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This is Lecture 16 of Stanford CS224W: Machine Learning with Graphs, Fall 2025, dated 2025-11-18. It follows the course schedule and the official slide artifact linked in that row; speaker attribution follows the slides.
Materials and gaps
Public materials include the official slides and optional readings on the schedule. Canvas video, live Q&A, board work, and Ed discussions are unavailable and are not reconstructed. The public 2021 videos are not evidence for a 2025 lecture. Where a slide filename differs from the lecture number, the Fall 2025 schedule row remains canonical.
Complete lecture agenda
1. Complementary gaps in LLMs and GNNs
LLMs excel at text and broad knowledge but do not guarantee multi-hop graph reasoning; GNNs aggregate along edges but often lack textual semantics and open vocabularies. The design question is which module understands language and which preserves structure.
2. Text-attributed graphs
A text-attributed graph attaches text to nodes or edges. One pipeline encodes text into features before a GNN; another serializes neighborhoods into a prompt. The former preserves graph inductive bias, while the latter is sensitive to context length and serialization order.
3. The LLM as predictor or encoder
An LLM may directly predict a graph task, produce node embeddings, or supply pseudo-labels and explanations. These roles have different costs: embedding an entire graph through an API is unlike processing only a query neighborhood.
4. Graph retrieval for LLMs
In the reverse direction, a graph retriever selects a query-relevant subgraph before an LLM reads its structure and text. A fluent generator cannot restore facts omitted by retrieval, so retrieval recall needs separate evaluation.
5. G-Retriever and the GraphRAG pipeline
G-Retriever composes a query, graph retrieval, subgraph pruning, and generation. Track retrieval metrics, answer metrics, and token cost separately to locate the source of any improvement.
Deep lecture agenda
Complementary gaps
GNNs exploit structure but may lack semantics; LLMs understand text but do not preserve topology or exact paths. A hybrid must identify which gap each component fills.
Text-attributed graphs
Nodes and edges carry documents or descriptions alongside connectivity. Text availability and duplication across splits require the same cutoff audit as edges.
LLM as encoder
An LLM turns node text into GNN features. Frozen embeddings reduce cost; fine-tuning adds adaptation, leakage risk, and versioning requirements.
LLM as predictor
Serialized neighborhoods can be prompted directly. Ordering, truncation, and structural invariance become part of the model.
GNN enhanced by an LLM
LLM features or pseudo-labels can enrich graph learning. Compare simpler text encoders and exclude target-bearing generated supervision.
LLM enhanced by a graph
Graph retrieval supplies connected evidence to generation. Retrieval quality and answer faithfulness need separate evaluation.
The G-Retriever pipeline
G-Retriever selects a compact query subgraph, encodes it, and conditions an LLM. Pruning saves context but may remove the decisive path.
GraphRAG evidence
GraphRAG retrieves multi-hop evidence before generation. Claims must trace to retrieved nodes and edges rather than parametric memory.
KG construction
Extraction, entity linking, relation extraction, and deduplication define the retrieval graph. Errors create false paths or fragmented entities.
Training
Frozen encoders, alignment projections, fine-tuning, and joint objectives have different cost and leakage boundaries. Record all trainable modules and corpora.
Evaluation
Measure answer quality, retrieval recall, evidence precision, faithfulness, latency, and cost. End-to-end accuracy cannot locate the failing stage.
Acceptance
Use known supporting paths, distractors, and missing-evidence queries; trace linking, retrieved edges, serialization, input, answer, and citations.
Implementation, failure modes, and acceptance
Entity linking
Ambiguity attaches queries to wrong nodes and missed aliases fragment evidence. Report candidates, confidence, and sensitivity.
Subgraph pruning
Top-k and path limits trade recall for context. Measure whether the gold path survives each budget.
Serialization
Preserve types, direction, IDs, and provenance, then reorder equivalent serializations to test robustness.
Fine-tuning leakage
Instruction data may contain benchmark answers or future facts. Deduplicate sources and enforce time boundaries.
Hallucination audit
Classify statements as supported, contradicted, or absent from retrieved evidence. Fluency without a path is not grounding.
Acceptance test
Remove the decisive edge and require abstention or answer change; add distractors and verify citations remain evidence-bound.
Self-study checkpoint
Decompose the pipeline into graph construction, retrieval or sampling, encoder, prediction head, and evaluation. Replace one component at a time and retain cost and failure traces so any improvement remains attributable.
Course video sources
Checked live: the archived Fall 2025 official page lists no public recording link (its Canvas entry is empty), and the current Fall 2026 official page says lecture videos are on Canvas for enrolled students only; the Canvas entry redirects to the Stanford sign-in page. The public Stanford Online YouTube playlists currently cover only the 2021 and 2023 offerings, whose lectures differ from the Fall 2025 offering this article follows, so they are not embedded or treated as Fall 2025 recordings.
Course and recording entries:
- Official course / lecture source
- CS224W Fall 2025 official archive
- Stanford Online CS224W public playlist (2021 offering, not Fall 2025)
- Stanford Online CS224W public playlist (2021 / 2023 offerings, not Fall 2025)
Checked: 2026-10-10.
Update Log
- 2026-10-10: Added explicit video status and checked recording sources and access notes.
- 2026-10-10: Rechecked video status. Confirmed the official pages list no public Fall 2025 recording, Canvas requires sign-in, and public playlists cover only 2021/2023; status unchanged and check date added.
References
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