Related papers: Multiple Sequence Alignment is not a Solved Proble…
Multimodal alignment of histopathology encoders with transcriptomic and genomic data has been shown to significantly improve performance in downstream diagnostic tasks. Hematological cytology is unique in that visual single-cell evaluation…
The aim of this research is twofold: Firstly, to model and solve a complex nurse scheduling problem with an integer programming formulation and evolutionary algorithms. Secondly, to detail a novel statistical method of comparing and hence…
Value alignment problems arise in scenarios where the specified objectives of an AI agent don't match the true underlying objective of its users. The problem has been widely argued to be one of the central safety problems in AI.…
Comparing and aligning large datasets is a pervasive problem occurring across many different knowledge domains. We introduce and study MREC, a recursive decomposition algorithm for computing matchings between data sets. The basic idea is to…
We describe a new global multiple alignment program capable of aligning a large number of genomic regions. Our progressive alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic…
Shifted combinatorial optimization is a new nonlinear optimization framework, which is a broad extension of standard combinatorial optimization, involving the choice of several feasible solutions at a time. It captures well studied and…
We study the problem of determining whether a given temporal specification can be implemented by a symmetric system, i.e., a system composed from identical components. Symmetry is an important goal in the design of distributed systems,…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
A variety of methods have been proposed for structure similarity calculation, which are called structure alignment or superposition. One major shortcoming in current structure alignment algorithms is in their inherent design, which is based…
Oscillation synchronization phenomenon is widely observed in natural systems through frequency modulated signals, especially in biological neural networks. Frequency modulation is also one of most widely used technologies in engineering.…
Within the context of topological data analysis, the problems of identifying topological significance and matching signals across datasets are important and useful inferential tasks in many applications. The limitation of existing solutions…
This paper presents new and effective algorithms for learning kernels. In particular, as shown by our empirical results, these algorithms consistently outperform the so-called uniform combination solution that has proven to be difficult to…
We develop a family of reformulations of an arbitrary consistent linear system into a stochastic problem. The reformulations are governed by two user-defined parameters: a positive definite matrix defining a norm, and an arbitrary discrete…
Value-alignment in normative multi-agent systems is used to promote a certain value and to ensure the consistent behavior of agents in autonomous intelligent systems with human values. However, the current literature is limited to…
Sequence alignment is a cornerstone of bioinformatics, widely used to identify similarities between DNA, RNA, and protein sequences and studying evolutionary relationships and functional properties. The Needleman-Wunsch algorithm remains a…
We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising…
In process mining, alignments quantify the degree of deviation between an observed event trace and a business process model and constitute the most important conformance checking technique. We study the algorithmic complexity of computing…
We consider the problem of consistently matching multiple sets of elements to each other, which is a common task in fields such as computer vision. To solve the underlying NP-hard objective, existing methods often relax or approximate it,…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
We introduce an algorithm for the alignment of protein- coding sequences accounting for frameshifts. The main specificity of this algorithm as compared to previously published protein-coding sequence alignment methods is the introduction of…