maximum-likelihood | Topic | Ecosyste.ms: Repos

Topic: "maximum-likelihood"

CamDavidsonPilon/lifelines

Survival analysis in Python

Language: Python - Size: 43.1 MB - Last synced at: 4 days ago - Pushed at: 7 months ago - Stars: 2,453 - Forks: 560

3dem/relion

Image-processing software for cryo-electron microscopy

Language: C++ - Size: 58.2 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 465 - Forks: 205

amkozlov/raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible

Language: C++ - Size: 1.46 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 427 - Forks: 63

Cibiv/IQ-TREE 📦

Efficient phylogenomic software by maximum likelihood

Language: C++ - Size: 65.4 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 180 - Forks: 45

stan-dev/cmdstanr

CmdStanR: the R interface to CmdStan

Language: R - Size: 27.7 MB - Last synced at: 1 day ago - Pushed at: 6 days ago - Stars: 150 - Forks: 65

cogent3/cogent3

Comparative Genomics Toolkit 3

Language: Python - Size: 45.3 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 130 - Forks: 64

jamiemcg/BUSCO_phylogenomics

BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins

Language: Python - Size: 347 KB - Last synced at: 2 months ago - Pushed at: 8 months ago - Stars: 64 - Forks: 9

vinuesa/get_phylomarkers

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

Language: Perl - Size: 115 MB - Last synced at: 17 days ago - Pushed at: 5 months ago - Stars: 55 - Forks: 9

jkirkby3/pymle

Maximum Likelihood estimation and Simulation for Stochastic Differential Equations (Diffusions)

Language: Python - Size: 218 KB - Last synced at: 5 days ago - Pushed at: 5 months ago - Stars: 51 - Forks: 13

r-spatial/spatialreg

spatialreg: spatial models estimation and testing

Language: R - Size: 8.16 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 47 - Forks: 11

jabbring/dynamic-discrete-choice

Matlab package for learning to specify, compute, and estimate dynamic discrete choice models

Language: MATLAB - Size: 262 KB - Last synced at: 18 days ago - Pushed at: over 1 year ago - Stars: 47 - Forks: 39

grenaud/deML

Maximum likelihood demultiplexing

Language: C++ - Size: 23.1 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 45 - Forks: 12

odubno/gauss-naive-bayes

Gauss Naive Bayes in Python From Scratch.

Language: Python - Size: 16.1 MB - Last synced at: 7 months ago - Pushed at: about 6 years ago - Stars: 45 - Forks: 21

pachadotdev/gravity Fork of jpburgard/gravity

R package that provides estimation methods for Gravity Models

Language: R - Size: 26.5 MB - Last synced at: 4 days ago - Pushed at: 7 months ago - Stars: 36 - Forks: 13

viodotcom/ppca_rs

Python+Rust implementation of the Probabilistic Principal Component Analysis model

Language: Rust - Size: 316 KB - Last synced at: 5 days ago - Pushed at: 10 months ago - Stars: 35 - Forks: 2

evolbioinfo/pastml

Ancestral character reconstruction and visualisation for rooted phylogenetic trees

Language: Python - Size: 35.9 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 33 - Forks: 6

reslp/phylociraptor

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

Language: Python - Size: 3.36 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 25 - Forks: 6

vinuesa/TIB-filoinfo

Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México

Language: Shell - Size: 160 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 22 - Forks: 5

mashephe/AmpTools

A utility library for performing amplitude analysis on particle physics data.

Language: C++ - Size: 140 MB - Last synced at: 18 days ago - Pushed at: 19 days ago - Stars: 21 - Forks: 13

Ensembl/treebest Fork of lh3/treebest

TreeBeST: Tree Building guided by Species Tree (Ensembl Compara modifications)

Language: C - Size: 368 KB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 20 - Forks: 8

mackelab/CorBinian

CorBinian: A toolbox for modelling and simulating high-dimensional binary and count-data with correlations

Language: MATLAB - Size: 688 KB - Last synced at: over 2 years ago - Pushed at: almost 4 years ago - Stars: 16 - Forks: 4

docnok/detection-estimation-learning

Python notebooks for my graduate class on Detection, Estimation, and Learning. Intended for in-class demonstration. Notebooks illustrate a variety of concepts, from hypothesis testing to estimation to image denoising to Kalman filtering. Feel free to use or modify for your instruction or self-study.

