Related papers: Reciprocal best hits are not a logically sufficien…
Many of the commonly used methods for orthology detection start from mutually most similar pairs of genes (reciprocal best hits) as an approximation for evolutionary most closely related pairs of genes (reciprocal best matches). This…
A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the…
Context-dependent identification of orthologs customarily relies on conserved gene order or whole-genome sequence alignment. It is shown here that short-range context--as short as single maximal matches--also provides an effective means to…
Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always…
Algorithmic statistics considers the following problem: given a binary string $x$ (e.g., some experimental data), find a "good" explanation of this data. It uses algorithmic information theory to define formally what is a good explanation.…
The recurring context in which objects appear holds valuable information that can be employed to predict their existence. This intuitive observation indeed led many researchers to endow appearance-based detectors with explicit reasoning…
Best-response mechanisms (Nisan, Schapira, Valiant, Zohar, 2011) provide a unifying framework for studying various distributed protocols in which the participants are instructed to repeatedly best respond to each others' strategies. Two…
Across a variety of ranking tasks, researchers use reciprocal rank to measure the effectiveness for users interested in exactly one relevant item. Despite its widespread use, evidence suggests that reciprocal rank is brittle when…
Synthesis of bulletproof strategies in imperfect information scenarios is a notoriously hard problem. In this paper, we suggest that it is sometimes a viable alternative to aim at "reasonably good" strategies instead. This makes sense not…
Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics and can be approximated with the help of similarity measures between gene sequences, albeit not without errors. The corresponding…
A series of papers has introduced the Heuristic Rating Estimation method, which evaluates a set of alternatives based on pairwise comparisons and the weights of reference alternatives. We formulate the conditions under which the HRE method…
Best match graphs (BMG) are a key intermediate in graph-based orthology detection and contain a large amount of information on the gene tree. We provide a near-cubic algorithm to determine whether a BMG is binary-explainable, i.e., whether…
Algorithms with (machine-learned) predictions is a powerful framework for combining traditional worst-case algorithms with modern machine learning. However, the vast majority of work in this space assumes that the prediction itself is…
Reciprocal best matches play an important role in numerous applications in computational biology, in particular as the basis of many widely used tools for orthology assessment. Nevertheless, very little is known about their mathematical…
Overlapping clusters are common in models of many practical data-segmentation applications. Suppose we are given $n$ elements to be clustered into $k$ possibly overlapping clusters, and an oracle that can interactively answer queries of the…
Binary search finds a given element in a sorted array with an optimal number of $\log n$ queries. However, binary search fails even when the array is only slightly disordered or access to its elements is subject to errors. We study the…
For many economic questions, the empirical results are not interesting unless they are strong. For these questions, theorizing before the results are known is not always optimal. Instead, the optimal sequencing of theory and empirics trades…
In this paper, we propose how to use objective arguments grounded in statistical mechanics concepts in order to obtain a single number, obtained after aggregation, which would allow to rank "agents", "opinions", ..., all defined in a very…
The paper deals with the problem of finding the best alternatives on the basis of pairwise comparisons when these comparisons need not be transitive. In this setting, we study a reinforcement urn model. We prove convergence to the optimal…
Considering the high heterogeneity of the ontologies pub-lished on the web, ontology matching is a crucial issue whose aim is to establish links between an entity of a source ontology and one or several entities from a target ontology.…