19 papers · ranked by Valyu relevance
Yiling Jia, Hongning Wang
Existing online learning to rank (OL2R) solutions are limited to linear models, which are incompetent to capture possible non-linear relations between queries and documents. In this work, to unleash the power of representation learning in OL2R, we propose to directly learn a neural ranking model from users' implicit…
Kosmas Pinitas, Konstantinos Makantasis, Antonios Liapis, Georgios N. Yannakakis
'Georgios N. Yannakakis'] Stochastic gradient descent (SGD) is a premium optimization method for training neural networks, especially for learning objectively defined labels such as image objects and events. When a neural network is instead faced with subjectively defined labels—such as human demonstrations or…
Vincent Thibeault, Antoine Allard, Patrick Desrosiers
Complex systems are high-dimensional nonlinear dynamical systems with intricate interactions among their constituents. To make interpretable predictions about their large-scale behavior, it is typically assumed, without a clear statement, that these dynamics can be reduced to a few number of equations involving a…
Vincent Moulton, Andreas Spillner
Ranked tree-child networks are a recently introduced class of rooted phylogenetic networks in which the evolutionary events represented by the network are ordered so as to respect the flow of time. This class includes the well-studied ranked phylogenetic trees (also known as ranked genealogies). An important problem in…
RT Pillich, J Chen, C Churas, D Fong + 7 more
The investigation of sets of genes using biological pathways is a common task for researchers and is supported by a wide variety of software tools. This type of analysis generates hypotheses about the biological processes active or modulated in a specific experimental context. The NDEx Integrated Query (IQuery) is a…
Andreas Orland, Max Padubrin
We collect a network dataset of tenured economics faculty in Austria, Germany and Switzerland. We rank the 100 institutions included with a minimum violation ranking. This ranking is positively and significantly correlated with the Times Higher Education ranking of economics institutions. According to the network…
Sebastian Morel-Balbi, Alec Kirkley
comparisons Authors: ['Sebastian Morel-Balbi' 'Alec Kirkley'] A common task arising in various domains is that of ranking items based on the outcomes of pairwise comparisons, from ranking players and teams in sports to ranking products or brands in marketing studies and recommendation systems. Statistical…
Shahar Somin, Yaniv Altshuler, Alex ‘Sandy’ Pentland, Erez Shmueli
Numerous studies over the past decades established that real-world networks typically follow preferential attachment and detachment principles. Subsequently, this implies that degree fluctuations monotonically increase while rising up the ‘degree ladder’, causing high-degree nodes to be prone for attachment of new…
Paolo Boldi, Flavio Furia, Sebastiano Vigna
Is it always beneficial to create a new relationship (have a new follower/friend) in a social network? This question can be formally stated as a property of the centrality measure that defines the importance of the actors of the network. Score monotonicity means that adding an arc increases the centrality score of the…
Uthsav Chitra, Tae Yoon Park, Benjamin J. Raphael
A standard paradigm in computational biology is to use interaction networks to analyze high-throughput biological data. Two common approaches for leveraging interaction networks are: (1) network ranking, where one ranks vertices in the network according to both vertex scores and network topology; (2) altered subnetwork…
Debasish Jana, Sven Malama, Sriram Narasimhan, Ertugrul Taciroglu + 1 more
Transportation networks play a crucial role in society by enabling the smooth movement of people and goods during regular times and acting as arteries for evacuations during catastrophes and natural disasters. Identifying the critical road segments in a large and complex network is essential for planners and emergency…
Xiao-Lu Liu, Chong Zhao, Tatsuro Kawamoto
Ranking user reputation and object quality in online rating systems is of great significance for the construction of reputation systems. In this paper we put forward an iterative algorithm for ranking reputation and quality in terms of eigenvector, named EigenRank algorithm, where the user reputation and object quality…
Bingjie Hao, István A. Kovács
As the current best practice, an experimental network dataset is validated by showing significant overlap with a gold standard network. Significance is assessed by comparison to a negative benchmark, often a randomized version of the same gold standard. While such analysis can reliably indicate the presence of signal…
Michael Schneider, Juri Rappsilber, Oliver Brock
The quality of biological data crucially affects progress in science. This quality can be improved with better measurement devices, more sophisticated experimental designs, or repetitious measurements. Each of these options is associated with substantial costs. We present a simple computational tool as an alternative.…
Matthew C. Perrone, Michael G. Lerner, Matthew Dunworth, Andrew J. Ewald + 2 more
'Andrew J. Ewald' 'Joel S. Bader' 'James Gallo'] Therapeutic interventions are designed to perturb the function of a biological system. However, there are many types of proteins that cannot be targeted with conventional small molecule drugs. Accordingly, many identified gene-regulatory drivers and downstream effectors…
Liang Zhang, Xin Lai
The exponential growth of data in biomedicine has created an urgent need for intuitive visualization tools. These tools must be able to effectively represent complex biological networks and remain accessible to domain experts without extensive computational training. Current network visualization approaches often…
Daniel Barter, Evan Walter Clark Spotte-Smith, Nikita S. Redkar, Shyam Dwaraknath + 2 more
Chemical reaction networks (CRNs) are powerful tools for obtaining mechanistic insight into complex reactive processes. However, they are limited in their applicability where reaction mechanisms are unintuitive, and products are unknown. Here we report new methods of CRN generation and analysis that overcome these…
Niclas Popp, Marco Stock, Jonathan Fiorentino, Antonio Scialdone
In recent years, many algorithms for inferring gene regulatory networks from single-cell transcriptomic data have been published. Several studies have evaluated their accuracy in estimating the presence of an interaction between pairs of genes. However, these benchmarking analyses do not quantify the algorithms’…
Rasmus Magnusson
Gene annotation enrichment analysis is the gold standard for studying the biological context of a set of genes, but available tools often overlook important network properties of the underlying gene regulatory system. This paper introduces the NETwork ANnotation enrichment package, NetAn, which augments annotation…