BRIDGE: Bottleneck-Aware Regulator-Set Inference and Diagnosis for Cooperative Gene Regulatory Recovery
Mirrored from arXiv — Machine Learning for archival readability. Support the source by reading on the original site.
Computer Science > Machine Learning
Title:BRIDGE: Bottleneck-Aware Regulator-Set Inference and Diagnosis for Cooperative Gene Regulatory Recovery
Abstract:Cooperative gene regulation often depends on groups of regulators acting jointly, but most gene regulatory network (GRN) inference methods output pairwise regulator-target rankings. We introduce Bottleneck-Aware Regulator-Set Inference and Diagnosis (BRIDGE), a framework for complete regulator-set recovery, and Targeted Recovery Attribution for Cooperative Evaluation (TRACE), a diagnostic suite that attributes failures to retrieval, set-level scoring, decoding, and evaluation bottlenecks.
TRACE includes a leak-free mechanism-mismatch cooperativity stress test in which cooperative targets are generated by random nonlinear mechanisms rather than product interactions. This design avoids feature-mechanism circularity: Residual higher-order set scoring (Residual HOS2) operates on raw expression vectors without handcrafted product-correlation features. Across 30 matched seed-cooperativity settings, Residual HOS2 improves Jaccard similarity from 0.382 to 0.460, recall from 0.522 to 0.597, and exact recovery from 0.053 to 0.113 over a decomposable pairwise set scorer (PairS2), although exact recovery remains low.
On SERGIO DS3, oracle retrieval and TRACE show that candidate coverage is necessary but insufficient because set-level misranking remains the dominant source of exact-recovery failure. PairS2 proposal followed by Residual HOS2 reranking reduces HOS2-scored candidate sets by 94-97% while largely preserving exact-recovery behavior. These results distinguish edge ranking, candidate retrieval, set-level scoring, and exact cooperative regulator-set recovery as separate objectives.
| Subjects: | Machine Learning (cs.LG) |
| Cite as: | arXiv:2607.18602 [cs.LG] |
| (or arXiv:2607.18602v1 [cs.LG] for this version) | |
| https://doi.org/10.48550/arXiv.2607.18602
arXiv-issued DOI via DataCite (pending registration)
|
Submission history
From: Maryam Rahimimovassagh [view email][v1] Tue, 21 Jul 2026 00:31:48 UTC (391 KB)
Access Paper:
- View PDF
- HTML (experimental)
- TeX Source
References & Citations
Bookmark
Bibliographic and Citation Tools
Code, Data and Media Associated with this Article
Demos
Recommenders and Search Tools
arXivLabs: experimental projects with community collaborators
arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website.
Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them.
Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.
More from arXiv — Machine Learning
-
LoKiFormer: Locality-aware Attention with Decoupled Knowledge Memory for Efficient Large Language Model Pretraining
Aug 14
-
Which Site, and When: A Free-Satellite-Data Test of Himalayan Glacial Lake Bursts, Landslides, and Ice Floods
Aug 14
-
MARCH: Scaling Recurrent Memory with Content-Routed State Anchors
Aug 14
-
Multi-AUV Ad-hoc network-based Target Tracking: A Value Gradient Guidance Multi-Agent Diffusion Reinforcement Learning Approach
Aug 14
Discussion (0)
Sign in to join the discussion. Free account, 30 seconds — email code or GitHub.
Sign in →No comments yet. Sign in and be the first to say something.