24 papers · ranked by Valyu relevance
Rund Tawfiq, Maxat Kulmanov, Robert Hoehndorf
Protein function annotation has traditionally followed a reductionist approach, assigning functions to individual proteins acting in isolation. This paradigm treats each annotation as an independent fact, disconnected from the broader biological system. However, proteins operate within integrated cellular networks…
Saeed Salehi
We argue that G¨odel's completeness theorem is equivalent to completability of consistent theories, and G¨odel's incompleteness theorem is equivalent to the fact that this completion is not constructive, in the sense that there are some consistent and recursively enumerable theories which cannot be extended to any…
Gerd Christian Krizek, Lukas Mairhofer, Marian Kupczynski
We explore the different notions of completeness applied in the EPR discussion following and amending the thorough analysis of Arthur Fine. To this aim, we propose a classification scheme for scientific theories that provides a methodology for analyzing the different levels at which interpretive approaches come into…
Nicklas Carpenter, Roberto Giacobazzi
We study local completeness and incompleteness of abstract interpretations from a recursion-theoretic perspective. Local completeness weakens global completeness and captures the absence of precision loss for a specific precondition: abstract computation yields exactly what is obtained by abstracting the corresponding…
Włodzimierz Drabent
Program correctness (in imperative and functional programming) splits in logic programming into correctness and completeness. Completeness means that a program produces all the answers required by its specification. Little work has been devoted to reasoning about completeness. This paper presents a few sufficient…
Iulian D. Toader
This paper provides an algebraic reconstruction of Einstein's own argument for the incompleteness of quantum mechanics – the one that he thought did not make it into the EPR paper – in order to clarify the assumptions that underlie an understanding of Einstein completeness as categoricity, the sense in which it is a…
Antonis Achilleos
We introduce the completeness problem for Modal Logic and examine its complexity. For a definition of completeness for formulas, given a formula of a modal logic, the completeness problem asks whether the formula is complete for that logic. We discover that completeness and validity have the same complexity — with…
Tim Adair, Alan D. Lopez, Bernardo Queiroz
We have proposed an empirical method to estimate the completeness of death registration that requires very few input variables and which performs well in reliably predicting completeness to guide policy action across a wide range of observed completeness, population age structures and under-five mortality rates. As…
Raphael Eisenhofer, Iñaki Odriozola, Antton Alberdi
Inferring the functional capabilities of bacteria from metagenome-assembled genomes (MAGs) is becoming a central process in microbiology. Here we show that the completeness of genomes has a significant impact on the recovered functional signal, spanning all domains of metabolic functions. We identify factors that…
Johnathan Wong, Lauren Coombe, René L Warren, Inanc Birol
In de novo sequencing projects, genome assembly optimization requires evaluating a number of candidate assemblies to identify optimal tool parameters. Yet, current completeness assessment tools like BUSCO and compleasm require 10-80 minutes per evaluation for gigabase-scale genomes, transforming what should be rapid…
Tim Adair, Alan D. Lopez, Bernardo Lanza Queiroz
[pone.0252140.g001] compares the completeness of birth registration according to the CRVS data (using both UN and GBD birth estimates) with completeness of birth registration and certification from the self-reported data. Self-reported completeness is consistently higher than that reported by the CRVS data…
Jessica Liu, Tre’Andice Williams, John A. Burns
Genome and transcriptome assemblies vary in their quality in terms of the connectedness of the assemblies and the amount of biological information captured. Interpreting de novo assemblies from new, poorly characterized, organisms in the context of complex traits can be challenging because, in the absence of a…
Nao Hirokawa, Aart Middeldorp, Christian Sternagel, Sarah Winkler
> Abstract. Completion is one of the most studied techniques in term rewriting and fundamental to automated reasoning with equalities. In this paper we present new correctness proofs of abstract completion, both for finite and infinite runs. For the special case of ground completion we present a new proof based on…
Callum J. Macgregor, Darren M. Evans, Michael J.O. Pocock
The analysis of ecological networks can be affected by sampling effort, potentially leading to bias. Ecological network structure is often summarised by descriptive metrics but these metrics can vary according to the proportion of the total interactions that have been observed. Therefore, to know the likely degree of…
Nancy Manchanda, John L. Portwood, Margaret R. Woodhouse, Arun S. Seetharam + 3 more
Genome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, genomic diversity and differences in gene expression across individuals and tissue types. Quality metrics for genome…
Bonchi Filippo, Pierre Ganty, Giacobazzi Roberto, Duško Pavlović
interpretation [7] is a general method for approximating invariants of dynamic systems. The key idea is that the analysis, or the possibility of proving invariance properties of a system, can be reduced to compute an approximate semantics of the system under inspection. Any monotone function b on a monotone lattice C…
Ruaan Kellerman, Alberto Zanardo, Valentin Goranko
Trees are partial orderings where every element has a linearly ordered set of smaller elements. We define and study several natural notions of completeness of trees, extending Dedekind completeness of linear orders and Dedekind-MacNeille completions of partial orders. We then define constructions of tree completions…
Uwe Waldmann, Sophie Tourret, Simon Robillard, Jasmin Blanchette
A crucial operation of saturation theorem provers is deletion of subsumed formulas. Designers of proof calculi, however, usually discuss this only informally, and the rare formal expositions tend to be clumsy. This is because the equivalence of dynamic and static refutational completeness holds only for derivations…
Chonghuan Zhang, Adarsh Arun, Alexei Lapkin
Computer Aided Synthesis Planning (CASP) development of reaction routes requires understanding of complete reaction structures. However, most reactions in the current databases are missing reaction co-participants. Although reaction prediction and atom mapping tools can predict major reaction participants and trace…
Authors not listed
We present a vector-based method to balance chemical reactions. The algorithm builds candidates in a deterministic way, removes duplicates, and always prints coefficients in the lowest whole-number form. For redox cases, electrons and protons/hydroxide are treated explicitly, so both mass and charge are balanced. We…
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Quantum state tomography has been widely used to reconstruct the quantum state of a system from a set of informationally-complete measurements. Obtaining enough information about, e.g., the wavefunction of a molecule allows its complete characterization. On the other hand, deep learning models for molecular property…
Authors not listed
SynTemp is a framework designed to extract and hierarchically cluster reaction templates from large-scale reaction data repositories. Reaction templates are partial Imaginary Transition State graphs representing the reaction center as well as surrounding context. These graphs are equivalent to Double Pushout graph…
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Step-by-step thinking is essential in all domains of chemical sciences and engineering. While machine learning tools are broadly used, algorithms that automate reasoning are far less common. We elaborate on seven categories of human reasoning activities and connect each to applications in chemical science and…
Miloje Rakočević
In some previous works (2018a,b; 2019, 2021a,b, 2022) we presented a new type of mirror symmetry, expressed in the set of protein amino acids; such a symmetry, that it simultaneously represents the semiotic essence of the genetic code. In this paper we provide new evidences that the genetic code represents the unity of…