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Codex/graph store multi supervision edge types - #728

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Codex/graph store multi supervision edge types#728
kmontemayor2-sc wants to merge 21 commits into
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codex/graph-store-multi-supervision-edge-types

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Scope of work done

Where is the documentation for this feature?: N/A

Did you add automated tests or write a test plan?

Updated Changelog.md? NO

Ready for code review?: NO

kmontemayor and others added 21 commits June 25, 2026 14:57
…racle

Factor the inline per-anchor label-remap loop in DistABLPLoader._set_labels
into a module-level function _loop_set_labels. The new function is a
behavior-preserving extraction: _set_labels delegates to it, producing
identical output. _loop_set_labels will serve as the equivalence oracle
for the vectorized kernel added in the next task.

Also imports PADDING_NODE from gigl.utils.data_splitters (used by the
vectorized kernel in the next task) and adds the contract test file
tests/unit/distributed/vectorized_set_labels_test.py.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…oop oracle

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…ls kernel

Add frozen dataclass AnchorLabels (anchor_index, label_index, num_anchors)
with to_dict() bridge; thin wrapper _remap_one_label_tensor_edge_list over
the shared _membership_remap; and edge_list_set_labels driver. Proves
to_dict() reproduces _loop_set_labels bit-for-bit via parametrized equivalence
tests (11 new tests, all classes pass).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…eous training

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…eneous training

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…test

Line-wrapping only (ruff format) for the edge-list label reads in the four
link-prediction training examples and the loader equivalence test. No logic
change.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…ctors

**Behavioral change:** Drop the composite-key stable argsort from
`_membership_remap` (the `composite_key = anchor_kept * (num_nodes + 1) +
local_idx` / `torch.argsort(composite_key, stable=True)` block). The pair
stream is now emitted in column-visit (row-major masked flatten) order rather
than ascending-local-index (torch.nonzero) order.

**Why this is safe:** `RetrievalLoss` (`gigl/nn/loss.py`) is
`CrossEntropyLoss(reduction="sum")` over a diagonal-targeted score matrix that
masks collisions by id VALUE, not position. It is invariant to any joint
permutation of `(anchor_index, label_index)` pairs. The only constraint is
co-indexing (pair k stays intact) and per-anchor grouping, both of which are
preserved. Within-anchor label order was an implementation artifact of the loop
oracle -- never a loss requirement.

**Why the dict path is unaffected:** `anchor_of_entry` is built as
`arange(N).repeat_interleave(M)` (row-major), so the masked flatten is already
non-decreasing in anchor_index. `bincount`/`split` requires only contiguous
grouping by anchor, which row-major flatten guarantees without any argsort.

**Readability refactors in `_membership_remap`:**
- Rename terse tensors: `valid` -> `is_present`, `found` -> `is_exact_match`,
  `positions` -> `sorted_positions`, `local_idx` -> `local_index`,
  `anchor_kept` -> `anchor_of_matched`
- Add numbered step comments explaining the searchsorted membership lookup

**Readability refactors in outer kernels:**
- Add `_remap_group` helper to collapse the ~40-line duplicated positive/
  negative per-edge-type loops in both `vectorized_set_labels` and
  `edge_list_set_labels` (uses TypeVar for generic return type)
- `_sorted_for` closure pattern preserved, inlined per-kernel (memoizes
  torch.sort across pos/neg edge types of the same node type)

**Other improvements:**
- Add doctest to `AnchorLabels` showing a 2-anchor case + `to_dict()` round-trip
- Update `AnchorLabels` docstring: document column-visit order and
  loss-permutation-invariance rationale
- Update all docstrings to drop "bit-for-bit"/"torch.nonzero order" language

