lambda-or 0.0.2__tar.gz

lambda_or-0.0.2/LICENSE

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+MIT License
+
+Copyright (c) 2021 ZeD Labs
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

lambda_or-0.0.2/MANIFEST.in

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+include version.py
+recursive-include lambda_or/examples  *
+recursive-include lambda_or *.ipynb *.joblib *.c *.so *.pyx *.pkl *.csv *.txt

lambda_or-0.0.2/PKG-INFO

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+Metadata-Version: 2.1
+Name: lambda_or
+Version: 0.0.2
+Summary: Lambda Odds Ratio
+Home-page: https://github.com/zeroknowledgediscovery/lambda_or
+Download-URL: https://github.com/zeroknowledgediscovery/lambda_or/archive/0.0.2.tar.gz
+Author: Ishanu Chattopadhyay
+Author-email: zeroknowledgediscovery@gmail.com
+License: LICENSE
+Keywords: robust odds ratio,misclassification correction,machine learning,EHR databases
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Software Development :: Libraries
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.9
+Requires-Python: >=3.6
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+
+===============
+Qbiome
+===============
+
+.. class:: no-web no-pdf
+
+:Info: Draft link will be posted here
+:Author: ZeD Lab <zed.createuky.net>
+:Description: Robust Odds Ratio correcting label noise 
+:Documentation: 
+
+
+**Usage:**
+
+.. code-block::
+
+    from lambda_or import lambda_or, pq_from_two_gates
+
+    tilde = np.array([[100, 50],[ 80, 70]], dtype=float)
+    # Suppose selection-conditional rates from two-gate ROC:
+    p_sel, q_sel = 0.92, 0.90
+    res = lambda_or(tilde, p_sel, q_sel, n_val=2000)
+    
+    print(res.log_or, res.neglog10_p, res.z, res.se)
+    print(res.counts)   # corrected a,b,c,d
+

lambda_or-0.0.2/README.rst

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+===============
+Qbiome
+===============
+
+.. class:: no-web no-pdf
+
+:Info: Draft link will be posted here
+:Author: ZeD Lab <zed.createuky.net>
+:Description: Robust Odds Ratio correcting label noise 
+:Documentation: 
+
+
+**Usage:**
+
+.. code-block::
+
+    from lambda_or import lambda_or, pq_from_two_gates
+
+    tilde = np.array([[100, 50],[ 80, 70]], dtype=float)
+    # Suppose selection-conditional rates from two-gate ROC:
+    p_sel, q_sel = 0.92, 0.90
+    res = lambda_or(tilde, p_sel, q_sel, n_val=2000)
+    
+    print(res.log_or, res.neglog10_p, res.z, res.se)
+    print(res.counts)   # corrected a,b,c,d
+

lambda_or-0.0.2/lambda_or/__init__.py

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+from .lambda_or import lambda_or, pq_from_two_gates, LambdaORResult
+__all__ = ["lambda_or", "pq_from_two_gates", "LambdaORResult"]
+__version__ = "0.1.0"
+

