Add improved goodness of fit implementation (#190)

* Started implementing improved goodness of fit implementation

* add tests and improve implementation

* Fix examples

* Fix docstring error

* Handle batch size = None for goodness of fit computation

* adapt GoF implementation

* Fix docstring tests

* Update docstring for goodness_of_fit_score

Co-authored-by: Célia Benquet <[email protected]>

* add annotations to goodness_of_fit_history

Co-authored-by: Célia Benquet <[email protected]>

* fix typo

Co-authored-by: Célia Benquet <[email protected]>

* improve err message

Co-authored-by: Célia Benquet <[email protected]>

* make numerical test less conversative

* Add tests for exception handling

* fix tests

---------

Co-authored-by: Célia Benquet <[email protected]>

cebra/integrations/sklearn/metrics.py

@@ -108,6 +108,149 @@ def infonce_loss(
     return avg_loss
 
 
+def goodness_of_fit_score(cebra_model: cebra_sklearn_cebra.CEBRA,
+                          X: Union[npt.NDArray, torch.Tensor],
+                          *y,
+                          session_id: Optional[int] = None,
+                          num_batches: int = 500) -> float:
+    """Compute the goodness of fit score on a *single session* dataset on the model.
+
+    This function uses the :func:`infonce_loss` function to compute the InfoNCE loss
+    for a given `cebra_model` and the :func:`infonce_to_goodness_of_fit` function
+    to derive the goodness of fit from the InfoNCE loss.
+
+    Args:
+        cebra_model: The model to use to compute the InfoNCE loss on the samples.
+        X: A 2D data matrix, corresponding to a *single session* recording.
+        y: An arbitrary amount of continuous indices passed as 2D matrices, and up to one
+            discrete index passed as a 1D array. Each index has to match the length of ``X``.
+        session_id: The session ID, an :py:class:`int` between 0 and :py:attr:`cebra.CEBRA.num_sessions`
+            for multisession, set to ``None`` for single session.
+        num_batches: The number of iterations to consider to evaluate the model on the new data.
+            Higher values will give a more accurate estimate. Set it to at least 500 iterations.
+
+    Returns:
+        The average GoF score estimated over ``num_batches`` batches from the data distribution.
+
+    Related:
+        :func:`infonce_to_goodness_of_fit`
+
+    Example:
+
+        >>> import cebra
+        >>> import numpy as np
+        >>> neural_data = np.random.uniform(0, 1, (1000, 20))
+        >>> cebra_model = cebra.CEBRA(max_iterations=10, batch_size = 512)
+        >>> cebra_model.fit(neural_data)
+        CEBRA(batch_size=512, max_iterations=10)
+        >>> gof = cebra.sklearn.metrics.goodness_of_fit_score(cebra_model, neural_data)
+    """
+    loss = infonce_loss(cebra_model,
+                        X,
+                        *y,
+                        session_id=session_id,
+                        num_batches=num_batches,
+                        correct_by_batchsize=False)
+    return infonce_to_goodness_of_fit(loss, cebra_model)
+
+
+def goodness_of_fit_history(model: cebra_sklearn_cebra.CEBRA) -> np.ndarray:
+    """Return the history of the goodness of fit score.
+
+    Args:
+        model: A trained CEBRA model.
+
+    Returns:
+        A numpy array containing the goodness of fit values, measured in bits.
+
+    Related:
+        :func:`infonce_to_goodness_of_fit`
+
+    Example:
+
+        >>> import cebra
