Merge branch 'main' into add_options_mixed

CODE_OF_CONDUCT.md

@@ -6,7 +6,7 @@ In the interest of fostering an open and welcoming environment, we as
 contributors and maintainers pledge to making participation in our project and
 our community a harassment-free experience for everyone, regardless of age, body
 size, disability, ethnicity, sex characteristics, gender identity and expression,
-level of experience, education, socio-economic status, nationality, personal
+level of experience, education, socioeconomic status, nationality, personal
 appearance, race, religion, or sexual identity and orientation.
 
 ## Our Standards

cebra/data/datasets.py

@@ -222,9 +222,9 @@ def __init__(
         else:
             self._cindex = None
         if discrete:
-            raise NotImplementedError(
-                "Multisession implementation does not support discrete index yet."
-            )
+            self._dindex = torch.cat(list(
+                self._iter_property("discrete_index")),
+                                     dim=0)
         else:
             self._dindex = None
 

cebra/data/multi_session.py

@@ -160,7 +160,16 @@ def index(self):
 
 @dataclasses.dataclass
 class DiscreteMultiSessionDataLoader(MultiSessionLoader):
-    pass
+    """Contrastive learning conditioned on a discrete behavior variable."""
+
+    # Overwrite sampler with the discrete implementation
+    # Generalize MultisessionSampler to avoid doing this?
+    def __post_init__(self):
+        self.sampler = cebra_distr.DiscreteMultisessionSampler(self.dataset)
+
+    @property
+    def index(self):
+        return self.dataset.discrete_index
 
 
 @dataclasses.dataclass

cebra/datasets/demo.py

@@ -111,15 +111,17 @@ def discrete_index(self):
         return self.dindex
 
 
-# TODO(stes) remove this from the demo datasets until multi-session training
-# with discrete indices is implemented in the sklearn API.
-# @register("demo-discrete-multisession")
+@register("demo-discrete-multisession")
 class MultiDiscrete(cebra.data.DatasetCollection):
     """Demo dataset for testing."""
 
-    def __init__(self, nums_neural=[3, 4, 5]):
+    def __init__(
+        self,
+        nums_neural=[3, 4, 5],
+        num_timepoints=_DEFAULT_NUM_TIMEPOINTS,
+    ):
         super().__init__(*[
-            DemoDatasetDiscrete(_DEFAULT_NUM_TIMEPOINTS, num_neural)
+            DemoDatasetDiscrete(num_timepoints, num_neural)
             for num_neural in nums_neural
         ])
 

cebra/datasets/make_neuropixel.py

@@ -171,7 +171,7 @@ def read_neuropixel(
 ):
     """Load 120Hz Neuropixels data recorded in the specified cortex during the movie1 stimulus.
 
-    The Neuropixels recordin is filtered and transformed to spike counts in a bin size specified by the sampling rat.
+    The Neuropixels recording is filtered and transformed to spike counts in a bin size specified by the sampling rat.
 
     Args:
         path: The wildcard file path where the neuropixels .nwb files are located.

