fpembed 0.1.4__tar.gz → 0.1.5__tar.gz

{fpembed-0.1.4/src/fpembed.egg-info → fpembed-0.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fpembed
-Version: 0.1.4
+Version: 0.1.5
 Summary: Generalized fingerprint embedding library
 License-Expression: MIT
 Requires-Python: >=3.9
@@ -66,12 +66,12 @@ FPembed supports six compression methods, selectable via the `method` parameter
 
 | Method (`method` value) | Category | `method_params` | Dynamic Range / Distance Preservation | Complexity |
 |-------------------------|----------|-----------------|---------------------------------------|------------|
-| `geometric` | block-wise | `interleave` (bool) | 65,536:1 dynamic range | O(L) |
-| `linear` | block-wise | `interleave` (bool) | S:1 dynamic range | O(L) |
-| `log` | block-wise | `interleave` (bool) | ~4.1:1 dynamic range | O(L) |
-| `uniform` | block-wise | `interleave` (bool) | 1:1 (mean pooling) | O(L) |
+| `geometric` | block-wise | `interleave` (bool) | 65,536:1 dynamic range | O(L)       |
+| `linear` | block-wise | `interleave` (bool) | S:1 dynamic range | O(L)       |
+| `log` | block-wise | `interleave` (bool) | ~4.1:1 dynamic range | O(L)       |
+| `uniform` | block-wise | `interleave` (bool) | 1:1 (mean pooling) | O(L)       |
 | `hadamard` | global | `seed` (int) | orthogonal projection | O(L log L) |
-| `random_projection` | global | `seed` (int) + `sparse` (bool) | JL distance preservation | O(L·D) |
+| `random_projection` | global | `seed` (int) + `sparse` (bool) | JL distance preservation | O(L D)     |
 
 ### The `method` Parameter
 
@@ -132,7 +132,7 @@ print(emb.shape)  # (1, 128)
 
 ### Choosing a Method
 
-Block-wise methods (`geometric`, `linear`, `log`, `uniform`) are fast (O(L)) and simple - use them when speed matters or compression ratios are modest. Among these, `geometric` preserves the most dynamic range while `uniform` treats all bits equally (mean pooling). Global projection methods (`hadamard`, `random_projection`) mix information across all input bits, which helps retain more information at high compression ratios. `hadamard` is efficient (O(L log L)) and requires power-of-2 fingerprint sizes; `random_projection` offers the strongest theoretical distance-preservation guarantees (Johnson-Lindenstrauss lemma) at the cost of O(L·D) complexity.
+Block-wise methods (`geometric`, `linear`, `log`, `uniform`) are fast (O(L)) and simple - use them when speed matters or compression ratios are modest. Among these, `geometric` preserves the most dynamic range while `uniform` treats all bits equally (mean pooling). Global projection methods (`hadamard`, `random_projection`) mix information across all input bits, which helps retain more information at high compression ratios. `hadamard` is efficient (O(L log L)) and requires power-of-2 fingerprint sizes; `random_projection` offers the strongest theoretical distance-preservation guarantees (Johnson-Lindenstrauss lemma) at the cost of O(L D) complexity.
 
 ### Performance Characteristics
 
@@ -141,7 +141,7 @@ All methods produce the same output dimensionality (D = L / compression) but dif
 | Method | Speed                                    | Precomputed Memory                   | Best For |
 |--------|------------------------------------------|--------------------------------------|----------|
 | Block-wise (all four) | Fastest - single vectorized einsum, O(L) | Negligible (C-length weight vector)  | Default choice; large batches |
-| Random projection | Fast - BLAS matmul, O(L·D)               | DxL matrix (~2 MB for L=2048, D=128) | Best theoretical guarantees (JL lemma) |
+| Random projection | Fast - BLAS matmul, O(L D)               | DxL matrix (~2 MB for L=2048, D=128) | Best theoretical guarantees (JL lemma) |
 | Hadamard (SRHT) | Slowest - pure-Python FWHT, O(L log L)   | L-length sign vector (~16 KB)        | Small-scale experiments; future optimization |
 
 Block-wise methods are ~2–5x faster than random projection and orders of magnitude faster than Hadamard in practice. Random projection's memory cost grows quadratically with fingerprint size.

