Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2610.00672

ORBIT-FMIB: Tracking Order-Resolved Epistatic Information Through ESM-2

Maryam Rahimimovassagh·Ivan Garibay·Niloofar Yousefi
View original source ↗Read source document ↗Export metadata ↓

Abstract

Protein foundation models support mutation-effect and structural prediction, but predictive performance alone does not reveal which forms of biological interaction information remain accessible through model depth. We ask whether ESM-2 retains higher-order epistatic information as strongly as first- and second-order information across its representation hierarchy, introducing ORBIT-FMIB, a diagnostic framework combining Walsh-based interaction decomposition with subset-conditioned neural dependence estimation. The method is validated on synthetic landscapes with known interaction structure before being applied to the dense four-site GB1 fitness landscape using frozen ESM-2 representations. An initial production run suggested ESM-2 retains higher-order epistatic information less well than lower-order information ($Δ_{\mathrm{HO-LO}}=-0.107$). An independent replication of the complete measurement grid, under matched GPU hardware and identical critic seeds, substantially reduced this contrast ($Δ_{\mathrm{HO-LO}}=-0.017$), and its sign was unstable across otherwise-defensible evaluation-pairing choices applied to the same trained critics ($-0.011$ to $+0.015$). We therefore do not currently have robust evidence that ESM-2 selectively loses higher-order epistatic information, nor that retention is equal across orders; the directional question remains open. The measurement protocol itself, including its documented removal of a positional-subset shortcut in pooled critics, remains validated and is unaffected by this finding. ORBIT-FMIB is offered as a diagnostic framework for probing interaction structure in protein foundation models; this study's own replication result illustrates why such probing requires adequately-powered reproducibility checks before its output is treated as a biological finding.

Explore related subjects

cs.LGq-bio.QM

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Maryam Rahimimovassagh, Ivan Garibay, Niloofar Yousefi. 2026-09-30. ORBIT-FMIB: Tracking Order-Resolved Epistatic Information Through ESM-2. https://arxiv.org/abs/2610.00672

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Roto-translated Local Coordinate Frames For Interacting Dynamical Systems

Modelling interactions is critical in learning complex dynamical systems, namely systems of interacting objects with highly non-linear and time-dependent behaviour. A large class of such systems can be formalized as $\textit{geometric graphs}$, $\textit{i.e.}$, graphs with nodes positioned in the Euclidean space given an $\textit{arbitrarily}$ chosen global coordinate system, for instance vehicles in a traffic scene. Notwithstanding the arbitrary global coordinate system, the governing dynamics of the respective dynamical systems are invariant to rotations and translations, also known as $\textit{Galilean invariance}$. As ignoring these invariances leads to worse generalization, in this work we propose local coordinate frames per node-object to induce roto-translation invariance to the geometric graph of the interacting dynamical system. Further, the local coordinate frames allow for a natural definition of anisotropic filtering in graph neural networks. Experiments in traffic scenes, 3D motion capture, and colliding particles demonstrate that the proposed approach comfortably outperforms the recent state-of-the-art.

cs.LG↗
arXiv2026

Geometry-Aware Adaptation for Pretrained Models

Machine learning models -- including prominent zero-shot models -- are often trained on datasets whose labels are only a small proportion of a larger label space. Such spaces are commonly equipped with a metric that relates the labels via distances between them. We propose a simple approach to exploit this information to adapt the trained model to reliably predict new classes -- or, in the case of zero-shot prediction, to improve its performance -- without any additional training. Our technique is a drop-in replacement of the standard prediction rule, swapping argmax with the Fréchet mean. We provide a comprehensive theoretical analysis for this approach, studying (i) learning-theoretic results trading off label space diameter, sample complexity, and model dimension, (ii) characterizations of the full range of scenarios in which it is possible to predict any unobserved class, and (iii) an optimal active learning-like next class selection procedure to obtain optimal training classes for when it is not possible to predict the entire range of unobserved classes. Empirically, using easily-available external metrics, our proposed approach, Loki, gains up to 29.7% relative improvement over SimCLR on ImageNet and scales to hundreds of thousands of classes. When no such metric is available, Loki can use self-derived metrics from class embeddings and obtains a 10.5% improvement on pretrained zero-shot models such as CLIP.

cs.LG↗
arXiv2026

Information propagation dynamics in Deep Graph Networks

Graphs are a highly expressive abstraction for modeling entities and their relations, such as molecular structures, social networks, and traffic networks. Deep Graph Networks (DGNs) have emerged as a family of deep learning models that can effectively process and learn such structured information. However, learning effective information propagation patterns within DGNs remains a critical challenge that heavily influences the model capabilities, both in the static domain and in the temporal domain (where features and/or topology evolve). Given this challenge, this thesis investigates the dynamics of information propagation within DGNs for static and dynamic graphs, focusing on their design as dynamical systems. Throughout this work, we provide theoretical and empirical evidence to demonstrate the effectiveness of our proposed architectures in propagating and preserving long-term dependencies between nodes, and in learning complex spatio-temporal patterns from irregular and sparsely sampled dynamic graphs. In summary, this thesis provides a comprehensive exploration of the intersection between graphs, deep learning, and dynamical systems, offering insights and advancements for the field of graph representation learning and paving the way for more effective and versatile graph-based learning models.

cs.LG↗