Ecosyste.ms: Issues

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GitHub / OHBA-analysis/osl-dynamics issues and pull requests

#183 - New Fully TensorFlow Implementation of the SE-HMM

Pull Request - State: closed - Opened by cgohil8 about 1 year ago

#182 - Counting batches is slow

Issue - State: closed - Opened by cgohil8 about 1 year ago - 1 comment
Labels: enhancement

#181 - TFRecord dataset not being updated

Issue - State: closed - Opened by cgohil8 about 1 year ago - 1 comment
Labels: bug

#180 - `np.memmap` issues

Issue - State: closed - Opened by evanr70 about 1 year ago
Labels: bug

#179 - Feat: Learning rate decay.

Pull Request - State: closed - Opened by RukuangHuang about 1 year ago

#178 - Mean over time rather than sum over time in loss calculation

Issue - State: closed - Opened by RukuangHuang about 1 year ago - 3 comments
Labels: enhancement

#177 - Add argument to model.fit for a learning rate decay.

Issue - State: closed - Opened by cgohil8 about 1 year ago - 2 comments
Labels: enhancement

#176 - TFRecords raises an error with TensorFlow v2.9.1+

Issue - State: closed - Opened by cgohil8 about 1 year ago
Labels: bug

#175 - Power normalisation fixes

Pull Request - State: closed - Opened by cgohil8 about 1 year ago

#174 - Fix: Importing `tensorflow` package for `Data.dataset` function

Pull Request - State: closed - Opened by scho97 about 1 year ago
Labels: bug

#173 - Toolbox Paper

Pull Request - State: closed - Opened by cgohil8 about 1 year ago

#172 - Buffer size in initialisation methods

Pull Request - State: closed - Opened by RukuangHuang about 1 year ago - 4 comments

#171 - Refact/dataset

Pull Request - State: closed - Opened by RukuangHuang about 1 year ago - 1 comment

#170 - Separate method to get instantaneous covariances.

Pull Request - State: closed - Opened by cgohil8 about 1 year ago

#169 - Reduce flake8 E501 warnings

Pull Request - State: closed - Opened by cgohil8 about 1 year ago

#168 - Feature/tf records

Pull Request - State: closed - Opened by RukuangHuang about 1 year ago - 1 comment
Labels: enhancement

#167 - Fix/default arguments

Pull Request - State: closed - Opened by evanr70 about 1 year ago

#166 - Improved Documentation

Pull Request - State: closed - Opened by cgohil8 about 1 year ago

#165 - Tutorials

Pull Request - State: closed - Opened by cgohil8 about 1 year ago

#164 - Use TFRecords rather than Dataset.from_tensor_slices

Issue - State: closed - Opened by cgohil8 over 1 year ago
Labels: enhancement

#163 - Refact: Scaling factor

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago - 1 comment

#162 - Feature/dual_estimation

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago

#161 - Data class refactor

Pull Request - State: closed - Opened by cgohil8 over 1 year ago - 1 comment

#160 - Remove observation model modules

Pull Request - State: closed - Opened by cgohil8 over 1 year ago - 1 comment

#159 - Option to set buffer size for shuffling

Issue - State: closed - Opened by cgohil8 over 1 year ago - 1 comment
Labels: enhancement

#158 - Removed OSL_HMM/HMM_MAR

Pull Request - State: closed - Opened by cgohil8 over 1 year ago

#157 - Smooth edge effects in inferred alphas

Pull Request - State: closed - Opened by cgohil8 over 1 year ago - 1 comment

#156 - Fix: reinitialisation bug

Pull Request - State: closed - Opened by cgohil8 over 1 year ago

#155 - Remove OSL_HMM/HMM_MAR object

Issue - State: closed - Opened by cgohil8 over 1 year ago - 3 comments

#154 - Fix: asymmetric colour bar in power.save

Pull Request - State: closed - Opened by cgohil8 over 1 year ago

#153 - Feat: Subject Fine Tuning

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago - 6 comments
Labels: enhancement