+        >>> import numpy as np
+        >>> neural_data = np.random.uniform(0, 1, (1000, 20))
+        >>> cebra_model = cebra.CEBRA(max_iterations=10, batch_size = 512)
+        >>> cebra_model.fit(neural_data)
+        CEBRA(batch_size=512, max_iterations=10)
+        >>> gof_history = cebra.sklearn.metrics.goodness_of_fit_history(cebra_model)
+    """
+    infonce = np.array(model.state_dict_["log"]["total"])
+    return infonce_to_goodness_of_fit(infonce, model)
+
+
+def infonce_to_goodness_of_fit(
+        infonce: Union[float, np.ndarray],
+        model: Optional[cebra_sklearn_cebra.CEBRA] = None,
+        batch_size: Optional[int] = None,
+        num_sessions: Optional[int] = None) -> Union[float, np.ndarray]:
+    """Given a trained CEBRA model, return goodness of fit metric.
+
+    The goodness of fit ranges from 0 (lowest meaningful value)
+    to a positive number with the unit "bits", the higher the
+    better.
+
+    Values lower than 0 bits are possible, but these only occur
+    due to numerical effects. A perfectly collapsed embedding
+    (e.g., because the data cannot be fit with the provided
+    auxiliary variables) will have a goodness of fit of 0.
+
+    The conversion between the generalized InfoNCE metric that
+    CEBRA is trained with and the goodness of fit computed with this
+    function is
+
+    .. math::
+
+        S = \\log N - \\text{InfoNCE}
+
+    To use this function, either provide a trained CEBRA model or the
+    batch size and number of sessions.
+
+    Args:
+        infonce: The InfoNCE loss, either a single value or an iterable of values.
+        model: The trained CEBRA model.
+        batch_size: The batch size used to train the model.
+        num_sessions: The number of sessions used to train the model.
+
+    Returns:
+        Numpy array containing the goodness of fit values, measured in bits
+
+    Raises:
+        RuntimeError: If the provided model is not fit to data.
+        ValueError: If both ``model`` and ``(batch_size, num_sessions)`` are provided.
+    """
+    if model is not None:
+        if batch_size is not None or num_sessions is not None:
+            raise ValueError(
+                "batch_size and num_sessions should not be provided if model is provided."
+            )
+        if not hasattr(model, "state_dict_"):
+            raise RuntimeError("Fit the CEBRA model first.")
+        if model.batch_size is None:
+            raise ValueError(
+                "Computing the goodness of fit is not yet supported for "
+                "models trained on the full dataset (batchsize = None). ")
+        batch_size = model.batch_size
+        num_sessions = model.num_sessions_
+        if num_sessions is None:
+            num_sessions = 1
+
+        if model.batch_size is None:
+            raise ValueError(
+                "Computing the goodness of fit is not yet supported for "
+                "models trained on the full dataset (batchsize = None). ")
+    else:
+        if batch_size is None or num_sessions is None:
+            raise ValueError(
+                f"batch_size ({batch_size}) and num_sessions ({num_sessions})"
+                f"should be provided if model is not provided.")
+
+    nats_to_bits = np.log2(np.e)
+    chance_level = np.log(batch_size * num_sessions)
+    return (chance_level - infonce) * nats_to_bits
+
+
 def _consistency_scores(
     embeddings: List[Union[npt.NDArray, torch.Tensor]],
     datasets: List[Union[int, str]],

