Merge branch 'master' into master

CHANGELOG.md

@@ -8,6 +8,10 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 ### Added
 
 - Update Dockerfile to use latest from NVIDIA ([#9794](https://github.com/pyg-team/pytorch_geometric/pull/9794))
+- Added various GRetriever Architecture Benchmarking examples ([#9666](https://github.com/pyg-team/pytorch_geometric/pull/9666))
+- Added `profiler.nvtxit` with some examples ([#9666](https://github.com/pyg-team/pytorch_geometric/pull/9666))
+- Added `loader.RagQueryLoader` with Remote Backend Example ([#9666](https://github.com/pyg-team/pytorch_geometric/pull/9666))
+- Added `data.LargeGraphIndexer` ([#9666](https://github.com/pyg-team/pytorch_geometric/pull/9666))
 - Added `GIT-Mol` ([#9730](https://github.com/pyg-team/pytorch_geometric/pull/9730))
 - Added comment in `g_retriever.py` pointing to `Neo4j` Graph DB integration demo ([#9748](https://github.com/pyg-team/pytorch_geometric/pull/9797))
 - Added `MoleculeGPT` example ([#9710](https://github.com/pyg-team/pytorch_geometric/pull/9710))

examples/llm/README.md

@@ -1,8 +1,11 @@
 # Examples for Co-training LLMs and GNNs
 
-| Example                                | Description                                                                                                                                                                                    |
-| -------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| [`g_retriever.py`](./g_retriever.py)   | Example for Retrieval-Augmented Generation (RAG) w/ GNN+LLM by co-training `LLAMA2` with `GAT` for answering questions based on knowledge graph information                                    |
-| [`git_mol.py`](./git_mol.py)           | Example for GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text                                                                                      |
-| [`molecule_gpt.py`](./molecule_gpt.py) | Example for MoleculeGPT: Instruction Following Large Language Models for Molecular Property Prediction                                                                                         |
-| [`glem.py`](./glem.py)                 | Example for [GLEM](https://arxiv.org/abs/2210.14709), a GNN+LLM co-training model via variational Expectation-Maximization (EM) framework on node classification tasks to achieve SOTA results |
+| Example                                      | Description                                                                                                                                                                                    |
+| -------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| [`g_retriever.py`](./g_retriever.py)         | Example for Retrieval-Augmented Generation (RAG) w/ GNN+LLM by co-training `LLAMA2` with `GAT` for answering questions based on knowledge graph information                                    |
+| [`g_retriever_utils/`](./g_retriever_utils/) | Contains multiple scripts for benchmarking GRetriever's architecture and evaluating different retrieval methods.                                                                               |
+| [`multihop_rag/`](./multihop_rag/)           | Contains starter code and an example run for building a Multi-hop dataset using WikiHop5M and 2WikiMultiHopQA                                                                                  |
+| [`nvtx_examples/`](./nvtx_examples/)         | Contains examples of how to wrap functions using the NVTX profiler for CUDA runtime analysis.                                                                                                  |
+| [`molecule_gpt.py`](./molecule_gpt.py)       | Example for MoleculeGPT: Instruction Following Large Language Models for Molecular Property Prediction                                                                                         |
+| [`glem.py`](./glem.py)                       | Example for [GLEM](https://arxiv.org/abs/2210.14709), a GNN+LLM co-training model via variational Expectation-Maximization (EM) framework on node classification tasks to achieve SOTA results |
+| [`git_mol.py`](./git_mol.py)                 | Example for GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text                                                                                      |

examples/llm/g_retriever.py

@@ -11,6 +11,7 @@
 https://github.com/neo4j-product-examples/neo4j-gnn-llm-example
 """
 import argparse
+import gc
 import math
 import os.path as osp
 import re
@@ -145,6 +146,9 @@ def adjust_learning_rate(param_group, LR, epoch):
     test_loader = DataLoader(test_dataset, batch_size=eval_batch_size,
                              drop_last=False, pin_memory=True, shuffle=False)
 
+    # To clean up after Data Preproc
+    gc.collect()
+    torch.cuda.empty_cache()
     gnn = GAT(
         in_channels=1024,
         hidden_channels=hidden_channels,

