Pith Number

pith:UXKJKG3G

pith:2026:UXKJKG3GJDEY7YBM46U5K7HRIK

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OgBench: A Framework for Evaluating Graph Neural Networks on Omics Data

Guillermo Bern\'ardez, Johan Mathe, Louisa Cornelis, Louis Van Langendonck, Nina Miolane

Graph neural networks often fail to outperform simple MLPs on omics data tasks with few samples and many nodes.

arxiv:2605.15511 v1 · 2026-05-15 · cs.LG

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3 Author claim open · sign in to claim

4 Citations open

5 Replications open

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The bundle contains the canonical record plus signed events. A mirror can host it anywhere and recompute the same current state with the deterministic merge algorithm.

Claims

C1strongest claim

Our results show that widely used GNNs often do not outperform simple MLPs and classical baselines. These findings challenge the prevailing assumption that graph structure inherently adds value in this domain.

C2weakest assumption

The constructed graphs from raw omics data capture biologically meaningful relationships that are relevant to the downstream prediction tasks, and the chosen datasets and tasks are representative of real omics applications.

C3one line summary

OgBench benchmarks GNNs on omics graphs in the n << p regime and reports that standard GNNs often fail to beat MLPs and classical baselines.

References

80 extracted · 80 resolved · 1 Pith anchors

[1] Francis E. Agamah, Jumamurat R. Bayjanov, Anna Niehues, Kelechi F. Njoku, Michelle Skelton, Gaston K. Mazandu, Thomas H. A. Ederveen, Nicola Mulder, Emile R. Chimusa, and Peter A. C. ’t Hoen. Computat 2022

[2] Elbashir, and Mohanad Mo- hammed 2025

[3] Network biology: understanding the cell’s functional organization.Nature reviews genetics, 5(2):101–113, 2004 2004

[4] Bronstein, Mathias Niepert, Bryan Perozzi, Mikhail Galkin, and Christopher Morris 2025

[5] Bench- mark of filter methods for feature selection in high-dimensional gene expression survival data 2021

Receipt and verification

First computed	2026-05-20T00:01:02.390963Z
Builder	pith-number-builder-2026-05-17-v1
Signature	Pith Ed25519 (`pith-v1-2026-05`) · public key
Schema	pith-number/v1.0

Canonical hash

a5d4951b6648c98fe02ce7a9d57cf142a8604759543f7b80f12e1f2db382f659

Aliases

arxiv: 2605.15511 · arxiv_version: 2605.15511v1 · doi: 10.48550/arxiv.2605.15511 · pith_short_12: UXKJKG3GJDEY · pith_short_16: UXKJKG3GJDEY7YBM · pith_short_8: UXKJKG3G

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Verify this Pith Number yourself

curl -sH 'Accept: application/ld+json' https://pith.science/pith/UXKJKG3GJDEY7YBM46U5K7HRIK \
  | jq -c '.canonical_record' \
  | python3 -c "import sys,json,hashlib; b=json.dumps(json.loads(sys.stdin.read()), sort_keys=True, separators=(',',':'), ensure_ascii=False).encode(); print(hashlib.sha256(b).hexdigest())"
# expect: a5d4951b6648c98fe02ce7a9d57cf142a8604759543f7b80f12e1f2db382f659

Canonical record JSON

{
  "metadata": {
    "abstract_canon_sha256": "c643ffad124702754f682bfb927972900c98c8a053cb467674cf77b68c71c771",
    "cross_cats_sorted": [],
    "license": "http://creativecommons.org/licenses/by/4.0/",
    "primary_cat": "cs.LG",
    "submitted_at": "2026-05-15T01:12:09Z",
    "title_canon_sha256": "9b61f5031366aff14187d71aa99c2eb8770718f2f89e14640db44fe252f36821"
  },
  "schema_version": "1.0",
  "source": {
    "id": "2605.15511",
    "kind": "arxiv",
    "version": 1
  }
}