Predicting Transmembrane Protein Topology from 3D Structure

Sitong Chen; Xiaopeng Mao

Home/Archive/arXiv

arXiv · 2609.30446

Predicting Transmembrane Protein Topology from 3D Structure

Sitong Chen·Xiaopeng Mao

View original source ↗Read source document ↗Export metadata ↓

Abstract

This paper presents a novel approach to infer protein topology using the state-of-the-art graph neural network (GNN), SchNet. The model is trained on the same dataset used to develop the recent DeepTMHMM model with 5-fold cross-validation. Unlike the conventional approaches based on using only the protein sequences or the $α$-carbons as features, we have decoded our classifier in this way, so all atom-level embeddings are used. Without applying any pre-trained weight, the final results have shown great potential that GNNs can be used for topological predictions.

Explore related subjects

cs.AI

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Sitong Chen, Xiaopeng Mao. 2026-09-24. Predicting Transmembrane Protein Topology from 3D Structure. https://arxiv.org/abs/2609.30446

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

KEEP EXPLORING

Related papers

arXiv2026

Sequence Variables: A Constraint Programming Computational Domain for Routing and Sequencing

Constraint Programming (CP) offers an intuitive, declarative framework for modeling Vehicle Routing Problems (VRP). While classical successor-based CP models can be adapted to handle optional visits or insertion-based heuristics, sequence variables provide a significantly more natural and elegant formulation for these requirements. Building upon our prior work that introduced the initial concept, the main contribution of this article is the complete semantic and operational formalization of sequence variables as a computational domain. Specifically, we formally define the sequence domain and its update operations, and detail the implementation and data structures required to integrate sequence variables into trail-based CP solvers. Furthermore, we introduce consistency levels for associated constraints on this domain alongside specialized global constraints tailored for routing problems. Finally, we demonstrate that sequence variables simplify problem modeling while achieving competitive computational performance on Pickup and Delivery Problems with and without Time Windows, the Dial-a-Ride Problem, and a Prize-Collecting Scheduling Problem.

cs.AI↗

arXiv2026

Agentic AI for Clustering, Relationship Discovery, and Semantic Trading in Prediction Markets

Prediction markets allow users to trade on outcomes of real-world events, but are prone to fragmentation with overlapping questions, implicit equivalences, and hidden contradictions across markets. We present an agentic AI (AAI) pipeline that autonomously recovers cross-market structure from contract text before prices enter the analysis. The workflow first clusters markets into coherent topical groups using natural-language understanding over contract text and metadata, and then identifies contracts within each cluster, but from different event markets, that exhibit strong dependence or leader--follower relationships. We evaluate this system, along with a natural language inference (NLI) benchmark, on a large prediction market dataset from early 2026. Using resolved outcomes to evaluate identified relations, we find that AAI-identified relations are 62.8\% consistent with exchange-recorded settlements, whereas the NLI benchmark only achieves 40.6\% accuracy. Within clusters, the AAI output is sparse and also remarkably compatible as a signed graph with a frustration rate of 0.324\%. As an application, we show how discovered relations inform semantics-based trading strategies on prediction markets. One such strategy yields 14.12\% net ROI after fees in a two-month period in 2026. Overall, we demonstrate the potential for agentic AI as a structural discovery layer for prediction markets.

cs.AI↗

arXiv2026

Nonlinearity as Rank: Generative Low-Rank Adapter with Radial Basis Functions

Low-rank adaptation (LoRA) approximates the update of a pretrained weight matrix using the product of two low-rank matrices. However, standard LoRA follows an explicit-rank paradigm, where increasing model capacity requires adding more rows or columns (i.e., basis vectors) to the low-rank matrices, leading to substantial parameter growth. In this paper, we find that these basis vectors exhibit significant parameter redundancy and can be compactly represented by lightweight nonlinear functions. Therefore, we propose Generative Low-Rank Adapter (GenLoRA), which replaces explicit basis vector storage with nonlinear basis vector generation. Specifically, GenLoRA maintains a latent vector for each low-rank matrix and employs a set of lightweight radial basis functions (RBFs) to synthesize the basis vectors. Each RBF requires far fewer parameters than an explicit basis vector, enabling higher parameter efficiency in GenLoRA. Extensive experiments across multiple datasets and architectures show that GenLoRA attains higher effective LoRA ranks under smaller parameter budgets, resulting in superior fine-tuning performance. The code is available at https://anonymous.4open.science/r/GenLoRA.

cs.AI↗