1. 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
  2. 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
  3. 20 Jun, 2020 1 commit
  4. 19 Jun, 2020 1 commit
  5. 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
  6. 16 Jun, 2020 3 commits
  7. 13 Jun, 2020 1 commit
  8. 12 Jun, 2020 2 commits