robot in the presence of risk zones. The robot is allowed to travel in these zones but is penalized in a super-linear fashion for consecutive accumulative time spent there. We suggest a natural cost function that balances path length and…
Aditya Shirwatkar, Aman Singh, Jana Ravi Kiran
— Autonomous agents face the challenge of coordinating multiple tasks (perception, motion planning, controller) which are computationally expensive on a single onboard computer. To utilize the onboard processing capacity optimally, it is imperative to arrive at computationally efficient algorithms for global path…
Shin-ichi Koda, Shinji Saito
Rapid generation of a plausible reaction path connecting a given reactant and product in advance is crucial for the efficient computation of precise reaction paths or transition states. We propose a computationally efficient potential energy based on molecular structure to generate such paths. This potential energy has…
Pablo Muñoz, Paolo Bellutta, Maria D. R-Moreno
The on-ground operation of Mars rovers is a complex task that requires comprehensive planning in which path planning plays a fundamental role. The selection of paths has to be carefully chosen considering the scientific objectives, terrain, energy, and safety. In this regard, operators are assisted by path-planning…
Marvin Rüdt, Constantin Enke, Kai Furmans
—Efficient routing of mobile robot fleets is crucial in intralogistics, where delays and deadlocks can substantially reduce system throughput. Roadmap design, specifying feasible transport routes, directly affects fleet coordination and computational performance. Existing approaches are either grid-based, compromising…
Daniel Rakita, Bilge Mutlu, Michael Gleicher
— In this paper, we present a meta-algorithm intended to accelerate many existing path optimization algorithms. The central idea of our work is to strategically break up a waypoint path into consecutive groupings called "pods," then optimize over various pods concurrently using parallel processing. Each pod is assigned…
David Pellow, Lianrong Pu, Bariş Ekim, Lior Kotlar + 3 more
'Ron Shamir' 'Yaron Orenstein'] Minimizers are ubiquitously used in data structures and algorithms for efficient searching, mapping, and indexing of high-throughput DNA sequencing data. Minimizer schemes select a minimum k-mer in every L-long subsequence of the target sequence, where minimality is with respect to a…
Shin-ichi Koda, Shinji Saito
This study introduces correlated flat-bottom elastic network model (CFB-ENM), an extension of our recently developed flat-bottom elastic network model (FB-ENM) for generating plausible reaction paths. While FB-ENM improved upon the widely used image-dependent pair potential (IDPP) by addressing unintended structural…
Guillaume Marçais, Dan DeBlasio, Carl Kingsford
The minimizers technique is a method to sample k-mers that is used in many bioinformatics software to reduce computation, memory usage and run time. The number of applications using minimizers keeps on growing steadily. Despite its many uses, the theoretical understanding of minimizers is still very limited. In many…
Jian Dai, Bin Yang, Chenjuan Guo, Christian S. Jensen
Using the growing volumes of vehicle trajectory data, it becomes increasingly possible to capture time-varying and uncertain travel costs in a road network, including travel time and fuel consumption. The current paradigm represents a road network as a graph, assigns weights to the graph's edges by fragmenting…
Denise Slenter, M. Kutmon, Chris T. Evelo, Egon L. Willighagen
Metabolomics data analysis for phenotype identification commonly reveals only a small set of biochemical markers, often containing overlapping metabolites for individual phenotypes. Differentiation between distinctive sample groups requires understanding the underlying causes of metabolic changes. However, combining…
Michael Hutcheon, Andrew Teale
Algorithms are presented for performing a topological analysis of an arbitrary function, evaluated on an arbitrary grid of points. These algorithms work strictly by post-processing the data and require no additional function evaluations. This is achieved by connecting the grid points with a neighbourhood graph…
Ryan Miller, Sebastian Muraru, Ana Belén Malpartida, Josh Low + 7 more
Within the next twenty years, the number of cancer patients is expected to rise by 70%. Current cancer treatments still face several limitations, such as severe side effects and a high incidence of disease recurrence. Drug combination therapies are a promising strategy to achieve higher therapeutic effects while…
Ruth Stoney, Jean-Mark Schwartz, David L Robertson, Goran Nenadic
The consolidation of pathway databases, such as KEGG[1], Reactome[2]and ConsensusPathDB[3], has generated widespread biological interest, however the issue of pathway redundancy impedes the use of these consolidated datasets. Attempts to reduce this redundancy have focused on visualizing pathway overlap or merging…