Language: Jupyter Notebook - Size: 3.29 MB - Last synced at: over 2 years ago - Pushed at: about 7 years ago - Stars: 15 - Forks: 8

4ment/physher

A multi-algorithmic framework for phylogenetic inference

Language: C - Size: 2.37 MB - Last synced at: about 2 months ago - Pushed at: 11 months ago - Stars: 14 - Forks: 2

jkirkby3/BsplineDensity

B-Spline Density Estimation Library - nonparametric density estimation using B-Spline density estimator from univariate sample.

Language: MATLAB - Size: 24.4 KB - Last synced at: 3 months ago - Pushed at: almost 4 years ago - Stars: 14 - Forks: 3

apallath/WHAM

Python package to construct free energy profiles from biased molecular simulation data using both log-likelihood maximization and self-consistent iteration approaches.

Language: Python - Size: 33.6 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 11 - Forks: 1

ddegras/switch-ssm

Markov-Switching State-Space Models

Language: MATLAB - Size: 1.22 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 11 - Forks: 8

gokhanntosun/channel-estimation

Channel estimations based on RLS, LMS and ML methods.

Language: MATLAB - Size: 39.1 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 11 - Forks: 7

justincbagley/piranha

Scripts for file processing and analysis in phylogenetics and phylogeography

Language: Shell - Size: 13.7 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 10 - Forks: 3

JonasMoss/univariateML

An R package for maximum likelihood estimation of univariate densities.

Language: R - Size: 9.06 MB - Last synced at: 8 days ago - Pushed at: 3 months ago - Stars: 8 - Forks: 6

fpv-iplab/Differentiable-Task-Graph-Learning

Code for the paper "Differentiable Task Graph Learning: Procedural Activity Representation and Online Mistake Detection from Egocentric Videos" [NeurIPS (spotlight), 2024]

Language: Python - Size: 51 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 8 - Forks: 1

xzluo97/X-metric

X-Metric: An N-Dimensional Information-Theoretic Framework for Groupwise Registration and Deep Combined Computing (TPAMI 2023)

Language: Python - Size: 38 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 8 - Forks: 2

welschma/TemplateFitter

Perform template likelihood fits on binned datasets to extract contribution to the dataset from different processes .

Language: Python - Size: 1.36 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 1

egarpor/sdetorus

Statistical tools for toroidal diffusions. Software companion for "Langevin diffusions on the torus: estimation and applications"

Language: C++ - Size: 45.2 MB - Last synced at: 29 days ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 1

oguzhan-baser/Channel-Estimation

Estimating unknown static channel coefficients on a communication system utilizing Maximum Likelihood Single-Shot Estimation algorithm.

Language: MATLAB - Size: 595 KB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 3

justincbagley/MAGNET

Shell script pipeline for inferring ML gene trees for many loci (e.g. genomic RAD loci)

Language: Shell - Size: 1.22 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 6 - Forks: 1

markjolah/Mappel

Maximum a posteriori Point Emitter Localization -- High-performance, parallel, robust, cross-platform localization for EMCCD and SCMOS microscopy.

Language: C++ - Size: 33.5 MB - Last synced at: 2 months ago - Pushed at: almost 6 years ago - Stars: 6 - Forks: 1

matthewwolak/gremlin

R package for mixed-effects REML incorporating Generalized Inverses

Language: R - Size: 1020 KB - Last synced at: about 1 month ago - Pushed at: 7 months ago - Stars: 5 - Forks: 1

lkazantzi/tilted-cosmology

The numerical analysis files corresponding to arxiv: 2202.00962

Language: Mathematica - Size: 3.73 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 5 - Forks: 0

jabbring/mht-likelihood

Replication package for Abbring and Salimans (2021), "The Likelihood of Mixed Hitting Times," with MATLAB code for estimating mixed hitting-time models

Language: MATLAB - Size: 2.35 MB - Last synced at: 10 months ago - Pushed at: about 4 years ago - Stars: 5 - Forks: 2

jb262/MaximumLikelihoodGammaDist

A basic implementation for the maximum likelihood estimators of a gamma distribution's parameters.

