Discover mackelab/IdentifyMechanisticModels

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Code for "Training deep neural density estimators to identify mechanistic models of neural dynamics"

sbi

Simulation-based inference toolkit

Python

433

delfi

Density estimation likelihood-free inference. No longer actively developed see https://github.com/mackelab/sbi instead

Python

neural_timeseries_diffusion

This repository contains research code for the paper "Generating realistic neurophysiological time series with denoising diffusion probabilistic models".

Python

simformer

Combination of transformers and diffusion models for flexible all-in-one simulation-based inference

Jupyter Notebook

machine-learning-I

Slides and lecture notes for the course 'machine learning I' taught at the Graduate School Neural Information Processing in Tuebingen.

TeX

pyknos

don't regress

Python

autohmm

Hidden Markov Models (HMMs) with tied states and autoregressive observations

Python

CorBinian

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

MATLAB

poisson-gpfa

Gaussian process factor analysis with Poisson observations

Python

gatsbi

GATSBI: Generative Adversarial Training for Simulation-Based Inference

Python

mnle-for-ddms

Research code for Mixed Neural Likelihood Estimation (MNLE, Boelts et al. 2022)

Jupyter Notebook

multispike_tempotron

To identify features by aggregate-label learning in spiking neurons

Jupyter Notebook

smc_rnns

Code accompanying Inferring stochastic low-rank RNNs from neural data. @matthijspals

Jupyter Notebook

DeepSpike

Jupyter Notebook

neuralgbi

Richard @rdgao & Michael @michaeldeistler: using neural network-based regression and density estimation for Generalized Bayesian Inference

Jupyter Notebook

epiphyte

Python toolkit for working with high-dimensional neural data recorded during naturalistic, continuous stimuli @a-darcher @rachrapp

Jupyter Notebook

S3ID

subspace identficiation for partially observed high-dimensional data

Python

phase-limit-cycle-RNNs

Code for "Trained recurrent neural networks develop phase-locked limit cycles in a working memory task" - Matthijs Pals (@matthijspals) , Jakob Macke and Omri Barak.

Python

neuro-behavior-conditioning

Masked variational autoencoders for modeling conditional distributions of neural and behavioral data

Python

dg_python

Dichotomized Gaussian model implemented in python

Jupyter Notebook

msne-datascience-2020

Fundamentals of Computer Science for Computational Neuroengineering 2020

Jupyter Notebook

snvi_repo

Reproduce results from the SVNI paper, Glöckler et al. 2022, ICLR

Jupyter Notebook

msne-datascience-2018

Course material for the Fundamentals of Computer Science for Computational Neuroengineering course at TUM

HTML

apt_icml

Anonymized code for ICML 2019 submission

Python

grassmann_binary_distribution

Implementation of binary distribution in the Grassmann formalism, including conditional version. Main contributor: Cornelius Schröder (@coschroeder)

Jupyter Notebook

RABI

Code for robust amortized bayesian inference package

Jupyter Notebook

automind

Automated Model Inference from Neural Dynamics

Jupyter Notebook

labproject

Labproject about comparing distributions metrics by @mackelab

Python

ddm_stride

Pipeline for applying simulation-based inference to Drift-Diffusion Models

Jupyter Notebook

pyrnn

General code for training (biologically inspired) recurrent neural networks. Code by Matthijs Pals (@matthijspals)

Jupyter Notebook

pyloric

Simulator of the pyloric network in cython.

Jupyter Notebook

tsnpe_neurips

Code to reproduce results from `Truncated proposals for scalable and hassle-free simulation-based inference`

Jupyter Notebook

msne-lsmlsda-2019

Programming exercises and mini-projects for LSMLSDA course, summer semester 2019

Jupyter Notebook

sbi_AIMS

Public repository for the sbi course at AIMS 2024

Jupyter Notebook

amortized-decision-making

Repository for the paper "Amortized Bayesian Decision Making for simulation-based models" - Mila @milagorecki and Michael @michaeldeistler

Jupyter Notebook

sbi-for-connectomics

Research code and results for the paper "Simulation-based inference for computational connectomics" (Boelts et al. 2023 PLoS CB, @janfb)

Jupyter Notebook

gp-maps-python

Gaussian process method for inferring cortical maps (Python version), code by Dominik Straub @dominikstrb

Python

critical_retina

Code and data for 'Signatures of criticality arise in simple neural populations models with correlations'

MATLAB

sequence-memory

Code for Liebe et al. "Phase of firing does not reflect temporal order in sequence memory of humans and recurrent neural networks", code by Matthijs Pals (@matthijspals)

Jupyter Notebook

msne-datascience-2019

Fundamentals of Computer Science for Computational Neuroengineering

Jupyter Notebook

DECODE

by @aspeiser

Jupyter Notebook

simulation_based_model_inference

Repository for the paper "Simultaneous identification of models and parameters of scientific simulators" -- Cornelius: @coschroeder

Jupyter Notebook

sourcerer

Code for the preprint "Sourcerer: Sample-based Maximum Entropy Source Distribution Estimation"

Python

pyLDS_dev

large-scale implementation of the expectation-maximisation algoithm in python for the linear dynamical system

Jupyter Notebook

neonatal_apnea_prediction

Neonatal apnea and hypopnea prediction in infants with Robin sequence with neural additive models for time series.

Python

spikefinder_SV-DeepSpike

Code for submission of Speiser et al to spike-finder-challenge 2017

Jupyter Notebook

LDNS

lsmlsda2020

Repo for students of the class 'Large Scale Modelling and Large Scale Data Analysis'

Jupyter Notebook

sinn

A library for both Simulation and INference of dynamical systems. Maintained by @alcrene

Python

open-comp-neuro

A first start as a resource for pooling lecture materials for computational neuroscience course

Jupyter Notebook

STG_energy

Repo for STG energy paper. Michael (@michaeldeistler) and Pedro (@ppjgoncalves).

Jupyter Notebook

mesoGIF

This repository archives the code used to obtain the results in René et al., 2020. Maintainer: @alcrene

Jupyter Notebook

sbi-ice

Simulation-Based Inference of Surface Accumulation and Basal Melt Rates of an Antarctic Ice Shelf from Isochronal Layers

Python

lfi-experiments

Applications of likelihoodfree to different problems

Jupyter Notebook

mackelab/IdentifyMechanisticModels_2020

mackelab

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