pyg-nightly 2.7.0.dev20250114__tar.gz → 2.7.0.dev20250118__tar.gz

{pyg_nightly-2.7.0.dev20250114 → pyg_nightly-2.7.0.dev20250118}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pyg-nightly
-Version: 2.7.0.dev20250114
+Version: 2.7.0.dev20250118
 Summary: Graph Neural Network Library for PyTorch
 Keywords: deep-learning,pytorch,geometric-deep-learning,graph-neural-networks,graph-convolutional-networks
 Author-email: Matthias Fey <matthias@pyg.org>

{pyg_nightly-2.7.0.dev20250114 → pyg_nightly-2.7.0.dev20250118}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend="flit_core.buildapi"
 
 [project]
 name="pyg-nightly"
-version="2.7.0.dev20250114"
+version="2.7.0.dev20250118"
 authors=[
     {name="Matthias Fey", email="matthias@pyg.org"},
 ]

{pyg_nightly-2.7.0.dev20250114 → pyg_nightly-2.7.0.dev20250118}/torch_geometric/__init__.py

@@ -30,7 +30,7 @@ from .lazy_loader import LazyLoader
 contrib = LazyLoader('contrib', globals(), 'torch_geometric.contrib')
 graphgym = LazyLoader('graphgym', globals(), 'torch_geometric.graphgym')
 
-__version__ = '2.7.0.dev20250114'
+__version__ = '2.7.0.dev20250118'
 
 __all__ = [
     'Index',

{pyg_nightly-2.7.0.dev20250114 → pyg_nightly-2.7.0.dev20250118}/torch_geometric/datasets/ppi.py

@@ -107,7 +107,8 @@ class PPI(InMemoryDataset):
         for s, split in enumerate(['train', 'valid', 'test']):
             path = osp.join(self.raw_dir, f'{split}_graph.json')
             with open(path) as f:
-                G = nx.DiGraph(json_graph.node_link_graph(json.load(f)))
+                G = nx.DiGraph(
+                    json_graph.node_link_graph(json.load(f), edges="links"))
 
             x = np.load(osp.join(self.raw_dir, f'{split}_feats.npy'))
             x = torch.from_numpy(x).to(torch.float)

