Merge pull request #14 from Adamits/faster-logsumexp

replaces scipy.logsumexp with numpy.logaddexp
CUNY-CL · Apr 22, 2024 · 41d97d5 · 41d97d5
2 parents abd17f5 + 22cd4f0
commit 41d97d5
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Showing 3 changed files with 8 additions and 12 deletions.
diff --git a/maxwell/sed.py b/maxwell/sed.py
@@ -17,8 +17,6 @@
 import numpy
 import tqdm
 
-from scipy import special
-
 from . import actions, util
 
 LARGE_NEG_CONST = -1e6
@@ -70,7 +68,7 @@ def sum(self) -> float:
         for vs in (self.delta_sub, self.delta_ins, self.delta_del):
             values.extend(vs.values())
         # Uses sum of exponentiation to maintain logarithmic values.
-        return special.logsumexp(values)
+        return numpy.logaddexp.reduce(values)
 
     @classmethod
     def from_params(cls, other: ParamDict) -> ParamDict:
@@ -248,7 +246,7 @@ def forward_evaluate(
                         )
                         + alpha[t - 1, v - 1]
                     )
-                alpha[t, v] = special.logsumexp(summands)
+                alpha[t, v] = numpy.logaddexp.reduce(summands)
         alpha[T, V] += self.params.delta_eos
         return alpha
 
@@ -292,7 +290,7 @@ def backward_evaluate(
                         )
                         + beta[t + 1, v + 1]
                     )
-                beta[t, v] = special.logsumexp(summands)
+                beta[t, v] = numpy.logaddexp.reduce(summands)
         return beta
 
     def log_likelihood(
@@ -348,7 +346,7 @@ def e_step(
         """
         alpha = self.forward_evaluate(source, target)
         beta = self.backward_evaluate(source, target)
-        gammas.delta_eos = special.logsumexp([gammas.delta_eos, 0.0])
+        gammas.delta_eos = numpy.logaddexp(gammas.delta_eos, 0.0)
         T = len(source)
         V = len(target)
         for t in range(T + 1):
@@ -358,7 +356,7 @@ def e_step(
                 tchar = target[v - 1]
                 stpair = schar, tchar
                 if t > 0 and schar in gammas.delta_del:
-                    gammas.delta_del[schar] = special.logsumexp(
+                    gammas.delta_del[schar] = numpy.logaddexp.reduce(
                         [
                             gammas.delta_del[schar],
                             alpha[t - 1, v]
@@ -367,7 +365,7 @@ def e_step(
                         ]
                     )
                 if v > 0 and tchar in gammas.delta_ins:
-                    gammas.delta_ins[tchar] = special.logsumexp(
+                    gammas.delta_ins[tchar] = numpy.logaddexp.reduce(
                         [
                             gammas.delta_ins[tchar],
                             alpha[t, v - 1]
@@ -376,7 +374,7 @@ def e_step(
                         ]
                     )
                 if t > 0 and v > 0 and stpair in gammas.delta_sub:
-                    gammas.delta_sub[stpair] = special.logsumexp(
+                    gammas.delta_sub[stpair] = numpy.logaddexp.reduce(
                         [
                             gammas.delta_sub[stpair],
                             alpha[t - 1, v - 1]

diff --git a/pyproject.toml b/pyproject.toml
@@ -10,7 +10,7 @@ include = ["maxwell*"]
 
 [project]
 name = "maxwell"
-version = "0.2.2.post2"
+version = "0.2.3"
 description = "Stochastic Edit Distance aligenr for string transduction"
 readme = "README.md"
 requires-python = "> 3.9"
@@ -28,7 +28,6 @@ keywords = [
 ]
 dependencies = [
     "numpy >= 1.20.1",
-    "scipy >= 1.6",
     "tqdm >= 4.64.1",
 ]
 classifiers = [

diff --git a/requirements.txt b/requirements.txt
@@ -3,6 +3,5 @@ build>=0.10.0
 flake8>=3.9.2
 numpy>=1.20.1
 pytest>=7.4.0
-scipy>=1.6
 twine>=4.0.2
 tqdm>=4.64.1