unicorn-eval 1.0__tar.gz

unicorn_eval-1.0/LICENSE

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unicorn_eval-1.0/MANIFEST.in

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+include README.md
+include LICENSE
+recursive-include src/unicorn_eval *.py

unicorn_eval-1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: unicorn_eval
+Version: 1.0
+Summary: Evaluation and adaption method for the UNICORN Challenge
+Home-page: https://github.com/DIAGNijmegen/unicorn_eval
+Author: Joeran Bosma, Clément Grisi, Marina D`Amato, Luc Builtjes, Lena Philipp, Fennie van der Graaf, Judith Lefkes, Michelle Stegeman, Rianne Weber
+Author-email: Clement.Grisi@radboudumc.nl
+Project-URL: Bug Tracker, https://github.com/DIAGNijmegen/unicorn_eval/issues
+Platform: unix
+Platform: linux
+Platform: osx
+Platform: cygwin
+Platform: win32
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: scikit-learn==1.1.1
+Requires-Dist: numpy==1.26.1
+Requires-Dist: pandas
+Requires-Dist: psutil
+Requires-Dist: torch==2.0.1
+Requires-Dist: torchvision==0.15.2
+Requires-Dist: scikit-survival
+Requires-Dist: pycocoevalcap
+Requires-Dist: transformers==4.28.1
+Requires-Dist: bert_score
+Requires-Dist: evalutils==0.3.1
+Requires-Dist: openslide-python
+Requires-Dist: pycm
+Provides-Extra: testing
+Requires-Dist: pytest>=6.0; extra == "testing"
+Requires-Dist: pytest-cov>=2.0; extra == "testing"
+Requires-Dist: mypy>=0.910; extra == "testing"
+Requires-Dist: flake8>=3.9; extra == "testing"
+Requires-Dist: tox>=3.24; extra == "testing"
+Dynamic: author-email
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: project-url
+
+# 🧪 UNICORN Evaluation Toolkit
+
+Welcome to the official evaluation repository for the [UNICORN Challenge](https://unicorn.grand-challenge.org/) — a benchmark for foundation models in pathology, radiology and medical language processing. This repository provides the code used to evaluate submissions using frozen foundation model features. It ships with a set of feature adaptors that convert features into predictions and expects to community to contribute with custom & more fancy adaptors.
+
+## 🚀 Goal
+
+The challenge evaluates how well foundation models generalize across tasks without extensive fine-tuning. For language and vision-language tasks, the model should yield the prediction. For vision tasks, we adapt features using light-weight methods (adaptors). Participants are invited to use built-in adaptors or propose their own!
+
+## 🧩 Custom Adaptors
+
+Want to use a custom method to convert vision features to predictions?
+
+- add your adaptor under the adaptors/ directory
+- submit a pull request with a short description of your method, giving it a unique name that can be selected at submission time
+
+Once approved and merged, you’ll be able to submit your model using your custom adaptor.
+
+⚠️ All adaptors must follow the base adaptor interface (see `adaptors/base.py`).

unicorn_eval-1.0/README.md

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+# 🧪 UNICORN Evaluation Toolkit
+
+Welcome to the official evaluation repository for the [UNICORN Challenge](https://unicorn.grand-challenge.org/) — a benchmark for foundation models in pathology, radiology and medical language processing. This repository provides the code used to evaluate submissions using frozen foundation model features. It ships with a set of feature adaptors that convert features into predictions and expects to community to contribute with custom & more fancy adaptors.
+
+## 🚀 Goal
+
+The challenge evaluates how well foundation models generalize across tasks without extensive fine-tuning. For language and vision-language tasks, the model should yield the prediction. For vision tasks, we adapt features using light-weight methods (adaptors). Participants are invited to use built-in adaptors or propose their own!
+
+## 🧩 Custom Adaptors
+
+Want to use a custom method to convert vision features to predictions?
+
+- add your adaptor under the adaptors/ directory
+- submit a pull request with a short description of your method, giving it a unique name that can be selected at submission time
+
+Once approved and merged, you’ll be able to submit your model using your custom adaptor.
+
+⚠️ All adaptors must follow the base adaptor interface (see `adaptors/base.py`).

unicorn_eval-1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=42.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.pytest.ini_options]
+addopts = "--cov=unicorn_eval"
+testpaths = [
+    "tests",
+]
+
+[tool.mypy]
+mypy_path = "."
+check_untyped_defs = true
+disallow_any_generics = true
+ignore_missing_imports = true
+no_implicit_optional = true
+show_error_codes = true
+strict_equality = true
+warn_redundant_casts = true
+warn_return_any = true
+warn_unreachable = true
+warn_unused_configs = true
+no_implicit_reexport = true

