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Graphormer-IR: Graph Transformers Can Predict Experimental IR Spectra Using Highly Specialized Attention

Authors: Cailum M. K. Stienstra; Liam Hebert; Patrick Thomas; Alexander Haack; Jason Guo; W. Scott Hopkins;

Graphormer-IR: Graph Transformers Can Predict Experimental IR Spectra Using Highly Specialized Attention

Abstract

Infrared (IR) spectroscopy is crucial in various chemical and forensic domains, but faster in silico methods for predicting experimental spectra are needed due to the time and accuracy limitations of ab initio methods. We employ Graphormer, a graph neural network (GNN) transformer, to predict IR spectra using only Simplified Molecular-Input Line-Entry System (SMILES) strings. Our dataset includes 53,528 high-quality spectra with elements H, C, N, O, F, Si, S, P, Cl, Br, and I in five solvent phases. When using only atomic numbers for node encodings, Graphormer-IR achieved SIS_μ test scores of 0.8449±0.0012 (n=5), surpassing the state-of-the-art Chemprop-IR (SIS_μ = 0.8409 ± 0.0014, n=5), with only 36% of the encoded information. Augmenting node embeddings with additional node-level descriptors in learned embeddings generated through a multi-layer perceptron improves scores to SIS_μ = 0.8523±0.0006, a total improvement of 19.7σ. These improved scores show how Graphormer-IR excels in capturing long-range interactions like hydrogen bonding, anharmonic peak positions in experimental spectra, and stretching frequencies of uncommon functional groups. Scaling our architecture to 210 attention heads demonstrates specialist-like behavior for distinct IR frequencies that improves model performance. Our model utilizes novel architectures, including a global node for solvent phase encoding, learned node feature embeddings, and a 1D smoothing CNN. Graphormer-IR’s innovations underscore its potency over traditional message-passing neural networks (MPNNs) due to its expressive embeddings and ability to capture long-range intra-molecular relationships.

Keywords

Spectrophotometry, Infrared, Neural Networks, Computer

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
6
Top 10%
Average
Top 10%
hybrid