pyg_nightly-2.7.0.dev20250118/torch_geometric/metrics/link_pred.py

@@ -0,0 +1,515 @@
+from dataclasses import dataclass
+from typing import Dict, List, Optional, Tuple, Union
+
+import torch
+from torch import Tensor
+
+from torch_geometric.utils import cumsum, scatter
+
+try:
+    import torchmetrics  # noqa
+    WITH_TORCHMETRICS = True
+    BaseMetric = torchmetrics.Metric
+except Exception:
+    WITH_TORCHMETRICS = False
+    BaseMetric = torch.nn.Module  # type: ignore
+
+
+@dataclass(repr=False)
+class LinkPredMetricData:
+    pred_index_mat: Tensor
+    edge_label_index: Union[Tensor, Tuple[Tensor, Tensor]]
+    edge_label_weight: Optional[Tensor] = None
+
+    @property
+    def pred_rel_mat(self) -> Tensor:
+        r"""Returns a matrix indicating the relevance of the `k`-th prediction.
+        If :obj:`edge_label_weight` is not given, relevance will be denoted as
+        binary.
+        """
+        if hasattr(self, '_pred_rel_mat'):
+            return self._pred_rel_mat  # type: ignore
+
+        # Flatten both prediction and ground-truth indices, and determine
+        # overlaps afterwards via `torch.searchsorted`.
+        max_index = max(  # type: ignore
+            self.pred_index_mat.max()
+            if self.pred_index_mat.numel() > 0 else 0,
+            self.edge_label_index[1].max()
+            if self.edge_label_index[1].numel() > 0 else 0,
+        ) + 1
+        arange = torch.arange(
+            start=0,
+            end=max_index * self.pred_index_mat.size(0),  # type: ignore
+            step=max_index,  # type: ignore
+            device=self.pred_index_mat.device,
+        ).view(-1, 1)
+        flat_pred_index = (self.pred_index_mat + arange).view(-1)
+        flat_label_index = max_index * self.edge_label_index[0]
+        flat_label_index = flat_label_index + self.edge_label_index[1]
+        flat_label_index, perm = flat_label_index.sort()
+        edge_label_weight = self.edge_label_weight
+        if edge_label_weight is not None:
+            assert edge_label_weight.size() == self.edge_label_index[0].size()
+            edge_label_weight = edge_label_weight[perm]
+
+        pos = torch.searchsorted(flat_label_index, flat_pred_index)
+        pos = pos.clamp(max=flat_label_index.size(0) - 1)  # Out-of-bounds.
+
+        pred_rel_mat = flat_label_index[pos] == flat_pred_index  # Find matches
+        if edge_label_weight is not None:
+            pred_rel_mat = edge_label_weight[pos].where(
+                pred_rel_mat,
+                pred_rel_mat.new_zeros(1),
+            )
+        pred_rel_mat = pred_rel_mat.view(self.pred_index_mat.size())
+
+        self._pred_rel_mat = pred_rel_mat
+        return pred_rel_mat
+
+    @property
+    def label_count(self) -> Tensor:
+        r"""The number of ground-truth labels for every example."""
+        if hasattr(self, '_label_count'):
+            return self._label_count  # type: ignore
+
+        label_count = scatter(
+            torch.ones_like(self.edge_label_index[0]),
+            self.edge_label_index[0],
+            dim=0,
+            dim_size=self.pred_index_mat.size(0),
+            reduce='sum',
+        )
+
+        self._label_count = label_count
+        return label_count
+
+    @property
+    def label_weight_sum(self) -> Tensor:
+        r"""The sum of edge label weights for every example."""
+        if self.edge_label_weight is None:
+            return self.label_count
+
+        if hasattr(self, '_label_weight_sum'):
+            return self._label_weight_sum  # type: ignore
+
+        label_weight_sum = scatter(
+            self.edge_label_weight,
+            self.edge_label_index[0],
+            dim=0,
+            dim_size=self.pred_index_mat.size(0),
+            reduce='sum',
+        )
+
+        self._label_weight_sum = label_weight_sum
+        return label_weight_sum
+
+    @property
+    def edge_label_weight_pos(self) -> Optional[Tensor]:
+        r"""Returns the position of edge label weights in descending order
+        within example-wise buckets.
+        """
+        if self.edge_label_weight is None:
+            return None
+
+        if hasattr(self, '_edge_label_weight_pos'):
+            return self._edge_label_weight_pos  # type: ignore
+
+        # Get the permutation via two sorts: One globally on the weights,
+        # followed by a (stable) sort on the example indices.
+        perm1 = self.edge_label_weight.argsort(descending=True)
+        perm2 = self.edge_label_index[0][perm1].argsort(stable=True)
+        perm = perm1[perm2]
+        # Invert the permutation to get the final position:
+        pos = torch.empty_like(perm)
+        pos[perm] = torch.arange(perm.size(0), device=perm.device)
+        # Normalize position to zero within all buckets:
+        pos = pos - cumsum(self.label_count)[self.edge_label_index[0]]
+
+        self._edge_label_weight_pos = pos
+        return pos
+
+
+class LinkPredMetric(BaseMetric):
+    r"""An abstract class for computing link prediction retrieval metrics.
+
+    Args:
+        k (int): The number of top-:math:`k` predictions to evaluate against.
+    """
+    is_differentiable: bool = False
+    full_state_update: bool = False
+    higher_is_better: Optional[bool] = None
+    weighted: bool = False
+
+    def __init__(self, k: int) -> None:
+        super().__init__()
+
+        if k <= 0:
+            raise ValueError(f"'k' needs to be a positive integer in "
+                             f"'{self.__class__.__name__}' (got {k})")
+
+        self.k = k
+
+        self.accum: Tensor
+        self.total: Tensor
+
+        if WITH_TORCHMETRICS:
+            self.add_state('accum', torch.tensor(0.), dist_reduce_fx='sum')
+            self.add_state('total', torch.tensor(0), dist_reduce_fx='sum')
+        else:
+            self.register_buffer('accum', torch.tensor(0.))
+            self.register_buffer('total', torch.tensor(0))
+
+    def update(
+        self,
+        pred_index_mat: Tensor,
+        edge_label_index: Union[Tensor, Tuple[Tensor, Tensor]],
+        edge_label_weight: Optional[Tensor] = None,
+    ) -> None:
+        r"""Updates the state variables based on the current mini-batch
+        prediction.
+
+        :meth:`update` can be repeated multiple times to accumulate the results