lambda_or-0.0.2/lambda_or/lambda_or.py

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+"""
+lambda_or.py — Λ-OR (Lambda Odds Ratio) for misclassification-corrected attribution.
+
+This module implements a ridge-stabilized inversion of a misclassified 2x2 contingency
+table to recover corrected counts and compute the corrected log-odds ratio, its
+variance (including uncertainty from selection-conditional sensitivity/specificity),
+a Wald z-statistic, and a -log10 p-value with a large-|z| tail approximation.
+
+Core API
+--------
+lambda_or(tilde_counts, p_sel, q_sel, n_val, lambda_start=1e-6, lambda_max=1e6,
+          step=10.0, eps=1e-9) -> dict
+
+Helpers
+-------
+pq_from_two_gates(pi_H1, pi_L1, pi_H0, pi_L0) -> (p_sel, q_sel)
+
+Notation
+--------
+- tilde_counts: observed (misclassified) 2x2 counts as [[ã, b̃],[ĉ, d̃]]
+- p_sel = P(tilde Y=1 | Y=1, selected), q_sel = P(tilde Y=0 | Y=0, selected)
+- n_val: size of validation cohort used to estimate (p_sel, q_sel)
+
+References
+----------
+See manuscript text for derivations and delta-method variance.
+"""
+
+from __future__ import annotations
+from dataclasses import dataclass
+from math import log, sqrt, isfinite, erfc, pi, log10
+from typing import Tuple, Dict, Any, Optional
+import numpy as np
+
+
+@dataclass
+class LambdaORResult:
+    log_or: float
+    neglog10_p: float
+    z: float
+    se: float
+    counts: np.ndarray      # corrected 2x2 matrix [ [a,b], [c,d] ]
+    lambda_used: float
+    converged: bool
+    meta: Dict[str, Any]
+
+
+def _normal_two_sided_p(z_abs: float) -> float:
+    """Two-sided p-value using complementary error function (numerically stable)."""
+    # sf(|z|) = 0.5 * erfc(|z|/sqrt(2))
+    return 2.0 * 0.5 * erfc(z_abs / sqrt(2.0))
+
+
+def pq_from_two_gates(pi_H1: float, pi_L1: float, pi_H0: float, pi_L0: float) -> Tuple[float, float]:
+    """
+    Compute selection-conditional sensitivity/specificity from two-gate ROC probabilities:
+    - pi_H1 = P(S in high-specificity gate | Y=1)
+    - pi_L1 = P(S in low-specificity gate  | Y=1)
+    - pi_H0 = P(S in high-specificity gate | Y=0)
+    - pi_L0 = P(S in low-specificity gate  | Y=0)
+    Returns (p_sel, q_sel).
+    """
+    denom1 = pi_H1 + pi_L1
+    denom0 = pi_H0 + pi_L0
+    if denom1 <= 0 or denom0 <= 0:
+        raise ValueError("Invalid gate probabilities: denominators must be positive.")
+    p_sel = pi_H1 / denom1
+    q_sel = pi_L0 / denom0
+    return p_sel, q_sel
+
+
+def lambda_or(tilde_counts: np.ndarray,
+              p_sel: float,
+              q_sel: float,
+              n_val: int,
+              lambda_start: float = 1e-6,
+              lambda_max: float = 1e6,
+              step: float = 10.0,
+              eps: float = 1e-9) -> LambdaORResult:
+    """
+    Compute Λ-OR given a misclassified 2x2 table and selection-conditional (p_sel, q_sel).
+
+    Parameters
+    ----------
+    tilde_counts : array-like shape (2,2)
+        Observed (misclassified) counts [[ã, b̃],[ĉ, d̃]].
+    p_sel, q_sel : float
+        Selection-conditional sensitivity and specificity (from ROC gates).
+    n_val : int
+        Validation cohort size used to estimate (p_sel, q_sel) for variance propagation.
+    lambda_start, lambda_max : float
+        Ridge path start and upper bound.
+    step : float
+        Multiplicative factor for ridge path (e.g., 10.0).
+    eps : float
+        Numerical/feasibility floor for corrected counts.
+
+    Returns
+    -------