**Test contract relaxation (tests remain non-vacuous):**
- `vectorized_set_labels_test.py` / `edge_list_set_labels_test.py`:
  `_assert_label_dicts_equal` -> `_assert_label_dicts_set_equal` (uses
  `sorted()` per anchor; still catches membership errors + multiplicity)
- `test_unsorted_node_map_exact_order` -> `test_unsorted_node_map_correct_membership`:
  asserts SET {0, 2} instead of sequence [0, 2]; docstring explains column
  vs ascending-local order difference
- `RemapOneEdgeListTest.test_unsorted_node_map_nontrivial_sort_perm` ->
  `test_unsorted_node_map_correct_membership`: pins column order [2, 0] and
  explains it is SET-equal to [0, 2]; verifies sort_perm mapping is correct
- `dist_ablp_neighborloader_test.py`: `_ordered_global_pairs` ->
  `_global_pair_set` (sorts within anchor); `_collect_homogeneous_labels`
  docstring updated; the in-process exact-tensor assertion
  (`label_index == cat(dict values)`) is preserved -- both paths draw from the
  same `_membership_remap` pair stream so they remain identical
- CUDA device test docstring: remove "stable-argsort tie-break" reference;
  keep the duplicate [15,15] row (still tests duplicate handling + device placement)

Device fix preserved: `anchor_of_entry` is still built on `label_tensor.device`.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…er-identical

After dropping the order-reproduction argsort, per-anchor label order is
column-visit order, not the loop's nonzero order. The (query, label) pairs are
unchanged and the contrastive loss is order-invariant, so the read is equivalent
for training; the comments now say so instead of implying byte-identical order.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
GiGL main resolved ABLP labels with a per-anchor Python loop. This replaces it
with one vectorized kernel and a single output type, plus a thin dict view for
backward compatibility.

- Resolve labels with a sorted-membership join (_membership_remap: sort the node
  map once, searchsorted the label ids, keep exact matches) instead of the
  O(N_anchors * M * N_nodes) per-anchor loop. Delete _loop_set_labels (no
  production callers) and the redundant dict-producing kernel.
- Collapse the remap to two functions, _membership_remap and edge_list_set_labels;
  the dict path is just AnchorLabels.to_dict(), selected by use_list_output on
  DistABLPLoader (default False keeps the ragged dict). Drop the _remap_group
  callback indirection, the _LabelT TypeVar, and the vestigial
  supervision_edge_types parity param.
- AnchorLabels stores labels as two parallel (anchor_index, label_index) tensors
  so the loss can index them directly; within-anchor order is unspecified because
  the ABLP contrastive loss is order-invariant over the pairs.
- Make the __debug__ unique-node-map check a cheap adjacent-difference test on the
  already-sorted map (it ran torch.unique every batch, and GiGL is not launched
  with -O).
- Tests assert against constructed expected values and per-anchor label SETS, not
  within-anchor order. Examples consume the edge-list directly.

Behavior-preserving: per-anchor label sets are unchanged.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…ions

Comments and docstrings only -- no behavior change (verified: the AST with
docstrings stripped is identical to the prior commit for every touched file).

- Docstrings lead with why over what; the membership-remap algorithm is shown as
  a small worked example (node map + [N_anchors, M] padded label tensor -> pairs)
  with labeled steps instead of dense prose.
- Inline comments reference those docstring steps rather than floating free.
- Tensor dimensions annotated throughout (N_anchors / M / N_nodes / K / E),
  including the K (non-padding candidates) vs E (matched pairs) distinction.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…uniqueness guard

- Add a use_list_output=True worked example to DistABLPLoader.__init__ that
  mirrors the use_list_output=False example (same graph, AnchorLabels values).
- Document AnchorLabels.to_dict()'s non-decreasing anchor_index precondition.
- Promote the _membership_remap duplicate-node-map guard from a __debug__
  assert to an always-on ValueError so it still fires under `python -O`; update
  the test to expect ValueError.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Comments should describe the code as it is, not as a delta from a prior or
never-committed version. Reword/remove comments that only parse if the reader
knows the code's development history:

- Drop the "Always-on (not __debug__) ... python -O" framing on the node-map
  uniqueness guard; keep the precondition + empty-slice safety rationale.
- Fix a stale _membership_remap docstring line still describing a __debug__
  assertion (it is now an always-on ValueError).
- Remove "with no argsort" / "no argsort needed" (presupposed the dropped
  order-reproduction argsort); state the grouped-by-anchor property directly.
- Reword "a sorted-membership join rather than a per-anchor scan ... trades a
  broadcast-compare for a search" to describe the algorithm and its complexity
  as-is.
- Drop "rather than maintaining a second kernel" in _set_labels.
- Same scrub in edge_list_set_labels_test.py (module docstring + guard test).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…dge types

_set_labels built the local->global node map from
self._supervision_edge_types[2]. Those edge types are stored reversed when
edge_dir="in" (dist_ablp_neighborloader.py:486-490), so that index is the anchor
node type there, while the label edge types reaching collation stay
outward-facing. Every heterogeneous edge_dir="in" batch therefore raised
KeyError on its supervision node type.