+        of successive predictions, *e.g.*, inside a mini-batch training or
+        evaluation loop.
+
+        Args:
+            pred_index_mat (torch.Tensor): The top-:math:`k` predictions of
+                every example in the mini-batch with shape
+                :obj:`[batch_size, k]`.
+            edge_label_index (torch.Tensor): The ground-truth indices for every
+                example in the mini-batch, given in COO format of shape
+                :obj:`[2, num_ground_truth_indices]`.
+            edge_label_weight (torch.Tensor, optional): The weight of the
+                ground-truth indices for every example in the mini-batch of
+                shape :obj:`[num_ground_truth_indices]`. If given, needs to be
+                a vector of positive values. Required for weighted metrics,
+                ignored otherwise. (default: :obj:`None`)
+        """
+        if self.weighted and edge_label_weight is None:
+            raise ValueError(f"'edge_label_weight' is a required argument for "
+                             f"weighted '{self.__class__.__name__}' metrics")
+        if not self.weighted:
+            edge_label_weight = None
+
+        data = LinkPredMetricData(
+            pred_index_mat=pred_index_mat,
+            edge_label_index=edge_label_index,
+            edge_label_weight=edge_label_weight,
+        )
+        self._update(data)
+
+    def _update(self, data: LinkPredMetricData) -> None:
+        metric = self._compute(data)
+
+        self.accum += metric.sum()
+        self.total += (data.label_count > 0).sum()
+
+    def compute(self) -> Tensor:
+        r"""Computes the final metric value."""
+        if self.total == 0:
+            return torch.zeros_like(self.accum)
+        return self.accum / self.total
+
+    def reset(self) -> None:
+        r"""Resets metric state variables to their default value."""
+        if WITH_TORCHMETRICS:
+            super().reset()
+        else:
+            self.accum.zero_()
+            self.total.zero_()
+
+    def _compute(self, data: LinkPredMetricData) -> Tensor:
+        r"""Computes the specific metric.
+        To be implemented separately for each metric class.
+
+        Args:
+            data (LinkPredMetricData): The mini-batch data for computing a link
+                prediction metric per example.
+        """
+        raise NotImplementedError
+
+    def __repr__(self) -> str:
+        weighted_repr = ', weighted=True' if self.weighted else ''
+        return f'{self.__class__.__name__}(k={self.k}{weighted_repr})'
+
+
+class LinkPredMetricCollection(torch.nn.ModuleDict):
+    r"""A collection of metrics to reduce and speed-up computation of link
+    prediction metrics.
+
+    .. code-block:: python
+
+        from torch_geometric.metrics import (
+            LinkPredMAP,
+            LinkPredMetricCollection,
+            LinkPredPrecision,
+            LinkPredRecall,
+        )
+
+        metrics = LinkPredMetricCollection([
+            LinkPredMAP(k=10),
+            LinkPredPrecision(k=100),
+            LinkPredRecall(k=50),
+        ])
+
+        metrics.update(pred_index_mat, edge_label_index)
+        out = metrics.compute()
+        metrics.reset()
+
+        print(out)
+        >>> {'LinkPredMAP@10': tensor(0.375),
+        ...  'LinkPredPrecision@100': tensor(0.127),
+        ...  'LinkPredRecall@50': tensor(0.483)}
+
+    Args:
+        metrics: The link prediction metrics.
+    """
+    def __init__(
+        self,
+        metrics: Union[
+            List[LinkPredMetric],
+            Dict[str, LinkPredMetric],
+        ],
+    ) -> None:
+        super().__init__()
+
+        if isinstance(metrics, (list, tuple)):
+            metrics = {
+                (f'{"Weighted" if metric.weighted else ""}'
+                 f'{metric.__class__.__name__}@{metric.k}'):
+                metric
+                for metric in metrics
+            }
+        assert len(metrics) > 0
+        assert isinstance(metrics, dict)
+
+        for name, metric in metrics.items():
+            self[name] = metric
+
+    @property
+    def max_k(self) -> int:
+        r"""The maximum number of top-:math:`k` predictions to evaluate
+        against.
+        """
+        return max([metric.k for metric in self.values()])
+
+    @property
+    def weighted(self) -> bool:
+        r"""Returns :obj:`True` in case the collection holds at least one
+        weighted link prediction metric.
+        """
+        return any([metric.weighted for metric in self.values()])
+
+    def update(  # type: ignore
+        self,
+        pred_index_mat: Tensor,
+        edge_label_index: Union[Tensor, Tuple[Tensor, Tensor]],
+        edge_label_weight: Optional[Tensor] = None,
+    ) -> None:
+        r"""Updates the state variables based on the current mini-batch
+        prediction.
+
+        :meth:`update` can be repeated multiple times to accumulate the results
+        of successive predictions, *e.g.*, inside a mini-batch training or
+        evaluation loop.
+
+        Args:
+            pred_index_mat (torch.Tensor): The top-:math:`k` predictions of
+                every example in the mini-batch with shape
+                :obj:`[batch_size, k]`.
+            edge_label_index (torch.Tensor): The ground-truth indices for every
+                example in the mini-batch, given in COO format of shape
+                :obj:`[2, num_ground_truth_indices]`.
+            edge_label_weight (torch.Tensor, optional): The weight of the
+                ground-truth indices for every example in the mini-batch of
+                shape :obj:`[num_ground_truth_indices]`. If given, needs to be
+                a vector of positive values. Required for weighted metrics,
+                ignored otherwise. (default: :obj:`None`)
+        """
+        if self.weighted and edge_label_weight is None:
+            raise ValueError(f"'edge_label_weight' is a required argument for "
+                             f"weighted '{self.__class__.__name__}' metrics")
+        if not self.weighted:
+            edge_label_weight = None
+
+        data = LinkPredMetricData(  # Share metric data across metrics.
+            pred_index_mat=pred_index_mat,
+            edge_label_index=edge_label_index,