cebra/distributions/multisession.py

@@ -259,3 +259,127 @@ def __getitem__(self, pos_idx):
         for i in range(self.num_sessions):
             pos_samples[i] = self.data[i][pos_idx[i]]
         return pos_samples
+
+
+class DiscreteMultisessionSampler(cebra_distr.PriorDistribution,
+                                  cebra_distr.ConditionalDistribution):
+    """Discrete multi-session sampling.
+
+    Discrete indices don't need to be aligned. Positive pairs are found
+    by matching the discrete index in randomly assigned sessions.
+
+    After data processing, the dimensionality of the returned features
+    matches. The resulting embeddings can be concatenated, and shuffling
+    (across the session axis) can be applied to the reference samples, or
+    reversed for the positive samples.
+
+    TODO:
+        * Add better CUDA support and refactor ``numpy`` implementation.
+    """
+
+    def __init__(self, dataset):
+        self.dataset = dataset
+
+        # TODO(stes): implement in pytorch
+        self.all_data = self.dataset.discrete_index.cpu().numpy()
+        self.session_lengths = np.array(self.dataset.session_lengths)
+
+        self.lengths = np.cumsum(self.session_lengths)
+        self.lengths[1:] = self.lengths[:-1]
+        self.lengths[0] = 0
+
+        self.index = [
+            cebra_distr.DiscreteUniform(
+                dataset.discrete_index.int().to(_device))
+            for dataset in self.dataset.iter_sessions()
+        ]
+
+    @property
+    def num_sessions(self) -> int:
+        """The number of sessions in the index."""
+        return len(self.lengths)
+
+    def mix(self, array: np.ndarray, idx: np.ndarray):
+        """Re-order array elements according to the given index mapping.
+
+        The given array should be of the shape ``(session, batch, ...)`` and the
+        indices should have length ``session x batch``, representing a mapping
+        between indices.
+
+        The resulting array will be rearranged such that
+        ``out.reshape(session*batch, -1)[i] = array.reshape(session*batch, -1)[idx[i]]``
+
+        For the inverse mapping, convert the indices first using ``_invert_index``
+        function.
+
+        Args:
+            array: A 2D matrix containing samples for each session.
+            idx: A list of indexes to re-order ``array`` on.
+        """
+        n, m = array.shape[:2]
+        return array.reshape(n * m, -1)[idx].reshape(array.shape)
+
+    def sample_prior(self, num_samples):
+        # TODO(stes) implement empirical/uniform resampling
+        ref_idx = np.random.uniform(0, 1, (self.num_sessions, num_samples))
+        ref_idx = (ref_idx * self.session_lengths[:, None]).astype(int)
+        return ref_idx
+
+    def sample_conditional(self, idx: torch.Tensor) -> torch.Tensor:
+        """Sample from the conditional distribution.
+
+        Note:
+            * Reference samples are sampled equally between sessions.
+            * In order to guarantee the same number of positive samples per
+              session, reference samples are randomly assigned to a session and its
+              corresponding positive sample is searched in that session only.
+            * As a result, ref/pos pairing is shuffled and can be recovered
+              the reverse shuffle operation.
+
+        Args:
+            idx: Reference indices, with dimension ``(session, batch)``.
+
+        Returns:
+            Positive indices (1st return value), which will be grouped by
+            session and *not* match the reference indices.
+            In addition, a mapping will be returned to apply the same shuffle operation
+            that was applied to assign reference samples to a session along session/batch dimension
+            (2nd return value), or reverse the shuffle operation (3rd return value).
+            Returned shapes are ``(session, batch), (session, batch), (session, batch)``.
+
+        TODO:
+            * re-implement in pytorch for additional speed gains
+        """
+
+        shape = idx.shape
+        # TODO(stes) unclear why we cannot restrict to 2d overall
+        # idx has shape (2, #samples per batch)
+        s = idx.shape[:2]
+        idx_all = (idx + self.lengths[:, None]).flatten()
+
+        # get discrete indices
+        query = self.all_data[idx_all]
+
+        # shuffle operation to assign each index to a session
+        idx = np.random.permutation(len(query))
+
+        # TODO this part fails in Pytorch
+        # apply shuffle
+        query = query[idx.reshape(s)]
+        query = torch.from_numpy(query).to(_device)
+
+        # sample conditional for each assigned session
+        pos_idx = torch.zeros(shape, device=_device).long()
+        for i in range(self.num_sessions):
+            pos_idx[i] = self.index[i].sample_conditional(query[i])
+        pos_idx = pos_idx.cpu().numpy()
+
+        # reverse indices to recover the ref/pos samples matching
+        idx_rev = _invert_index(idx)
+        return pos_idx, idx, idx_rev
+
+    def __getitem__(self, pos_idx):
+        pos_samples = np.zeros(pos_idx.shape[:2] + (self.data.shape[2],))
+        for i in range(self.num_sessions):
+            pos_samples[i] = self.data[i][pos_idx[i]]
+        return pos_samples

cebra/integrations/sklearn/cebra.py

@@ -153,6 +153,7 @@ def _require_arg(key):
 