#152 - Config API: Burst Detection Pipeline

Pull Request - State: closed - Opened by cgohil8 over 1 year ago

#151 - Dual-estimation method for DyNeMo/HMM

Issue - State: closed - Opened by RukuangHuang over 1 year ago - 3 comments
Labels: enhancement

#150 - Updated example scripts for the toolbox paper

Pull Request - State: closed - Opened by cgohil8 over 1 year ago

#149 - Feat: plot wavelet transform

Pull Request - State: closed - Opened by cgohil8 over 1 year ago

#148 - Feat: BIC.

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago - 4 comments

#147 - Enhancement: option to get the inferred thetas (rather than alphas)

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago - 7 comments

#146 - Strange bursting activity around sequence boundaries.

Issue - State: closed - Opened by evanr70 over 1 year ago - 7 comments

#145 - Continue next initialisation when KL blows up.

Issue - State: closed - Opened by RukuangHuang over 1 year ago - 1 comment
Labels: enhancement

#144 - Fix: Bug in SE-DyNeMo observation model.

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago - 1 comment

#143 - Get thetas from DyNeMo

Issue - State: closed - Opened by evanr70 over 1 year ago - 5 comments
Labels: enhancement

#142 - Potential bug with random_subset_initialisation in sehmm.

Issue - State: closed - Opened by RukuangHuang over 1 year ago - 9 comments
Labels: bug

#141 - Fix variable names in tinda.py

Pull Request - State: closed - Opened by matsvanes over 1 year ago - 3 comments

#140 - Tinda examples error out

Issue - State: closed - Opened by evanr70 over 1 year ago
Labels: bug

#139 - Regularisation on MLP layers

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago
Labels: enhancement

#138 - Scaling factor for regularisation and KL loss terms.

Issue - State: closed - Opened by RukuangHuang over 1 year ago - 1 comment
Labels: enhancement

#136 - Refactored config API

Pull Request - State: closed - Opened by cgohil8 over 1 year ago

#135 - Tinda

Pull Request - State: closed - Opened by matsvanes over 1 year ago - 2 comments
Labels: enhancement

#134 - feat: add ability to plot asymmetric maps

Pull Request - State: closed - Opened by evanr70 over 1 year ago - 2 comments

#133 - Fix: Prevent in-place operation when rescaling PSD

Pull Request - State: closed - Opened by scho97 over 1 year ago - 2 comments
Labels: enhancement

#132 - SE-HMM inherits from HMM

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago

#131 - SE-HMM can inherit the HMM class

Issue - State: closed - Opened by cgohil8 over 1 year ago - 1 comment

#130 - Prevent `NaN` values in mean lifetimes and intervals

Pull Request - State: closed - Opened by scho97 over 1 year ago
Labels: enhancement

#129 - Fix input dimension errors in fractional occupancy and switching rate computation

Pull Request - State: closed - Opened by scho97 over 1 year ago
Labels: bug

#128 - Modification of mode analysis to use slices

Pull Request - State: closed - Opened by evanr70 over 1 year ago

#127 - HMM with subject variability

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago

#126 - Added FAQ

Pull Request - State: closed - Opened by cgohil8 over 1 year ago
Labels: documentation

#125 - Add FAQ to docs

Issue - State: closed - Opened by cgohil8 over 1 year ago - 4 comments
Labels: documentation

#124 - Fix: More stable sedynemo and fixed reinitialize function.