+            edge_label_weight=edge_label_weight,
+        )
+
+        for metric in self.values():
+            if metric.weighted:
+                metric._update(data)
+                if WITH_TORCHMETRICS:
+                    metric._update_count += 1
+
+        data.edge_label_weight = None
+        if hasattr(data, '_pred_rel_mat'):
+            data._pred_rel_mat = data._pred_rel_mat != 0.0
+        if hasattr(data, '_label_weight_sum'):
+            del data._label_weight_sum
+        if hasattr(data, '_edge_label_weight_pos'):
+            del data._edge_label_weight_pos
+
+        for metric in self.values():
+            if not metric.weighted:
+                metric._update(data)
+                if WITH_TORCHMETRICS:
+                    metric._update_count += 1
+
+    def compute(self) -> Dict[str, Tensor]:
+        r"""Computes the final metric values."""
+        return {name: metric.compute() for name, metric in self.items()}
+
+    def reset(self) -> None:
+        r"""Reset metric state variables to their default value."""
+        for metric in self.values():
+            metric.reset()
+
+    def __repr__(self) -> str:
+        names = [f'  {name}: {metric},\n' for name, metric in self.items()]
+        return f'{self.__class__.__name__}([\n{"".join(names)}])'
+
+
+class LinkPredPrecision(LinkPredMetric):
+    r"""A link prediction metric to compute Precision @ :math:`k`.
+
+    Args:
+        k (int): The number of top-:math:`k` predictions to evaluate against.
+    """
+    higher_is_better: bool = True
+    weighted: bool = False
+
+    def _compute(self, data: LinkPredMetricData) -> Tensor:
+        pred_rel_mat = data.pred_rel_mat[:, :self.k]
+        return pred_rel_mat.sum(dim=-1) / self.k
+
+
+class LinkPredRecall(LinkPredMetric):
+    r"""A link prediction metric to compute Recall @ :math:`k`.
+
+    Args:
+        k (int): The number of top-:math:`k` predictions to evaluate against.
+    """
+    higher_is_better: bool = True
+
+    def __init__(self, k: int, weighted: bool = False):
+        super().__init__(k=k)
+        self.weighted = weighted
+
+    def _compute(self, data: LinkPredMetricData) -> Tensor:
+        pred_rel_mat = data.pred_rel_mat[:, :self.k]
+        return pred_rel_mat.sum(dim=-1) / data.label_weight_sum.clamp(min=1e-7)
+
+
+class LinkPredF1(LinkPredMetric):
+    r"""A link prediction metric to compute F1 @ :math:`k`.
+
+    Args:
+        k (int): The number of top-:math:`k` predictions to evaluate against.
+    """
+    higher_is_better: bool = True
+    weighted: bool = False
+
+    def _compute(self, data: LinkPredMetricData) -> Tensor:
+        pred_rel_mat = data.pred_rel_mat[:, :self.k]
+        isin_count = pred_rel_mat.sum(dim=-1)
+        precision = isin_count / self.k
+        recall = isin_count / data.label_count.clamp(min=1e-7)
+        return 2 * precision * recall / (precision + recall).clamp(min=1e-7)
+
+
+class LinkPredMAP(LinkPredMetric):
+    r"""A link prediction metric to compute MAP @ :math:`k` (Mean Average
+    Precision).
+
+    Args:
+        k (int): The number of top-:math:`k` predictions to evaluate against.
+    """
+    higher_is_better: bool = True
+    weighted: bool = False
+
+    def _compute(self, data: LinkPredMetricData) -> Tensor:
+        pred_rel_mat = data.pred_rel_mat[:, :self.k]
+        device = pred_rel_mat.device
+        arange = torch.arange(1, pred_rel_mat.size(1) + 1, device=device)
+        cum_precision = pred_rel_mat.cumsum(dim=1) / arange
+        return ((cum_precision * pred_rel_mat).sum(dim=-1) /
+                data.label_count.clamp(min=1e-7, max=self.k))
+
+
+class LinkPredNDCG(LinkPredMetric):
+    r"""A link prediction metric to compute the NDCG @ :math:`k` (Normalized
+    Discounted Cumulative Gain).
+
+    Args:
+        k (int): The number of top-:math:`k` predictions to evaluate against.
+        weighted (bool, optional): If set to :obj:`True`, assumes sorted lists
+            of ground-truth items according to a relevance score as given by
+            :obj:`edge_label_weight`. (default: :obj:`False`)
+    """
+    higher_is_better: bool = True
+
+    def __init__(self, k: int, weighted: bool = False):
+        super().__init__(k=k)
+        self.weighted = weighted
+
+        dtype = torch.get_default_dtype()
+        discount = torch.arange(2, k + 2, dtype=dtype).log2()
+
+        self.discount: Tensor
+        self.register_buffer('discount', discount)
+
+        if not weighted:
+            self.register_buffer('idcg', cumsum(1.0 / discount))
+        else:
+            self.idcg = None
+
+    def _compute(self, data: LinkPredMetricData) -> Tensor:
+        pred_rel_mat = data.pred_rel_mat[:, :self.k]
+        discount = self.discount[:pred_rel_mat.size(1)].view(1, -1)
+        dcg = (pred_rel_mat / discount).sum(dim=-1)
+
+        if not self.weighted:
+            assert self.idcg is not None
+            idcg = self.idcg[data.label_count.clamp(max=self.k)]
+        else:
+            assert data.edge_label_weight is not None
+            pos = data.edge_label_weight_pos
+            assert pos is not None
+
+            discount = torch.cat([
+                self.discount,
+                self.discount.new_full((1, ), fill_value=float('inf')),
+            ])
+            discount = discount[pos.clamp(max=self.k + 1)]
+
+            idcg = scatter(  # Apply discount and aggregate:
+                data.edge_label_weight / discount,
+                data.edge_label_index[0],
+                dim_size=data.pred_index_mat.size(0),
+                reduce='sum',
+            )
+
+        out = dcg / idcg
+        out[out.isnan() | out.isinf()] = 0.0
+        return out
+
+
+class LinkPredMRR(LinkPredMetric):
+    r"""A link prediction metric to compute the MRR @ :math:`k` (Mean
+    Reciprocal Rank).
+
+    Args:
+        k (int): The number of top-:math:`k` predictions to evaluate against.
+    """
+    higher_is_better: bool = True
+    weighted: bool = False
+
+    def _compute(self, data: LinkPredMetricData) -> Tensor:
+        pred_rel_mat = data.pred_rel_mat[:, :self.k]
+        device = pred_rel_mat.device
+        arange = torch.arange(1, pred_rel_mat.size(1) + 1, device=device)
+        return (pred_rel_mat / arange).max(dim=-1)[0]

