Systems-Theory-in-Systems-Biology/EPI

Issues

• Plotting produces error for low vertical resolutions

  #135 opened 2 months ago
  0

• Other density estimation possibilities

  #134 opened 2 months ago
  0

• Test the jupyter notebook tutorial

  #113 opened 3 months ago
  0

• Redundant function in core

  #111 opened 3 months ago
  1

• Issues with jax usage

  #110 opened 9 months ago
  1

• Extend tutorial to include loading results (e.g. using result manager or dict) and plotting

  #107 opened 9 months ago
  1

• Show only EPI core in api doc

  #106 opened 9 months ago
  0

• Kolmogorov-Distance as quantitative check for inference results

  #104 opened 9 months ago
  3

• How to (properly) vectorize the forward function

  #103 opened 9 months ago
  0

• Docstrings for example models

  #102 opened 9 months ago
  0

• Extensive Tutorial

  #101 opened 9 months ago
  0

• model(param) is unequal to model.forward(param)

  #99 opened 9 months ago
  2

• Fix jax warning about config import

  #96 opened 9 months ago
  0

• Model test

  #94 opened 9 months ago
  4

• Basic plotting quick EPI results check

  #92 opened 10 months ago
  0

• Dependencies in the documentation lead to the wrong version

  #91 opened 10 months ago
  1

• Future Work

  #85 opened 3 months ago
  2

• Spatial discretization of heat equation isn't proper second order central derivative.

  #78 opened a year ago
  0

• Use linear interpolation for the heat model evaluation points

  #74 opened a year ago
  0

• SBML Model not supporting time series

  #71 opened a year ago
  4

• Value error in inference with heat model and PCA

  #68 opened a year ago
  1

• Dense grid does not generate a grid with correct values for certain slices

  #67 opened a year ago
  1

• Add a way for the user to provide more complex parameter domains

  #63 opened a year ago
  1

• Add a way to handle exceptions raised in the model

  #62 opened a year ago
  0

• Update the tutorial to match the current state of the project

  #56 opened a year ago
  0

• Use principal component analysis (PCA) to reduce number of data dimesions

  #54 opened a year ago
  0

• Accelerate data normalization

  #52 opened a year ago
  0

• Use L2-Error to check quantitative tests

  #44 opened 3 months ago
  0

• Dense grid inference returns density that is not normalized to an intergral of 1

  #43 opened 10 months ago
  2

• Replace custom KDE with scipy.stats.gaussian_kde

  #42 opened a year ago
  0

• More and more qualitative tests needed

  #41 opened a year ago
  1

• Current MCMC move policy includes many tiny steps

  #39 opened a year ago
  0

• Scale all data to have mean 0 and variance 1 to improve numerical stability for high data dimensionality

  #38 opened a year ago
  3

• Inference for linear ODE model stops working if data sample size is larger than 2^16 = 65536 data points

  #36 opened a year ago
  5

• GitHub Actions CI - Pytest segmentation fault for amici models

  #34 opened a year ago
  1

• Create template for pull requests including a checklist

  #33 opened a year ago
  0

• Pytest gets stuck in test_examples[coronaartificial]

  #31 opened a year ago
  0

• Improve dependency management

  #30 opened 10 months ago
  4

• Temperature model does not use artificially created data

  #29 opened 10 months ago
  2

• Dense grid evaluation does not work for SBML model

  #28 opened a year ago
  1

• Menten SBML model inference simulation result dimension does not match single simulation result dimension

  #27 opened a year ago
  3

• load_sim_results in Results_manager should be refined

  #26 opened a year ago
  1

• SBML model assigend data dimension not consistent with dimension of model output

  #25 opened a year ago
  1

• Numburn samples has no sensible default / no documentation for recommended values

  #24 opened a year ago
  4

• Default result manager neglects all runs but the first when burning mcmc samples

  #23 opened a year ago
  2

• Output dimensions for dense grid evaluation inconsistent with mcmc evaluation

  #20 opened a year ago
  2

• Bug in Stock model; No intermediate results used

  #18 opened a year ago
  0

• User-specified burn-in period for saved samples

  #17 opened a year ago
  0

• Fix building the documentation

  #16 opened a year ago
  1

• Get results directly from inference method

  #15 opened a year ago
  1