unicorn_eval-1.0/setup.cfg

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+[metadata]
+name = unicorn_eval
+version = 1.0
+description = Evaluation and adaption method for the UNICORN Challenge
+author = Joeran Bosma, Clément Grisi, Marina D`Amato, Luc Builtjes, Lena Philipp, Fennie van der Graaf, Judith Lefkes, Michelle Stegeman, Rianne Weber
+platforms = unix, linux, osx, cygwin, win32
+classifiers = 
+	Programming Language :: Python :: 3
+	Programming Language :: Python :: 3 :: Only
+	Programming Language :: Python :: 3.10
+	Programming Language :: Python :: 3.11
+	Programming Language :: Python :: 3.12
+	Programming Language :: Python :: 3.13
+
+[options]
+packages = 
+	unicorn_eval
+install_requires = 
+	scikit-learn==1.1.1
+	numpy==1.26.1
+	pandas
+	psutil
+	torch==2.0.1
+	torchvision==0.15.2
+	scikit-survival
+	pycocoevalcap
+	transformers==4.28.1
+	bert_score
+	evalutils==0.3.1
+	openslide-python
+	pycm
+python_requires = >=3.10
+package_dir = 
+	=src
+zip_safe = no
+include_package_data = True
+
+[options.extras_require]
+testing = 
+	pytest>=6.0
+	pytest-cov>=2.0
+	mypy>=0.910
+	flake8>=3.9
+	tox>=3.24
+
+[options.package_data]
+unicorn_eval = py.typed
+
+[flake8]
+max-line-length = 160
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

unicorn_eval-1.0/setup.py

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+import setuptools
+
+if __name__ == "__main__":
+    with open("README.md", "r", encoding="utf-8") as fh:
+        long_description = fh.read()
+
+    setuptools.setup(
+        author_email="Clement.Grisi@radboudumc.nl",
+        long_description=long_description,
+        long_description_content_type="text/markdown",
+        url="https://github.com/DIAGNijmegen/unicorn_eval",
+        project_urls={
+            "Bug Tracker": "https://github.com/DIAGNijmegen/unicorn_eval/issues"
+        },
+        package_dir={"": "src"},  # our packages live under src, but src is not a package itself
+        packages=setuptools.find_packages("src", exclude=["tests"]),
+        exclude_package_data={"": ["tests"]},
+        entry_points={
+            "console_scripts": [
+                "unicorn_eval = unicorn_eval.evaluate:main",
+            ],
+        },
+    )

unicorn_eval-1.0/src/unicorn_eval/__init__.py

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+#  Copyright 2025 Diagnostic Image Analysis Group, Radboudumc, Nijmegen, The Netherlands
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.

unicorn_eval-1.0/src/unicorn_eval/adaptors/__init__.py

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+#  Copyright 2025 Diagnostic Image Analysis Group, Radboudumc, Nijmegen, The Netherlands
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+from unicorn_eval.adaptors.classification import (
+    KNN,
+    WeightedKNN,
+    LogisticRegression,
+    LinearProbing,
+    MLP,
+)
+from unicorn_eval.adaptors.detection import DensityMap
+from unicorn_eval.adaptors.segmentation import SegmentationUpsampling
+
+__all__ = [
+    "KNN",
+    "WeightedKNN",
+    "LogisticRegression",
+    "LinearProbing",
+    "MLP",
+    "DensityMap",
+    "SegmentationUpsampling",
+]

unicorn_eval-1.0/src/unicorn_eval/adaptors/base.py

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+from abc import ABC, abstractmethod
+import numpy as np
+
+
+class BaseAdaptor(ABC):
+    """
+    Base class for coarse-grained tasks like classification or regression.
+    Expects train_feats, train_labels, and test_feats.
+    """
+
+    def __init__(self, train_feats: np.ndarray, train_labels: np.ndarray, test_feats: np.ndarray):
+        self.train_feats = train_feats
+        self.train_labels = train_labels
+        self.test_feats = test_feats
+
+    @abstractmethod
+    def fit(self):
+        """
+        Fit the model using train_feats and train_labels.
+        """
+        pass
+
+    @abstractmethod
+    def predict(self) -> np.ndarray:
+        """
+        Predict using test_feats.
+        Returns:
+            np.ndarray: Predictions for the test set.
+        """
+        pass
+
+
+class DenseAdaptor(BaseAdaptor):
+    """
+    Base class for dense prediction tasks like detection or segmentation.
+    Expects train_feats, train_labels, test_feats, train_coordinates, and test_coordinates.
+    """
+
+    def __init__(
+        self,
+        train_feats: np.ndarray,
+        train_labels: np.ndarray,
+        test_feats: np.ndarray,
+        train_coordinates: np.ndarray,
+        test_coordinates: np.ndarray,
+    ):
+        super().__init__(train_feats, train_labels, test_feats)
+        self.train_coordinates = train_coordinates
+        self.test_coordinates = test_coordinates
+
+    @abstractmethod
+    def fit(self):
+        """
+        Fit the model using train_feats, train_labels, and train_coordinates.
+        """
+        pass
+
+    @abstractmethod
+    def predict(self) -> np.ndarray:
+        """
+        Predict using test_feats and test_coordinates.
+        Returns:
+            np.ndarray: Predictions for the test set.
+        """
+        pass