{fpembed-0.1.4 → fpembed-0.1.5}/README.md

@@ -46,12 +46,12 @@ FPembed supports six compression methods, selectable via the `method` parameter
 
 | Method (`method` value) | Category | `method_params` | Dynamic Range / Distance Preservation | Complexity |
 |-------------------------|----------|-----------------|---------------------------------------|------------|
-| `geometric` | block-wise | `interleave` (bool) | 65,536:1 dynamic range | O(L) |
-| `linear` | block-wise | `interleave` (bool) | S:1 dynamic range | O(L) |
-| `log` | block-wise | `interleave` (bool) | ~4.1:1 dynamic range | O(L) |
-| `uniform` | block-wise | `interleave` (bool) | 1:1 (mean pooling) | O(L) |
+| `geometric` | block-wise | `interleave` (bool) | 65,536:1 dynamic range | O(L)       |
+| `linear` | block-wise | `interleave` (bool) | S:1 dynamic range | O(L)       |
+| `log` | block-wise | `interleave` (bool) | ~4.1:1 dynamic range | O(L)       |
+| `uniform` | block-wise | `interleave` (bool) | 1:1 (mean pooling) | O(L)       |
 | `hadamard` | global | `seed` (int) | orthogonal projection | O(L log L) |
-| `random_projection` | global | `seed` (int) + `sparse` (bool) | JL distance preservation | O(L·D) |
+| `random_projection` | global | `seed` (int) + `sparse` (bool) | JL distance preservation | O(L D)     |
 
 ### The `method` Parameter
 
@@ -112,7 +112,7 @@ print(emb.shape)  # (1, 128)
 
 ### Choosing a Method
 
-Block-wise methods (`geometric`, `linear`, `log`, `uniform`) are fast (O(L)) and simple - use them when speed matters or compression ratios are modest. Among these, `geometric` preserves the most dynamic range while `uniform` treats all bits equally (mean pooling). Global projection methods (`hadamard`, `random_projection`) mix information across all input bits, which helps retain more information at high compression ratios. `hadamard` is efficient (O(L log L)) and requires power-of-2 fingerprint sizes; `random_projection` offers the strongest theoretical distance-preservation guarantees (Johnson-Lindenstrauss lemma) at the cost of O(L·D) complexity.
+Block-wise methods (`geometric`, `linear`, `log`, `uniform`) are fast (O(L)) and simple - use them when speed matters or compression ratios are modest. Among these, `geometric` preserves the most dynamic range while `uniform` treats all bits equally (mean pooling). Global projection methods (`hadamard`, `random_projection`) mix information across all input bits, which helps retain more information at high compression ratios. `hadamard` is efficient (O(L log L)) and requires power-of-2 fingerprint sizes; `random_projection` offers the strongest theoretical distance-preservation guarantees (Johnson-Lindenstrauss lemma) at the cost of O(L D) complexity.
 
 ### Performance Characteristics
 
@@ -121,7 +121,7 @@ All methods produce the same output dimensionality (D = L / compression) but dif
 | Method | Speed                                    | Precomputed Memory                   | Best For |
 |--------|------------------------------------------|--------------------------------------|----------|
 | Block-wise (all four) | Fastest - single vectorized einsum, O(L) | Negligible (C-length weight vector)  | Default choice; large batches |
-| Random projection | Fast - BLAS matmul, O(L·D)               | DxL matrix (~2 MB for L=2048, D=128) | Best theoretical guarantees (JL lemma) |
+| Random projection | Fast - BLAS matmul, O(L D)               | DxL matrix (~2 MB for L=2048, D=128) | Best theoretical guarantees (JL lemma) |
 | Hadamard (SRHT) | Slowest - pure-Python FWHT, O(L log L)   | L-length sign vector (~16 KB)        | Small-scale experiments; future optimization |
 
 Block-wise methods are ~2–5x faster than random projection and orders of magnitude faster than Hadamard in practice. Random projection's memory cost grows quadratically with fingerprint size.

