Related papers: R3F: An R package for evolutionary dates, rates, a…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
Real-time time-dependent density functional theory (rt-TDDFT) is a well-established method for studying the dynamic response of matter in the femtosecond or optical range. In this method, the Kohn-Sham (KS) wave functions are propagated…
We present a new RF fingerprinting technique for wireless emitters that is based on a simple, easily and efficiently retrainable Ridge Regression (RR) classifier. The RR learns to identify devices using bursts of waveform samples,…
A standard model for exposing structured provenance metadata of scientific assertions on the Semantic Web would increase interoperability, discoverability, reliability, as well as reproducibility for scientific discourse and evidence-based…
We study a set of linear transformations on the Fourier series representation of a sequence that can be used as the basis for similarity queries on time-series data. We show that our set of transformations is rich enough to formulate…
We present a comprehensive new framework for handling biologically accurate models of molecular evolution. This model provides a systematic framework for studying models of molecular evolution that implement heterogeneous rates,…
We present MRPC, an R package that learns causal graphs with improved accuracy over existing packages, such as pcalg and bnlearn. Our algorithm builds on the powerful PC algorithm, the canonical algorithm in computer science for learning…
The evolutionary processes of complex systems contain critical information regarding their functional characteristics. The generation time of edges provides insights into the historical evolution of various networked complex systems, such…
Random cut forest (RCF) algorithms have been developed for anomaly detection, particularly in time series data. The RCF algorithm is an improved version of the isolation forest (IF) algorithm. Unlike the IF algorithm, the RCF algorithm can…
We present a new method for estimating the Neural Reflectance Field (NReF) of an object from a set of posed multi-view images under unknown lighting. NReF represents 3D geometry and appearance of objects in a disentangled manner, and are…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
When examining the relationship between an exposure and an outcome, there is often a time lag between exposure and the observed effect on the outcome. A common statistical approach for estimating the relationship between the outcome and…
An adaptive kernel method in the Bayesian framework together with a new simulation program for Rutherford backscattering spectroscopy (RBS) have been applied to the analysis of RBS data. Even in the case of strongly overlapping RBS peaks a…
Calculation of the log-likelihood stands as the computational bottleneck for many statistical phylogenetic algorithms. Even worse is its gradient evaluation, often used to target regions of high probability. Order ${\cal…
Forward-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
Pathogen genome data offers valuable structure for spatial models, but its utility is limited by incomplete sequencing coverage. We propose a probabilistic framework for inferring genetic distances between unsequenced cases and known…
Background: Continuous traits evolution of a group of taxa that are correlated through a phylogenetic tree is commonly modelled using parametric stochastic differential equations to represent deterministic change of trait through time,…
Approximation of scattered geometric data is often a task in many engineering problems. The Radial Basis Function (RBF) approximation is appropriate for large scattered (unordered) datasets in d-dimensional space. This method is useful for…