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Commits on Jul 12, 2018

• Rename and drop unused methods

  maaskola

  committed
  f47d6f3

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Commits on Jul 10, 2018

• Move out of parallel section and constify

  maaskola

  committed
  767a6f9

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Commits on Jun 3, 2018

• Optionally fix GP means to zero

  maaskola

  committed
  008ba9a

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Commits on May 27, 2018

• By default, initialize GPs zero-centered

  maaskola

  committed
  940f212

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• Fix GP learning

  maaskola

  committed
  dda112f

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• Always calculate likelihood

  maaskola

  committed
  dff0e29

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• Copy GP pointers when cloning Model

  maaskola

  committed
  6de7bb8

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• Overhaul GP code

  maaskola

  committed
  e7a146e

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• Fix semantics of method

  maaskola

  committed
  126d4a4

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• Rename method

  maaskola

  committed
  151aac0

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• Rename member

  maaskola

  committed
  742b143

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Commits on May 8, 2018

• Polymorphic coefficient types; drop index vectors

  maaskola

  committed
  7fb75b0

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Commits on Mar 12, 2018

• Drop unused code

  maaskola

  committed
  996f043

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• Drop lBFGS support

  maaskola

  committed
  4519579

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Commits on Mar 8, 2018

• Some code comments

  maaskola

  committed
  c84ebab

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• Report which coefficients get optimized

  maaskola

  committed
  c2f74e5

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• Better variable and local function names

  maaskola

  committed
  13a856c

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Commits on Mar 1, 2018

• Use correct default value

  maaskola

  committed
  e06d3bb

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Commits on Feb 28, 2018

• Deactivate stochasticity in report iterations

  maaskola

  committed
  1041f59

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• Re-enable down-sampling and seq depth adjustment

  maaskola

  committed
  ff2b521

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Commits on Feb 21, 2018

• Don't base gradient on hidden counts

  maaskola

  committed
  0efdd6e

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Commits on Jan 30, 2018

• Compute and store means and variances at the end

  maaskola

  committed
  09e1c59

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Commits on Jan 11, 2018

• Merge branch 'llvm' into llvm-stage

  ludvb

  committed
  6e2b8d4

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• Add support for Nesterov momentum in Adam

  ludvb

  committed
  e461d4a

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Commits on Dec 31, 2017

• Optionally match read/spot ratio by down-sampling

  maaskola

  committed
  40dcf70

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Commits on Dec 29, 2017

• Save time by not calculating likelihood

  maaskola

  committed
  91c066e

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• Tree-balance sums and products of > 2 terms

  maaskola

  committed
  523e0ba

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Commits on Dec 28, 2017

• Simplify expressions

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  maaskola

  committed
  91064d8

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• Write LLVM IR to files

  maaskola

  committed
  c7d427b

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Commits on Dec 27, 2017

• More fine-grained staging

  maaskola

  committed
  c235d61

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Commits on Dec 25, 2017

• Fix: use same arguments for derivative functions

  maaskola

  committed
  d8a6507

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• Write out the model

  maaskola

  committed
  50eaf52

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• Fix: use dropout rate 0 in last iteration

  maaskola

  committed
  07b3f91

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Commits on Dec 22, 2017

• Merge branch 'llvm' into staging

  maaskola

  committed
  a9ac8ca

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Commits on Dec 17, 2017

• Ensure gradients of fixed coefficients are zero

  maaskola

  committed
  27c6656

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