update b_bit_minhash benchmark (#238)

benchmark/sketches/b_bit_minhash_benchmark.py

@@ -1,77 +1,112 @@
-'''
-Benchmarking the performance and accuracy of b-bi MinHash.
-'''
-import time, logging, random
-logging.basicConfig(level=logging.INFO)
-import pyhash
-import numpy as np
+"""
+Benchmarking the performance and accuracy of b-bit MinHash.
+"""
+import time, logging
+from numpy import random
+import matplotlib
+
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
 from datasketch.minhash import MinHash
 from datasketch.b_bit_minhash import bBitMinHash
-from similarity_benchmark import _get_exact, _gen_data,\
-        Hash, _b_bit_minhash_jaccard
-
-def _run_minhash(A, B, data, seed, bs, num_perm):
-    (a_start, a_end), (b_start, b_end) = A, B
-    hasher = pyhash.murmur3_32()
-    m1 = MinHash(num_perm=num_perm, hashobj=Hash)
-    m2 = MinHash(num_perm=num_perm, hashobj=Hash)
-    for i in xrange(a_start, a_end):
-        m1.update(hasher(data[i], seed=seed))
-    for i in xrange(b_start, b_end):
-        m2.update(hasher(data[i], seed=seed))
-    return [m1.jaccard(m2)] + \
-            [_b_bit_minhash_jaccard(m1, m2, b) for b in bs]
-
-def _run_test(A, B, data, n, bs, num_perm):
-    logging.info("Run tests with A = (%d, %d), B = (%d, %d), n = %d"
-            % (A[0], A[1], B[0], B[1], n))
-    runs = np.array([_run_minhash(A, B, data, i, bs, num_perm)
-        for i in xrange(n)]).T
-    return runs
-
-def run_full_tests(attr_pairs, data, n, bs, num_perm):
-    return [_run_test(A, B, data, n, bs, num_perm)
-            for A, B in attr_pairs]
-
-def plot(result, bs, exact_sims, num_perm, bins, save):
-    import matplotlib
-    matplotlib.use('Agg')
-    import matplotlib.pyplot as plt
-    num_row = 1
-    num_col = len(result)
-    basesize = 5
-    size = (basesize*num_col, basesize*num_row)
-    fig, axes = plt.subplots(num_row, num_col, sharey=True,
-            sharex=True, figsize=size)
-    for i, runs in enumerate(result):
-        minhash = sorted(runs[0])
-        bbits = [sorted(r) for r in runs[1:]]
-        exact_sim = exact_sims[i]
-        ax = axes[i]
-        l = ax.plot(minhash, label='MinHash')
-        for b, run in zip(bs, bbits):
-            l = ax.plot(run, label='%d-bit' % b)
-        ax.axhline(exact_sim, color='black', linestyle='--', label='Exact')
-        ax.set_title("%d perm funcs, exact = %.2f" % (num_perm, exact_sim))
-        ax.grid()
-        ax.set_xlabel("Runs with random hash functions")
-        if i == 0:
-            ax.set_ylabel('Jaccard')
-        if i == num_col - 1:
-            ax.legend(loc='lower right')
-    fig.savefig(save)
-
-
-if __name__ == "__main__":
-    data = _gen_data(5000)
-    attr_pairs = [((0, 3000), (2000, 5000)),
-                  ((0, 3500), (1500, 5000)),
-                  ((0, 4500), (500, 5000))]
-    num_perm = 128
-    bs = [1, 2, 3]
-    n = 100
-    save = "b_bit_minhash_benchmark.png"
-    bins = [i*0.02 for i in range(51)]
-    exact_sims = [_get_exact(A, B) for A, B in attr_pairs]
-    result = run_full_tests(attr_pairs, data, n, bs, num_perm)
-    plot(result, bs, exact_sims, num_perm, bins, save)
+from datasketch.hashfunc import *
+
+logging.basicConfig(level=logging.INFO)
+
+# Produce some bytes
+int_bytes = lambda x: ("a-%d-%d" % (x, x)).encode("utf-8")
+
+
+def run_perf(card, num_perm, num_bits):
+    dur = 0
+    n_trials = 5
+    for i in range(n_trials):
+        m = MinHash(num_perm=num_perm)
+        logging.info("MinHash using %d permutation functions" % num_perm)
+        start = time.perf_counter()
+        for i in range(card):
+            m.update(int_bytes(i))
+
+        b = bBitMinHash(m, num_bits)
+        duration = time.perf_counter() - start
+        dur += duration
+        logging.info("Digested %d hashes in %.4f sec" % (card, duration))
+    return dur / n_trials
+
+
+def _run_acc(size, seed, num_perm, num_bits):
+    m = MinHash(num_perm=num_perm)
+    s = set()
+    random.seed(seed)
+    for i in range(size):
+        v = int_bytes(random.randint(1, size))
+        m.update(v)
+        s.add(v)
+
+    b = bBitMinHash(m, num_bits)
+    return (b, s)
+
+
+def run_acc(size, num_perm, num_bits):
+    logging.info("MinHash using %d permutation functions" % num_perm)
+    m1, s1 = _run_acc(size, 1, num_perm, num_bits)
+    m2, s2 = _run_acc(size, 4, num_perm, num_bits)
+    j = float(len(s1.intersection(s2))) / float(len(s1.union(s2)))
+    j_e = m1.jaccard(m2)
+    err = abs(j - j_e)
+    return err
+
+
+num_perms = range(10, 256, 20)
+num_bits = [1, 2, 3, 4, 8, 12, 16, 32]
+bit_colors = colors = [
+    "#1f77b4",
+    "#ff7f0e",
+    "#2ca02c",
+    "#d62728",
+    "#9467bd",
+    "#8c564b",
+    "#e377c2",
+    "#7f7f7f",
+]
+output = "b_bit_minhash_benchmark.png"
+
+logging.info("> Running performance tests")
+card = 5000
+perf_times = {}
+for b in num_bits:
+    run_times = [run_perf(card, n, b) for n in num_perms]
+    perf_times[b] = run_times
+
+
+logging.info("> Running accuracy tests")
+size = 5000
+errors = {}
+for b in num_bits:
+    errs = [run_acc(size, n, b) for n in num_perms]
+    errors[b] = errs
+
+logging.info("> Plotting result")
+fig, axe = plt.subplots(1, 2, sharex=True, figsize=(10, 4))
+ax = axe[1]
+for i, b in enumerate(num_bits):
+    ax.plot(
+        num_perms, perf_times[b], marker="+", color=bit_colors[i], label=f"{b} bits"
+    )
+ax.set_xlabel("Number of permutation functions")
+ax.set_ylabel("Running time (sec)")
+ax.set_title("MinHash performance")
+ax.grid()
+ax.legend()
+ax = axe[0]
+for i, b in enumerate(num_bits):
+    ax.plot(num_perms, errors[b], marker="+", color=bit_colors[i], label=f"{b} bits")
+ax.set_xlabel("Number of permutation functions")
+ax.set_ylabel("Absolute error in Jaccard estimation")
+ax.set_title("MinHash accuracy")
+ax.grid()
+ax.legend()
+
+plt.tight_layout()
+fig.savefig(output)
+logging.info("Plot saved to %s" % output)