+    LambdaORResult
+        Structured result with fields (log_or, neglog10_p, z, se, counts, lambda_used, converged, meta).
+    """
+    Ttil = np.asarray(tilde_counts, dtype=float)
+    if Ttil.shape != (2,2):
+        raise ValueError("tilde_counts must be 2x2.")
+
+    if not (0.0 <= p_sel <= 1.0 and 0.0 <= q_sel <= 1.0):
+        raise ValueError("p_sel and q_sel must be in [0,1].")
+    if n_val <= 1:
+        raise ValueError("n_val must be > 1.")
+
+    # Misclassification matrix A
+    A = np.array([[p_sel, 1.0 - p_sel],
+                  [1.0 - q_sel, q_sel]], dtype=float)
+
+    lam = float(lambda_start)
+    converged = False
+    counts = None
+
+    while lam <= lambda_max:
+        A_lam = A + lam * np.eye(2)
+        try:
+            # counts = tilde T * (A_lam^{-T})
+            inv_AT = np.linalg.inv(A_lam).T
+            M = Ttil @ inv_AT
+        except np.linalg.LinAlgError:
+            lam *= step
+            continue
+
+        if np.all(M > eps) and np.all(np.isfinite(M)):
+            counts = M
+            converged = True
+            break
+        lam *= step
+
+    if not converged:
+        return LambdaORResult(
+            log_or=float('nan'),
+            neglog10_p=float('nan'),
+            z=float('nan'),
+            se=float('nan'),
+            counts=np.full((2,2), np.nan),
+            lambda_used=float('nan'),
+            converged=False,
+            meta={
+                "message": "Ridge path failed to find feasible counts.",
+                "lambda_max": lambda_max,
+                "p_sel": p_sel,
+                "q_sel": q_sel
+            }
+        )
+
+    a, b = counts[0,0], counts[0,1]
+    c, d = counts[1,0], counts[1,1]
+    # Corrected log odds ratio
+    log_or = log((a * d) / (b * c))
+
+    # Base variance
+    var_base = 1.0/a + 1.0/b + 1.0/c + 1.0/d
+
+    # Delta-method extra variance from (p_sel, q_sel)
+    J = p_sel + q_sel - 1.0
+    # Protect against divide by zero; if J ~ 0, variance will be huge anyway
+    denom = max(J*J, 1e-18)
+    ad = a * d
+    bc = b * c
+    dlog_dp = ((1.0 - q_sel) * (ad - bc)) / (denom * ad)
+    dlog_dq = ((1.0 - p_sel) * (bc - ad)) / (denom * ad)
+
+    var_p = p_sel * (1.0 - p_sel) / float(n_val)
+    var_q = q_sel * (1.0 - q_sel) / float(n_val)
+    var_extra = (dlog_dp ** 2) * var_p + (dlog_dq ** 2) * var_q
+
+    se = sqrt(var_base + var_extra)
+    z = log_or / se if se > 0 else float('inf')
+
+    # Two-sided p-value and -log10 p with asymptotic tail
+    z_abs = abs(z)
+    if z_abs <= 7.0:
+        p_two = _normal_two_sided_p(z_abs)
+        # Guard for underflow
+        p_two = max(min(p_two, 1.0), 1e-323)
+        neglog10_p = -log10(p_two)
+    else:
+        # Asymptotic: -log10 p ≈ z^2/(2 ln 10) - log10( sqrt(2π)*|z| )
+        neglog10_p = (z_abs*z_abs) / (2.0 * np.log(10.0)) - log10((2.0*pi)**0.5 * z_abs)
+
+    meta = {
+        "var_base": var_base,
+        "var_extra": var_extra,
+        "J": J,
+        "lambda_path_start": lambda_start,
+        "lambda_used": lam,
+        "step": step,
+        "eps": eps,
+        "p_sel": p_sel,
+        "q_sel": q_sel,
+        "n_val": n_val
+    }
+
+    return LambdaORResult(
+        log_or=log_or,
+        neglog10_p=neglog10_p,
+        z=z,
+        se=se,
+        counts=counts,
+        lambda_used=lam,
+        converged=converged,
+        meta=meta
+    )
+
+
+__all__ = ["lambda_or", "pq_from_two_gates", "LambdaORResult"]