The pre-refactor code inserted both endpoints of each supervision edge type,
which masked the direction ambiguity. Deriving the map from the label edge type
keys that _remap_labels_by_edge_type actually looks up drops the edge_dir
coupling entirely.

Add heterogeneous coverage for both output formats across both edge dirs. The
existing equivalence test is homogeneous and edge_dir="out", so it could not
catch this. Anchors and supervision nodes use distinct node types, so a label
remapped against the wrong node map yields a wrong global id instead of passing
silently.

Fixes the 5 unit errors and the het-dblp-sup{,-gs} e2e trainer failures in
https://github.com/Snapchat/GiGL/actions/runs/30379971583

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
@kmontemayor2-sc

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/all_test

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@ 20:06:49UTC : 🔄 Integration Test started.

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@ 20:06:50UTC : 🔄 E2E Test started.

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@ 20:06:53UTC : 🔄 Python Unit Test started.

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@ 20:06:55UTC : 🔄 Scala Unit Test started.

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validation_errors: list[Optional[str]] = [
None
] * torch.distributed.get_world_size()
torch.distributed.all_gather_object(validation_errors, validation_error)

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Semgrep identified an issue in your code:

Pickle-based object serialization in all_gather_object() can execute attacker-controlled code on remote ranks if validation errors are compromised.

More details about this

The torch.distributed.all_gather_object() call uses pickle serialization under the hood to share the validation_error string across distributed ranks. If an attacker can control the content of validation_error, they can craft a malicious pickled object that executes arbitrary code when deserialized on other ranks.

Exploit scenario:

  1. An attacker triggers a ValueError in _convert_graph_store_ablp_inputs() by providing malicious input (e.g., crafted node data, edge types, or edge direction that causes a specific error condition).
  2. The error message is converted to a string and stored in validation_error.
  3. When all_gather_object() serializes this string using pickle and sends it to other ranks, if the attacker has injected a specially-crafted pickle payload instead of a plain string, the deserialization on remote ranks will execute the attacker's code.
  4. The attacker gains code execution on all compute ranks in the distributed training job.

Even though str(error) is called here, if an exception object with a malicious __str__ method reaches this point, or if the exception's string representation is later pickled as part of a larger object, pickle exploitation becomes possible.

To resolve this comment:

✨ Commit fix suggestion
  1. Replace torch.distributed.all_gather_object(validation_errors, validation_error) with tensor-based collectives so PyTorch does not use pickle under the hood.

  2. Gather the error state as an integer tensor instead of a Python string.
    For example, create a local flag like has_error = torch.tensor([1 if validation_error is not None else 0], device=...) and gather it with torch.distributed.all_gather(...) into one tensor per rank.

  3. Change the validation check to use the gathered flags.
    For example, raise when any gathered value is 1 instead of checking a list of Python objects.

  4. Keep the exception message generic, or send only a numeric error code if you need rank-specific detail.
    For example, use error_code = torch.tensor([0 if validation_error is None else 1], device=...) and map codes to messages locally after all_gather(...).

  5. If you must preserve the text of the validation error, encode it into bytes and gather it with tensors instead of object collectives.
    For example, convert the message to utf-8, store its length in an integer tensor, store the bytes in a fixed-size torch.uint8 tensor, and call torch.distributed.all_gather(...) on those tensors. This avoids deserializing arbitrary Python objects from other ranks.

  6. Update the final ValueError to use the safe gathered result.
    For example, raise ValueError("Graph Store ABLP input validation failed across compute ranks.") or reconstruct messages only from tensor data gathered in the previous step.

💬 Ignore this finding

Reply with Semgrep commands to ignore this finding.

  • /fp <comment> for false positive
  • /ar <comment> for acceptable risk
  • /other <comment> for all other reasons

Alternatively, triage in Semgrep AppSec Platform to ignore the finding created by pickles-in-pytorch-distributed.

You can view more details about this finding in the Semgrep AppSec Platform.

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