{fpembed-0.1.4 → fpembed-0.1.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "fpembed"
-version = "0.1.4"
+version = "0.1.5"
 description = "Generalized fingerprint embedding library"
 requires-python = ">=3.9"
 dependencies = [

{fpembed-0.1.4 → fpembed-0.1.5}/src/fpembed/__init__.py

@@ -20,7 +20,7 @@ from fpembed.compression import compress_fingerprint
 from fpembed.smiles_utils import parse_smiles, canonicalize_smiles
 from fpembed.hashing import fp_params_hash
 
-__version__ = "0.1.4"
+__version__ = "0.1.5"
 
 __all__ = [
     "EmbeddedFingerprintGenerator",

{fpembed-0.1.4 → fpembed-0.1.5/src/fpembed.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fpembed
-Version: 0.1.4
+Version: 0.1.5
 Summary: Generalized fingerprint embedding library
 License-Expression: MIT
 Requires-Python: >=3.9
@@ -66,12 +66,12 @@ FPembed supports six compression methods, selectable via the `method` parameter
 
 | Method (`method` value) | Category | `method_params` | Dynamic Range / Distance Preservation | Complexity |
 |-------------------------|----------|-----------------|---------------------------------------|------------|
-| `geometric` | block-wise | `interleave` (bool) | 65,536:1 dynamic range | O(L) |
-| `linear` | block-wise | `interleave` (bool) | S:1 dynamic range | O(L) |
-| `log` | block-wise | `interleave` (bool) | ~4.1:1 dynamic range | O(L) |
-| `uniform` | block-wise | `interleave` (bool) | 1:1 (mean pooling) | O(L) |
+| `geometric` | block-wise | `interleave` (bool) | 65,536:1 dynamic range | O(L)       |
+| `linear` | block-wise | `interleave` (bool) | S:1 dynamic range | O(L)       |
+| `log` | block-wise | `interleave` (bool) | ~4.1:1 dynamic range | O(L)       |
+| `uniform` | block-wise | `interleave` (bool) | 1:1 (mean pooling) | O(L)       |
 | `hadamard` | global | `seed` (int) | orthogonal projection | O(L log L) |
-| `random_projection` | global | `seed` (int) + `sparse` (bool) | JL distance preservation | O(L·D) |
+| `random_projection` | global | `seed` (int) + `sparse` (bool) | JL distance preservation | O(L D)     |
 
 ### The `method` Parameter
 
@@ -132,7 +132,7 @@ print(emb.shape)  # (1, 128)
 
 ### Choosing a Method
 
-Block-wise methods (`geometric`, `linear`, `log`, `uniform`) are fast (O(L)) and simple - use them when speed matters or compression ratios are modest. Among these, `geometric` preserves the most dynamic range while `uniform` treats all bits equally (mean pooling). Global projection methods (`hadamard`, `random_projection`) mix information across all input bits, which helps retain more information at high compression ratios. `hadamard` is efficient (O(L log L)) and requires power-of-2 fingerprint sizes; `random_projection` offers the strongest theoretical distance-preservation guarantees (Johnson-Lindenstrauss lemma) at the cost of O(L·D) complexity.
+Block-wise methods (`geometric`, `linear`, `log`, `uniform`) are fast (O(L)) and simple - use them when speed matters or compression ratios are modest. Among these, `geometric` preserves the most dynamic range while `uniform` treats all bits equally (mean pooling). Global projection methods (`hadamard`, `random_projection`) mix information across all input bits, which helps retain more information at high compression ratios. `hadamard` is efficient (O(L log L)) and requires power-of-2 fingerprint sizes; `random_projection` offers the strongest theoretical distance-preservation guarantees (Johnson-Lindenstrauss lemma) at the cost of O(L D) complexity.
 
 ### Performance Characteristics
 
@@ -141,7 +141,7 @@ All methods produce the same output dimensionality (D = L / compression) but dif
 | Method | Speed                                    | Precomputed Memory                   | Best For |
 |--------|------------------------------------------|--------------------------------------|----------|
 | Block-wise (all four) | Fastest - single vectorized einsum, O(L) | Negligible (C-length weight vector)  | Default choice; large batches |
-| Random projection | Fast - BLAS matmul, O(L·D)               | DxL matrix (~2 MB for L=2048, D=128) | Best theoretical guarantees (JL lemma) |
+| Random projection | Fast - BLAS matmul, O(L D)               | DxL matrix (~2 MB for L=2048, D=128) | Best theoretical guarantees (JL lemma) |
 | Hadamard (SRHT) | Slowest - pure-Python FWHT, O(L log L)   | L-length sign vector (~16 KB)        | Small-scale experiments; future optimization |
 
 Block-wise methods are ~2–5x faster than random projection and orders of magnitude faster than Hadamard in practice. Random projection's memory cost grows quadratically with fingerprint size.