         # Discrete behavior contrastive training is selected with the default dataloader
         if not is_cont and is_disc:
+            kwargs = dict(**shared_kwargs,)
             if is_full:
                 if is_hybrid:
                     raise_not_implemented_error = True
@@ -162,7 +163,10 @@ def _require_arg(key):
                 if is_hybrid:
                     raise_not_implemented_error = True
                 else:
-                    raise_not_implemented_error = True
+                    return (
+                        cebra.data.DiscreteMultiSessionDataLoader(**kwargs),
+                        "multi-session",
+                    )
 
         # Mixed behavior contrastive training is selected with the default dataloader
         if is_cont and is_disc:
@@ -1030,7 +1034,6 @@ def _partial_fit(
             if callback is None:
                 raise ValueError(
                     "callback_frequency requires to specify a callback.")
-
         model.train()
 
         solver.fit(

docs/source/conf.py

@@ -108,7 +108,7 @@ def get_years(start_year=2021):
     "sklearn": ("https://scikit-learn.org/stable", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),
-    "pandas": ("http://pandas.pydata.org/pandas-docs/dev", None),
+    "pandas": ("https://pandas.pydata.org/docs/", None),
     "scipy": ("http://docs.scipy.org/doc/scipy/reference/", None),
     "joblib": ("https://joblib.readthedocs.io/en/latest/", None),
     "plotly": ("https://plotly.com/python-api-reference/", None)

docs/source/usage.rst

@@ -12,7 +12,7 @@ Firstly, why use CEBRA?
 
 CEBRA is primarily designed for producing robust, consistent extractions of latent factors from time-series data. It supports three modes, and is a self-supervised representation learning algorithm that uses our modified contrastive learning approach designed for multi-modal time-series data. In short, it is a type of non-linear dimensionality reduction, like `tSNE <https://www.jmlr.org/papers/v9/vandermaaten08a.html>`_ and `UMAP <https://arxiv.org/abs/1802.03426>`_. We show in our original paper that it outperforms tSNE and UMAP at producing closer-to-ground-truth latents and is more consistent.
 
-That being said, CEBRA can be used on non-time-series data and it does not strictly require multi-modal data. In general, we recommend considering using CEBRA for measuring changes in consistency across conditions (brain areas, cells, animals), for hypothesis-guided decoding, and for toplogical exploration of the resulting embedding spaces. It can also be used for visualization and considering dynamics within the embedding space. For examples of how CEBRA can be used to map space, decode natural movies, and make hypotheses for neural coding of sensorimotor systems, see our paper (Schneider, Lee, Mathis, 2023).
+That being said, CEBRA can be used on non-time-series data and it does not strictly require multi-modal data. In general, we recommend considering using CEBRA for measuring changes in consistency across conditions (brain areas, cells, animals), for hypothesis-guided decoding, and for topological exploration of the resulting embedding spaces. It can also be used for visualization and considering dynamics within the embedding space. For examples of how CEBRA can be used to map space, decode natural movies, and make hypotheses for neural coding of sensorimotor systems, see our paper (Schneider, Lee, Mathis, 2023).
 
 The CEBRA workflow
 ------------------
@@ -419,10 +419,10 @@ We can now fit the model in different modes.
 
 .. rubric:: Multi-session training
 
-For multi-sesson training, lists of data are provided instead of a single dataset and eventual corresponding auxiliary variables.
+For multi-session training, lists of data are provided instead of a single dataset and eventual corresponding auxiliary variables.
 
 .. warning::
-    For now, multi-session training can only handle a **unique set of continuous labels**. All other combinations will raise an error.
+    For now, multi-session training can only handle a **unique set of continuous labels** or a **unique discrete label**. All other combinations will raise an error. For the continuous case we provide the following example:
 
 
 .. testcode::
@@ -450,6 +450,29 @@ Once you defined your CEBRA model, you can run:
     multi_cebra_model.fit([neural_session1, neural_session2], [continuous_label1, continuous_label2])
 