examples/llm/g_retriever_utils/README.md

@@ -0,0 +1,11 @@
+# Examples for LLM and GNN co-training
+
+| Example                                                          | Description                                                                                                                                                               |
+| ---------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| [`rag_feature_store.py`](./rag_feature_store.py)                 | A Proof of Concept Implementation of a RAG enabled FeatureStore that can serve as a starting point for implementing a custom RAG Remote Backend                           |
+| [`rag_graph_store.py`](./rag_graph_store.py)                     | A Proof of Concept Implementation of a RAG enabled GraphStore that can serve as a starting point for implementing a custom RAG Remote Backend                             |
+| [`rag_backend_utils.py`](./rag_backend_utils.py)                 | Utility functions used for loading a series of Knowledge Graph Triplets into the Remote Backend defined by a FeatureStore and GraphStore                                  |
+| [`rag_generate.py`](./rag_generate.py)                           | Script for generating a unique set of subgraphs from the WebQSP dataset using a custom defined retrieval algorithm (defaults to the FeatureStore and GraphStore provided) |
+| [`benchmark_model_archs_rag.py`](./benchmark_model_archs_rag.py) | Script for running a GNN/LLM benchmark on GRetriever while grid searching relevent architecture parameters and datasets.                                                  |
+
+NOTE: Evaluating performance on GRetriever with smaller sample sizes may result in subpar performance. It is not unusual for the fine-tuned model/LLM to perform worse than an untrained LLM on very small sample sizes.

examples/llm/g_retriever_utils/benchmark_model_archs_rag.py

@@ -0,0 +1,105 @@
+"""Used to benchmark the performance of an untuned/fine tuned LLM against
+GRetriever with various architectures and layer depths.
+"""
+# %%
+import argparse
+import sys
+
+import torch
+
+from torch_geometric.datasets import WebQSPDataset
+from torch_geometric.nn.models import GAT, MLP, GRetriever
+
+sys.path.append('..')
+from minimal_demo import (  # noqa: E402 # isort:skip
+    benchmark_models, get_loss, inference_step,
+)
+
+# %%
+parser = argparse.ArgumentParser(
+    description="""Benchmarker for GRetriever\n""" +
+    """NOTE: Evaluating with smaller samples may result in poorer""" +
+    """ performance for the trained models compared to """ +
+    """untrained models.""")
+parser.add_argument("--hidden_channels", type=int, default=1024)
+parser.add_argument("--learning_rate", type=float, default=1e-5)
+parser.add_argument("--epochs", type=int, default=2)
+parser.add_argument("--batch_size", type=int, default=8)
+parser.add_argument("--eval_batch_size", type=int, default=16)
+parser.add_argument("--tiny_llama", action='store_true')
+
+parser.add_argument("--dataset_path", type=str, required=False)
+# Default to WebQSP split
+parser.add_argument("--num_train", type=int, default=2826)
+parser.add_argument("--num_val", type=int, default=246)
+parser.add_argument("--num_test", type=int, default=1628)
+
+args = parser.parse_args()
+
+# %%
+hidden_channels = args.hidden_channels
+lr = args.learning_rate
+epochs = args.epochs
+batch_size = args.batch_size
+eval_batch_size = args.eval_batch_size
+
+# %%
+if not args.dataset_path:
+    ds = WebQSPDataset('benchmark_archs', verbose=True, force_reload=True)
+else:
+    # We just assume that the size of the dataset accomodates the
+    # train/val/test split, because checking may be expensive.
+    dataset = torch.load(args.dataset_path)
+
+    class MockDataset:
+        """Utility class to patch the fields in WebQSPDataset used by
+        GRetriever.
+        """
+        def __init__(self) -> None:
+            pass
+
+        @property
+        def split_idxs(self) -> dict:
+            # Imitates the WebQSP split method
+            return {
+                "train":
+                torch.arange(args.num_train),
+                "val":
+                torch.arange(args.num_val) + args.num_train,
+                "test":
+                torch.arange(args.num_test) + args.num_train + args.num_val,
+            }
+
+        def __getitem__(self, idx: int):
+            return dataset[idx]
+
+    ds = MockDataset()
+
+# %%
+model_names = []
+model_classes = []
+model_kwargs = []
+model_type = ["GAT", "MLP"]
+models = {"GAT": GAT, "MLP": MLP}
+# Use to vary the depth of the GNN model
+num_layers = [4]
+# Use to vary the number of LLM tokens reserved for GNN output
+num_tokens = [1]
+for m_type in model_type:
+    for n_layer in num_layers:
+        for n_tokens in num_tokens:
+            model_names.append(f"{m_type}_{n_layer}_{n_tokens}")
+            model_classes.append(GRetriever)
+            kwargs = dict(gnn_hidden_channels=hidden_channels,
+                          num_gnn_layers=n_layer, gnn_to_use=models[m_type],
+                          mlp_out_tokens=n_tokens)
+            if args.tiny_llama:
+                kwargs['llm_to_use'] = 'TinyLlama/TinyLlama-1.1B-Chat-v0.1'
+                kwargs['mlp_out_dim'] = 2048
+                kwargs['num_llm_params'] = 1
+            model_kwargs.append(kwargs)
+
+# %%
+benchmark_models(model_classes, model_names, model_kwargs, ds, lr, epochs,
+                 batch_size, eval_batch_size, get_loss, inference_step,
+                 skip_LLMs=False, tiny_llama=args.tiny_llama, force=True)