1. 10 Jul, 2020 1 commit
  2. 09 Jul, 2020 1 commit
  3. 08 Jul, 2020 2 commits
    • Chris Jewell's avatar
      Fix in discrete_markov simulation code · 0b337d47
      Chris Jewell authored
      Bug in discrete_markov.propagate found, introduced after changes for vectorised
      likelihood.
      0b337d47
    • Chris Jewell's avatar
      Added occult inference capability · cad36259
      Chris Jewell authored
      Changes:
      
      1. Added occult Metropolis Hastings update.
      2. Factored out Categorical2 distribution for use by both event time move and occults.
      3. Refactored mcmc.py script for HDF5 output purposes
      4. Apply compression to HDF5 output file.
      cad36259
  4. 05 Jul, 2020 3 commits
  5. 04 Jul, 2020 2 commits
  6. 01 Jul, 2020 1 commit
  7. 29 Jun, 2020 1 commit
  8. 28 Jun, 2020 7 commits
  9. 27 Jun, 2020 2 commits
  10. 26 Jun, 2020 2 commits
    • Chris Jewell's avatar
      Changed storage order of events matrix. · 0291aa34
      Chris Jewell authored
      Previously, the Events matrix expected by model.log_prob was ordered
      [T, M, X] where T is the number of timpoints, M is the number of
      meta-populations and X is the number of transitions.  However, it was
      found more convenient to work with [M, T, X] for the purposes of data
      augmentation.  This meant extra tf.transpose calls.
      
      model.log_prob now expects [M, T, X], with any further batch
      dimensions added as outer dimensions.
      0291aa34
    • Chris Jewell's avatar
      Minor formatting changes to mcmc.py · 8f6ef578
      Chris Jewell authored
      8f6ef578
  11. 25 Jun, 2020 1 commit
  12. 24 Jun, 2020 1 commit
    • Chris Jewell's avatar
      Changes: · e72cfe76
      Chris Jewell authored
      1. Formatting -- black style!
      2. After profiling, implemented a better workaround for the
      tfd.Categorical bug.  Replaced with an inherited Categorical2 class,
      with overloaded log_prob function.
      3. Fixed a  bug in EventTimeProposal where tfd.FiniteDiscrete was
      being used on a non-strictly-increasing outcomes vector.
      4. Increased number of meta-populations to 149 to mirror UK UTLA regions.
      e72cfe76
  13. 22 Jun, 2020 1 commit
    • Chris Jewell's avatar
      Changes: · 705ce40b
      Chris Jewell authored
      1. Fixed bug in covid.impl.event_time_mh._reverse_move where Multinomial one_hot tensor wasn't being advanced for the reverse move.  This is a temporary workaround while tf.nn.sparse_softmax_cross_entropy_with_logits is fixed.
      
      2. Batched EventTimesProposal to move multiple meta-populations.
      
      3. Batched _move_events to allow for multiple meta-population updates
      
      4. Refactored covid.impl.event_time_proposal._abscumdiff so we calculate `bound_times` outside the function.  This allows clipping of times proposed outside [0, T] to [0, T], thus avoiding an error in tf.gather_nd in CPU mode.  The output of EventTimesProposal.sample and EventTimesProposal.log_prob might be inconsistent with what we expect, but that's okay as the move gets rejected as an out-of-bounds proposal anyway.
      705ce40b
  14. 20 Jun, 2020 1 commit
  15. 19 Jun, 2020 3 commits
  16. 18 Jun, 2020 1 commit
    • Chris Jewell's avatar
      Changes: · ac099f62
      Chris Jewell authored
      1. Edited _move_events to take into account metapopulation selection.
      2. Replace bound_t.ndim with bound_t.shape.rank for TF Graph Mode running.
      3. Revised index calculation in `_abscumdiff`.  Re-wrote test to accommodate.
      4. Code rationalisation in FilteredEventTimesProposal to return a simpler data structure.
      5. Changed dimension of results.extra field to trace `x_star`.
      6. Edited tests in `tests.test_mcmc.py` for new `_abscumdiff` interface.
      ac099f62
  17. 16 Jun, 2020 3 commits
  18. 13 Jun, 2020 1 commit
  19. 12 Jun, 2020 3 commits
  20. 05 Jun, 2020 1 commit
  21. 04 Jun, 2020 1 commit
  22. 03 Jun, 2020 1 commit