Writhe-Based Polymer Link Classification Using Machine Learning

Graph Neural Networks (GNNs) have achieved strong results in molecular property prediction, but polymers present distinct challenges: labeled datasets are scarce and small (typically in the order of hundreds of polymers) due to the need for expensive experimentation, and complex polymer chain distributions influence polymer properties. Established practice in polymer prediction represents polymers solely by graphs of their repeat units, discarding the chain-scale morphology that governs key properties such as the glass transition temperature ($T_g$). In this work, we propose a principled graph construction that addresses this gap. Given a polymer's molecular mass distribution (MMD), we sample representative chains from the Schulz-Zimm distribution and construct representative sets of large graphs encoding chain-scale topology directly, with atoms and bonds featurized using rich chemical descriptors. We further pretrain GNN encoders via masked graph modeling on 100,000 unlabeled PSMILES strings before fine-tuning on labeled data. On a dataset of 381 polymers (180 homopolymers and 201 copolymers), we show that graph construction and self-supervised pretraining are jointly necessary: without pretraining, the large graph method matches the repeat-unit baseline (28.40 K vs. 28.36 K RMSE); with pretraining, it achieves 24.76 K +/- 3.30 K, a 5.1% reduction in mean error over the pretrained repeat-unit baseline (26.08 K +/- 4.20 K, p < 0.001, 30 runs). An ablation removing chemical features degrades performance to 36.65 K, confirming both components are essential. Results are architecture-agnostic, holding for both GINE and GATv2 encoders.

Polymers underpin applications across energy, healthcare, and materials science, yet their vast chemical space makes systematic discovery challenging. Most machine learning approaches represent polymers as molecular graphs of a single repeating unit, thereby missing both the periodicity of polymer chains and many-body interactions beyond pairwise bonds. We introduce Periodic-TDL, a deep learning framework built on periodic Vietoris-Rips complexes that capture many-body interactions across multiple spatial scales, followed by a hierarchical simplicial message-passing (HSMP) encoder that propagates information from long-range interactions to covalent bonds, yielding representations enriched by higher-order topological features. Periodic-TDL outperforms all state-of-the-art models across polymer property prediction tasks spanning electronic, optical, physical, and thermal targets. Furthermore, we quantitatively validate how ester-to-amide substitution and $α$-methylation enhance thermal stability. Using a computationally synthesized dataset of 48,208 structures-generated via systematic substitution of acrylate and acrylamide polymers-we observed a mean $T_g$ increase of $\sim 55^\circ$C for ester-to-amide substitutions and $\sim 14^\circ$C for backbone $α$-methylation across matched polymer pairs. To verify these predicted trends, we use our Periodic-TDL model to analyze six novel polymer pairs from independent experimental measurements, including three newly synthesized polymers previously unreported in the literature. The experimental data successfully confirmed the model's predictions. Ultimately, these findings demonstrate that Periodic-TDL captures the underlying physical effects of specific functional group modifications, rather than merely optimizing predictive performance on benchmark datasets.

We study layered models, including feedforward networks, ResNets, and transformers, by limiting each layer to a width of $d = 3$, i.e., $\mathbb{R}^3$ as representation space. This allows us to track how a neural network changes low-dimensional topological invariants through its layers. Just about any topological structure may be simplified or even trivialized by simply increasing dimension; e.g., any knot is equivalent to an unknot in $\mathbb{R}^4$. By restricting to $\mathbb{R}^3$, we not only isolate the effects of activation and depth from that of width, we work in a space that lends itself to easy visualization. We focus on linking number here, deferring other invariants like link groups, Milnor's $\barμ$-invariants, knot types, ambient cobordisms, to a sequel. We provide full proofs and empirical experiments to justify the following insights: When measured by their power to effect changes in linking numbers, the layer-skipping feature in ResNets is as powerful as the attention mechanism in transformers; both ResNets and transformers are strictly more powerful than feedforward neural networks with monotonic activations, which are in turn more powerful than invertible and flow-based models; but replacing monotonic activation with a nonmonotonic one elevates a feedforward network into the same expressivity class as ResNets and transformers. These results suggest that low-dimensional topology can be a useful tool to guide designs of AI architectures. We also generalize our results from $d = 3$ to arbitrary $d > 3$.