lambda_or-0.0.2/lambda_or.egg-info/PKG-INFO

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+Metadata-Version: 2.1
+Name: lambda-or
+Version: 0.0.2
+Summary: Lambda Odds Ratio
+Home-page: https://github.com/zeroknowledgediscovery/lambda_or
+Download-URL: https://github.com/zeroknowledgediscovery/lambda_or/archive/0.0.2.tar.gz
+Author: Ishanu Chattopadhyay
+Author-email: zeroknowledgediscovery@gmail.com
+License: LICENSE
+Keywords: robust odds ratio,misclassification correction,machine learning,EHR databases
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Software Development :: Libraries
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.9
+Requires-Python: >=3.6
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+
+===============
+Qbiome
+===============
+
+.. class:: no-web no-pdf
+
+:Info: Draft link will be posted here
+:Author: ZeD Lab <zed.createuky.net>
+:Description: Robust Odds Ratio correcting label noise 
+:Documentation: 
+
+
+**Usage:**
+
+.. code-block::
+
+    from lambda_or import lambda_or, pq_from_two_gates
+
+    tilde = np.array([[100, 50],[ 80, 70]], dtype=float)
+    # Suppose selection-conditional rates from two-gate ROC:
+    p_sel, q_sel = 0.92, 0.90
+    res = lambda_or(tilde, p_sel, q_sel, n_val=2000)
+    
+    print(res.log_or, res.neglog10_p, res.z, res.se)
+    print(res.counts)   # corrected a,b,c,d
+

lambda_or-0.0.2/lambda_or.egg-info/SOURCES.txt

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+LICENSE
+MANIFEST.in
+README.rst
+setup.py
+version.py
+lambda_or/__init__.py
+lambda_or/lambda_or.py
+lambda_or.egg-info/PKG-INFO
+lambda_or.egg-info/SOURCES.txt
+lambda_or.egg-info/dependency_links.txt
+lambda_or.egg-info/requires.txt
+lambda_or.egg-info/top_level.txt

lambda_or-0.0.2/lambda_or.egg-info/dependency_links.txt

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+

lambda_or-0.0.2/lambda_or.egg-info/requires.txt

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+scikit-learn
+scipy
+numpy
+pandas

lambda_or-0.0.2/lambda_or.egg-info/top_level.txt

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+lambda_or

lambda_or-0.0.2/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

lambda_or-0.0.2/setup.py

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+from setuptools import setup, Extension, find_packages
+from codecs import open
+from os import path
+import warnings
+
+package_name = "lambda_or"
+example_dir = "examples/"
+example_data_dir = example_dir + "example_data/"
+
+version = {}
+with open("version.py") as fp:
+    exec(fp.read(), version)
+
+here = path.abspath(path.dirname(__file__))
+
+# Get the long description from the relevant file
+with open(path.join(here, "README.rst"), encoding="utf-8") as f:
+    long_description = f.read()
+
+
+setup(
+    name=package_name,
+    author="Ishanu Chattopadhyay",
+    author_email="zeroknowledgediscovery@gmail.com",
+    version=str(version["__version__"]),
+    packages=find_packages(),
+    scripts=[],
+    url="https://github.com/zeroknowledgediscovery/lambda_or",
+    license="LICENSE",
+    description="Lambda Odds Ratio",
+    keywords=[
+        "robust odds ratio",
+        "misclassification correction",
+        "machine learning",
+        "EHR databases",
+    ],
+    download_url="https://github.com/zeroknowledgediscovery/lambda_or/archive/"
+    + str(version["__version__"])
+    + ".tar.gz",
+    long_description=long_description,
+    long_description_content_type="text/x-rst",
+    install_requires=["scikit-learn", "scipy", "numpy", "pandas" ],
+    python_requires=">=3.6",
+    classifiers=[
+        "Development Status :: 4 - Beta",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "Topic :: Scientific/Engineering :: Information Analysis",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+        "Topic :: Software Development :: Libraries",
+        "License :: OSI Approved :: MIT License",
+        "Programming Language :: Python :: 3.9",
+    ],
+    include_package_data=True,
+)

lambda_or-0.0.2/version.py

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+__version__ = '0.0.2'