mackelab/sequence-memory

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mackelab/sequence-memory

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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)

sbi

Simulation-based inference toolkit

delfi

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

neural_timeseries_diffusion

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

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.

pyknos

autohmm

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

CorBinian

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

poisson-gpfa

Gaussian process factor analysis with Poisson observations

gatsbi

GATSBI: Generative Adversarial Training for Simulation-Based Inference

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

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smc_rnns

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

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DeepSpike

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neuralgbi

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

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epiphyte

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

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S3ID

subspace identficiation for partially observed high-dimensional data

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.

neuro-behavior-conditioning

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

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

apt_icml

Anonymized code for ICML 2019 submission

grassmann_binary_distribution

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

Jupyter Notebook

IdentifyMechanisticModels_2020

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

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RABI

Code for robust amortized bayesian inference package

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automind

Automated Model Inference from Neural Dynamics

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labproject

Labproject about comparing distributions metrics by @mackelab

ddm_stride

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

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pyrnn

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

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pyloric

Simulator of the pyloric network in cython.

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tsnpe_neurips

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

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msne-lsmlsda-2019

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

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sbi_AIMS

Public repository for the sbi course at AIMS 2024

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amortized-decision-making

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

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sbi-for-connectomics

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

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gp-maps-python

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

critical_retina

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

msne-datascience-2019

Fundamentals of Computer Science for Computational Neuroengineering

Jupyter Notebook

DECODE

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simulation_based_model_inference

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

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sourcerer

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

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.

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

open-comp-neuro

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

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STG_energy

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

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mesoGIF

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

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sbi-ice

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

lfi-experiments

Applications of likelihoodfree to different problems

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