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago

#123 - Add CLI interface for config_api

Pull Request - State: closed - Opened by evanr70 over 1 year ago

#122 - Sedynemo

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago

#121 - enhance: psd ordering and colormaps in `plot_psd_topo()`

Pull Request - State: closed - Opened by scho97 over 1 year ago
Labels: enhancement

#120 - Feature/fisher kernel

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago - 1 comment

#119 - Fix: plot_alphas bug when axes=None

Pull Request - State: closed - Opened by evanr70 over 1 year ago

#118 - Fix: update to reflect changed History objects

Pull Request - State: closed - Opened by evanr70 over 1 year ago

#117 - Config API: new wrappers and single subject bugs

Pull Request - State: closed - Opened by cgohil8 over 1 year ago

#116 - Add detail to logging format

Pull Request - State: closed - Opened by evanr70 over 1 year ago - 2 comments

#115 - Bug in single subject pipeline processing

Issue - State: closed - Opened by evanr70 over 1 year ago
Labels: bug

#114 - feat: github action to check black linting

Pull Request - State: closed - Opened by evanr70 over 1 year ago

#113 - feat: add axis argument to plot_alpha

Pull Request - State: closed - Opened by evanr70 over 1 year ago

#112 - feat: add axis argument to plot_alpha

Pull Request - State: closed - Opened by evanr70 over 1 year ago

#111 - Updated Config API

Pull Request - State: closed - Opened by cgohil8 over 1 year ago

#110 - Fixes bug in Data.trim_time_series()

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago - 1 comment

#109 - Statistics module

Pull Request - State: closed - Opened by cgohil8 over 1 year ago

#108 - docs: jupyter functions in mod_base + utils/model

Pull Request - State: closed - Opened by evanr70 over 1 year ago - 1 comment

#107 - Feature/sliding window power

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago

#106 - Methods/functions should be documented

Issue - State: closed - Opened by cgohil8 over 1 year ago
Labels: documentation

#105 - add: close figure window after saving

Pull Request - State: closed - Opened by scho97 over 1 year ago - 6 comments
Labels: enhancement

#104 - fix: plot GMM fittings per each mode

Pull Request - State: closed - Opened by scho97 over 1 year ago - 2 comments
Labels: enhancement

#103 - pre-commit not used

Issue - State: closed - Opened by cgohil8 over 1 year ago

#101 - feat: function for checking matrix symmetry

Pull Request - State: closed - Opened by scho97 over 1 year ago - 3 comments
Labels: enhancement

#100 - Save raw data in Data.save()

Issue - State: closed - Opened by cgohil8 over 1 year ago - 2 comments
Labels: enhancement, wontfix

#99 - Feature/multi sub simulation

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago

#98 - add: return weights for static power spectra

Pull Request - State: closed - Opened by scho97 over 1 year ago
Labels: enhancement

#97 - feat: tqdm -> tqdm.auto

Pull Request - State: closed - Opened by evanr70 over 1 year ago

#96 - feat: added use_tqdm option for HMM fit

Pull Request - State: closed - Opened by evanr70 over 1 year ago

#95 - Feature/sedynemo

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago

#94 - Removed initializer argument from various layers

Pull Request - State: closed - Opened by cgohil8 over 1 year ago

#93 - Initializer argument in multiple layers not used

Issue - State: closed - Opened by cgohil8 over 1 year ago
Labels: enhancement

#92 - Doc: Updated HMM write up.

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago

#91 - Parcellations + topomap plots in source space

Pull Request - State: closed - Opened by cgohil8 over 1 year ago

#90 - Add: Allow returning matplotlib objects when plotting power maps

Pull Request - State: closed - Opened by scho97 over 1 year ago - 4 comments
Labels: enhancement

#89 - Bug when resetting model weights.

Issue - State: closed - Opened by RukuangHuang over 1 year ago - 3 comments
Labels: bug

#88 - Feat: Method to calculate model evidence in HMM.

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago

#87 - HMM Free Energy Method + Updated Docs

Pull Request - State: closed - Opened by RukuangHuang over 1 year ago

#86 - Refactored HMM initialisation methods

Pull Request - State: closed - Opened by cgohil8 over 1 year ago

#84 - HMM Random State Time Course Initialisation Fix

Pull Request - State: closed - Opened by cgohil8 over 1 year ago