- 24 Jun, 2020 1 commit
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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.
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- 22 Jun, 2020 1 commit
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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.
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- 20 Jun, 2020 1 commit
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Chris Jewell authored
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- 19 Jun, 2020 1 commit
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Christopher Suter authored
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- 18 Jun, 2020 1 commit
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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.
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- 16 Jun, 2020 3 commits
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Chris Jewell authored
1. Wrote wrapper `FilteredEventTimesProposal` for EventTimesProposal to subset metapopulations. This currently selects just one meta-population, but the plan is to select more. 2. Moved test fixture to folder inside tests. 3. Wrote (failing) TestFilteredEventTimesProposal test.
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Chris Jewell authored
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Chris Jewell authored
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- 13 Jun, 2020 1 commit
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Chris Jewell authored
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- 12 Jun, 2020 2 commits
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Christopher Suter authored
- flatten out the distribution of delta_t; no longer a JointDistributionNamed, just a FiniteDiscrete - replaced OneHotCategorical with a Categorical (sample needs an expand dims after) - fix bug -- were using zeros instead of int max's for upper bounds - thread dtypes through various functions - inlined some arg-free distributions in JointDistributionNamed - minor reformatting to appease Chris Suter's formatting compulsions - pprint in tests; fix test data paths (weren't working for Chris Suter's setup)
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Chris Jewell authored
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