Language: VBA - Size: 5.86 KB - Last synced at: 6 months ago - Pushed at: about 4 years ago - Stars: 4 - Forks: 2

reslp/iqtreeGUI

iqtreeGUI - A graphical user interface for IQ-TREE

Language: Python - Size: 118 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 5

lyhsieh/NTHU-Machine-Learning

NTHU EE6550: Machine Learning

Language: Jupyter Notebook - Size: 6.12 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

lkndl/ab12phylo

AB12PHYLO: An integrated easy-to-use pipeline for ML phylogenetic tree inference

Language: Perl - Size: 24.3 MB - Last synced at: 22 days ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 3

zang-langyan/autolik

Provide the automatic differentiation for Likelihood maximization routine

Language: Python - Size: 3.19 MB - Last synced at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 1

poissonconsulting/ml 📦

An R package to perform Maximum Likelihood analysis using R expressions

Language: R - Size: 278 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 0

jamesjcai/MBEToolbox

MBEToolbox: Matlab toolbox for molecular evolution

Language: C - Size: 5.18 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 3

amarinderthind/CGRphylo

CGR package for phylogeny. Pipeline compare multiple whole genome sequences using alignment free approach Chaos Game Representation (CGR). CRG core function creates the frequencies object for each sequence which can be used to calculate distances among sequences.

Language: R - Size: 1.17 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 2 - Forks: 2

LinyunLiu/Bioinformatics

Unraveling Evolutionary Relationship between Fungi Species

Language: Shell - Size: 187 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0

GioStamoulos/Mnist_Analysis

Mnist dataset in specific forms (2,4,6 & 8 labels or mean brightness 2D arrays) was utilized for dimensionality reduction, clustering and classification implementations for educational purposes.

Language: Python - Size: 443 KB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 0

mozanunal/notebook-ml-map-comparasion

It is a jupyter notebook which examine the varience and bias parameters of maximum likelihood and maximum a posteriori approaches for biomedical imaging.

Language: Jupyter Notebook - Size: 3.77 MB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 2 - Forks: 0

samuelleach/miramare

Miramare healpix analysis tools and a composable maximum likelihood component separation technique.

Language: FORTRAN - Size: 922 KB - Last synced at: about 1 year ago - Pushed at: almost 11 years ago - Stars: 2 - Forks: 0

AlexStead/FronPy

Python package for frontier analysis

Language: Python - Size: 637 KB - Last synced at: about 2 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 1

donlapark/Dirichlet-Mechanism

The Dirichlet Mechanism for Differentially Private KL Divergence Minimization

Language: Jupyter Notebook - Size: 5.27 MB - Last synced at: 3 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

pharo-ai/gaussian-mixture-model

Gaussian Mixture Model (GMM) is an iterative algorithm for fitting the data with multiple normal distributions (gaussians). Can be used for classification

Language: Smalltalk - Size: 55.7 KB - Last synced at: 3 months ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 1

orl1k/mle-in-bearing-only-estimation

Language: Python - Size: 167 MB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

bcbi/MaximumLikelihoodProblems.jl

Formulate likelihood problems and solve them with maximum likelihood estimation (MLE)

Language: Julia - Size: 276 KB - Last synced at: 2 months ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

Gaurav927/Hidden_Markov_Model

HMM from scratch

Language: Python - Size: 39.1 KB - Last synced at: about 1 year ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 0

m-clark/mixed-models-estimation

Raw files for a document demonstrating some by hand estimation of mixed models.

Language: R - Size: 1.89 MB - Last synced at: 3 months ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 1

houtanb/aimad

Automatic Differentiation Applied to the Likelihood Function for Dynamic General Equilibrium Models

Language: Fortran - Size: 2.11 MB - Last synced at: almost 2 years ago - Pushed at: almost 8 years ago - Stars: 1 - Forks: 1

PierreBoyeau/rare_words_DNA

Language: Python - Size: 1.52 MB - Last synced at: almost 2 years ago - Pushed at: about 8 years ago - Stars: 1 - Forks: 0

xRiskLab/fastwoe

Fast Weight of Evidence (WOE) encoding and inference

Language: Python - Size: 4.01 MB - Last synced at: about 15 hours ago - Pushed at: about 16 hours ago - Stars: 0 - Forks: 0

Emmanuelprz1400/Logistic-Regression

Project where the Logistic Regression algorithm is used

Language: Jupyter Notebook - Size: 1.42 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

RezaDastranj/LMEASDRs.jl

Analysing Age-Specific Death Rates with MixedModels.jl

Language: Julia - Size: 22.6 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

ntyblco/Maximum-Likelihood-Estimation

Maximum Likelihood Estimation Using a Rotten tomatoes database.

Size: 138 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

juliawiggeshoff/astral-species-tree

This is a Snakemake workflow that calculates maximum-likelihood gene trees with IQ-TREE and 100 bootstrap replicates for each tree. Then, consensus trees are produced and combined to infer a species tree following the multispecies coalescent model with ASTRAL. Imported from my GitLab.

Language: Python - Size: 14.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0