{pyg_nightly-2.7.0.dev20250114 → pyg_nightly-2.7.0.dev20250118}/torch_geometric/nn/nlp/llm.py

@@ -51,17 +51,18 @@ class LLM(torch.nn.Module):
 
     model_name (str): The HuggingFace model name, *e.g.*, :obj:`"llama2"` or
         :obj:`"gemma"`.
-    num_params (int): An integer representing how many parameters the
+    num_params (int, optional): An integer representing how many parameters the
         HuggingFace model has, in billions. This is used to automatically
         allocate the correct number of GPUs needed, given the available GPU
-        memory of your GPUs.
+        memory of your GPUs. If not specified, the number of parameters
+        is determined using the `huggingface_hub` module.
     dtype (torch.dtype, optional): The data type to use for the LLM.
         (default :obj: `torch.bfloat16`)
     """
     def __init__(
         self,
         model_name: str,
-        num_params: int,
+        num_params: int = None,
         dtype=torch.bfloat16,
     ) -> None:
         super().__init__()
@@ -70,6 +71,12 @@ class LLM(torch.nn.Module):
 
         from transformers import AutoModelForCausalLM, AutoTokenizer
 
+        if num_params is None:
+            from huggingface_hub import get_safetensors_metadata
+            safetensors_metadata = get_safetensors_metadata(model_name)
+            param_count = safetensors_metadata.parameter_count
+            num_params = list(param_count.values())[0] // 10**9
+
         # A rough heuristic on GPU memory requirements, e.g., we found that
         # LLAMA2 (7B parameters) fits on a 85GB GPU.
         required_memory = 85 * num_params / 7