 
+Similarly, for the discrete case a discrete label can be provided and the CEBRA model will use the discrete multisession mode:
+
+.. testcode::
+
+    timesteps1 = 5000
+    timesteps2 = 3000
+    neurons1 = 50
+    neurons2 = 30
+    out_dim = 8
+
+    neural_session1 = np.random.normal(0,1,(timesteps1, neurons1))
+    neural_session2 = np.random.normal(0,1,(timesteps2, neurons2))
+    discrete_label1 = np.random.randint(0,10,(timesteps1, ))
+    discrete_label2 = np.random.randint(0,10,(timesteps2, ))
+
+    multi_cebra_model = cebra.CEBRA(batch_size=512,
+                                    output_dimension=out_dim,
+                                    max_iterations=10,
+                                    max_adapt_iterations=10)
+
+
+    multi_cebra_model.fit([neural_session1, neural_session2], [discrete_label1, discrete_label2])
+
 .. admonition:: See API docs
     :class: dropdown
 

setup.cfg

@@ -89,11 +89,11 @@ dev =
     isort
     toml
     coverage
-    pytest
+    pytest==7.4.4
     pytest-benchmark
     pytest-xdist
     pytest-timeout
-    pytest-sphinx
+    pytest-sphinx==0.5.0
     tables<=3.8
     licenseheaders
     # TODO(stes) Add back once upstream issue
@@ -105,3 +105,4 @@ dev =
 
 [bdist_wheel]
 universal=1
+

tests/test_distributions.py

@@ -298,6 +298,31 @@ def test_multi_session_time_contrastive(time_offset):
         len(rev_idx.flatten())).all())
 
 
+def test_multi_session_discrete():
+    dataset = cebra_datasets.init("demo-discrete-multisession")
+    sampler = cebra_distr.DiscreteMultisessionSampler(dataset)
+
+    num_samples = 5
+    sample = sampler.sample_prior(num_samples)
+    assert sample.shape == (dataset.num_sessions, num_samples)
+
+    positive, idx, rev_idx = sampler.sample_conditional(sample)
+    assert positive.shape == (dataset.num_sessions, num_samples)
+    assert idx.shape == (dataset.num_sessions * num_samples,)
+    assert rev_idx.shape == (dataset.num_sessions * num_samples,)
+    # NOTE(celia): test the private function ``_inverse_idx()``, with idx arrays flat
+    assert (idx.flatten()[rev_idx.flatten()].all() == np.arange(
+        len(rev_idx.flatten())).all())
+
+    # Check positive samples' labels match reference samples' labels
+    sample_labels = sampler.all_data[(sample +
+                                      sampler.lengths[:, None]).flatten()]
+    sample_labels = sample_labels[idx.reshape(sample.shape[:2])].flatten()
+    positive_labels = sampler.all_data[(positive +
+                                        sampler.lengths[:, None]).flatten()]
+    assert (sample_labels == positive_labels).all()
+
+
 class OldDeltaDistribution(cebra_distr_base.JointDistribution,
                            cebra_distr_base.HasGenerator):
     """

tests/test_integration_train.py

@@ -35,6 +35,11 @@
 import cebra.models
 import cebra.solver
 
+if torch.cuda.is_available():
+    _DEVICE = "cuda"
+else:
+    _DEVICE = "cpu"
+
 
 def _init_single_session_solver(loader, args):
     """Train a single session CEBRA model."""
@@ -77,6 +82,7 @@ def _list_data_loaders():
         cebra.data.HybridDataLoader,
         cebra.data.FullDataLoader,
         cebra.data.ContinuousMultiSessionDataLoader,
+        cebra.data.DiscreteMultiSessionDataLoader,
     ]
     # TODO limit this to the valid combinations---however this
     # requires to adapt the dataset API slightly; it is currently
@@ -95,7 +101,7 @@ def _list_data_loaders():
 @pytest.mark.requires_dataset
 @pytest.mark.parametrize("dataset_name, loader_type", _list_data_loaders())
 def test_train(dataset_name, loader_type):
-    args = cebra.config.Config(num_steps=1, device="cuda").as_namespace()
+    args = cebra.config.Config(num_steps=1, device=_DEVICE).as_namespace()
 
     dataset = cebra.datasets.init(dataset_name)
     if loader_type not in cebra_data_helper.get_loader_options(dataset):