tests/test_sklearn_metrics.py

@@ -383,3 +383,132 @@ def test_sklearn_runs_consistency():
     with pytest.raises(ValueError, match="Invalid.*embeddings"):
         _, _, _ = cebra_sklearn_metrics.consistency_score(
             invalid_embeddings_runs, between="runs")
+
+
+@pytest.mark.parametrize("seed", [42, 24, 10])
+def test_goodness_of_fit_score(seed):
+    """
+    Ensure that the GoF score is close to 0 for a model fit on random data.
+    """
+    cebra_model = cebra_sklearn_cebra.CEBRA(
+        model_architecture="offset1-model",
+        max_iterations=5,
+        batch_size=512,
+    )
+    generator = torch.Generator().manual_seed(seed)
+    X = torch.rand(5000, 50, dtype=torch.float32, generator=generator)
+    y = torch.rand(5000, 5, dtype=torch.float32, generator=generator)
+    cebra_model.fit(X, y)
+    score = cebra_sklearn_metrics.goodness_of_fit_score(cebra_model,
+                                                        X,
+                                                        y,
+                                                        session_id=0,
+                                                        num_batches=500)
+    assert isinstance(score, float)
+    assert np.isclose(score, 0, atol=0.01)
+
+
+@pytest.mark.parametrize("seed", [42, 24, 10])
+def test_goodness_of_fit_history(seed):
+    """
+    Ensure that the GoF score is higher for a model fit on data with underlying
+    structure than for a model fit on random data.
+    """
+
+    # Generate data
+    generator = torch.Generator().manual_seed(seed)
+    X = torch.rand(1000, 50, dtype=torch.float32, generator=generator)
+    y_random = torch.rand(len(X), 5, dtype=torch.float32, generator=generator)
+    linear_map = torch.randn(50, 5, dtype=torch.float32, generator=generator)
+    y_linear = X @ linear_map
+
+    def _fit_and_get_history(X, y):
+        cebra_model = cebra_sklearn_cebra.CEBRA(
+            model_architecture="offset1-model",
+            max_iterations=150,
+            batch_size=512,
+            device="cpu")
+        cebra_model.fit(X, y)
+        history = cebra_sklearn_metrics.goodness_of_fit_history(cebra_model)
+        # NOTE(stes): Ignore the first 5 iterations, they can have nonsensical values
+        # due to numerical issues.
+        return history[5:]
+
+    history_random = _fit_and_get_history(X, y_random)
+    history_linear = _fit_and_get_history(X, y_linear)
+
+    assert isinstance(history_random, np.ndarray)
+    assert history_random.shape[0] > 0
+    # NOTE(stes): Ignore the first 5 iterations, they can have nonsensical values
+    # due to numerical issues.
+    history_random_non_negative = history_random[history_random >= 0]
+    np.testing.assert_allclose(history_random_non_negative, 0, atol=0.075)
+
+    assert isinstance(history_linear, np.ndarray)
+    assert history_linear.shape[0] > 0
+
+    assert np.all(history_linear[-20:] > history_random[-20:])
+
+
+@pytest.mark.parametrize("seed", [42, 24, 10])
+def test_infonce_to_goodness_of_fit(seed):
+    """Test the conversion from InfoNCE loss to goodness of fit metric."""
+    # Test with model
+    cebra_model = cebra_sklearn_cebra.CEBRA(
+        model_architecture="offset10-model",
+        max_iterations=5,
+        batch_size=128,
+    )
+    generator = torch.Generator().manual_seed(seed)
+    X = torch.rand(1000, 50, dtype=torch.float32, generator=generator)
+    cebra_model.fit(X)
+
+    # Test single value
+    gof = cebra_sklearn_metrics.infonce_to_goodness_of_fit(1.0,
+                                                           model=cebra_model)
+    assert isinstance(gof, float)
+
+    # Test array of values
+    infonce_values = np.array([1.0, 2.0, 3.0])
+    gof_array = cebra_sklearn_metrics.infonce_to_goodness_of_fit(
+        infonce_values, model=cebra_model)
+    assert isinstance(gof_array, np.ndarray)
+    assert gof_array.shape == infonce_values.shape
+
+    # Test with explicit batch_size and num_sessions
+    gof = cebra_sklearn_metrics.infonce_to_goodness_of_fit(1.0,
+                                                           batch_size=128,
+                                                           num_sessions=1)
+    assert isinstance(gof, float)
+
+    # Test error cases
+    with pytest.raises(ValueError, match="batch_size.*should not be provided"):
+        cebra_sklearn_metrics.infonce_to_goodness_of_fit(1.0,
+                                                         model=cebra_model,
+                                                         batch_size=128)
+
+    with pytest.raises(ValueError, match="batch_size.*should not be provided"):
+        cebra_sklearn_metrics.infonce_to_goodness_of_fit(1.0,
+                                                         model=cebra_model,
+                                                         num_sessions=1)
+
+    # Test with unfitted model
+    unfitted_model = cebra_sklearn_cebra.CEBRA(max_iterations=5)
+    with pytest.raises(RuntimeError, match="Fit the CEBRA model first"):
+        cebra_sklearn_metrics.infonce_to_goodness_of_fit(1.0,
+                                                         model=unfitted_model)
+
+    # Test with model having batch_size=None
+    none_batch_model = cebra_sklearn_cebra.CEBRA(batch_size=None,
+                                                 max_iterations=5)
+    none_batch_model.fit(X)
+    with pytest.raises(ValueError, match="Computing the goodness of fit"):
+        cebra_sklearn_metrics.infonce_to_goodness_of_fit(1.0,
+                                                         model=none_batch_model)
+
+    # Test missing batch_size or num_sessions when model is None
+    with pytest.raises(ValueError, match="batch_size.*and num_sessions"):
+        cebra_sklearn_metrics.infonce_to_goodness_of_fit(1.0, batch_size=128)
+
+    with pytest.raises(ValueError, match="batch_size.*and num_sessions"):
+        cebra_sklearn_metrics.infonce_to_goodness_of_fit(1.0, num_sessions=1)