Discretization-Aware Fine-Tuning for Quantum Machine Learning with Chemical Foundation Models

Quantum Physics arXiv:2609.03220 (quant-ph) [Submitted on 2 Sep 2026] Title:Discretization-Aware Fine-Tuning for Quantum Machine Learning with Chemical Foundation Models Authors:Shunji Matsuura, Sonika Johri View a PDF of the paper titled Discretization-Aware Fine-Tuning for Quantum Machine Learning with Chemical Foundation Models, by Shunji Matsuura and 1 other authors View PDF HTML (experimental) Abstract:A key challenge in practical quantum machine learning (QML), particularly for discriminative tasks such as classification, is the limited capacity of near-term quantum devices to encode high-dimensional classical data into small quantum registers. In optimized basis-encoded (bit-bit) settings, this constraint leads to cross-class collisions, where samples with different labels are mapped to the same discrete bit-string and thus become indistinguishable to any downstream model. In this work, we investigate how data representation affects QML performance under such severe information bottlenecks. We introduce discretization-aware fine-tuning (DAFT), a method that adapts a pre-trained chemical foundation model to produce representations that remain informative after quantization. DAFT reduces collision probability through a differentiable soft collision loss. We evaluate both quantum and classical models under a controlled setting in which they receive identical discretized bit-string inputs, isolating the effect of representation from model architecture. On the blood-brain barrier penetration (BBBP) molecular property prediction benchmark using ChemBERTa-77M, DAFT reduces collision counts by several orders of magnitude and improves quantum classification accuracy by more than 12 percentage points compared to a frozen backbone. Importantly, without DAFT, classical models outperform QML under the same input constraints. With DAFT, however, this comparison reverses at higher qubit counts. At 10 qubits, the quantum model surpasses a matched classical baseline trained on identical bit-strings (0.883 vs. 0.855, $p = 0.026$). These results show that, in information-constrained regimes, achieving a quantum advantage critically depends on aligning continuous representations with discrete quantum encodings. Comments: Subjects: Quantum Physics (quant-ph) Report number: RIKEN-iTHEMS-Report-26 Cite as: arXiv:2609.03220 [quant-ph] (or arXiv:2609.03220v1 [quant-ph] for this version) https://doi.org/10.48550/arXiv.2609.03220 Focus to learn more arXiv-issued DOI via DataCite (pending registration) Submission history From: Shunji Matsuura [view email] [v1] Wed, 2 Sep 2026 23:36:29 UTC (26 KB) Full-text links: Access Paper: View a PDF of the paper titled Discretization-Aware Fine-Tuning for Quantum Machine Learning with Chemical Foundation Models, by Shunji Matsuura and 1 other authorsView PDFHTML (experimental)TeX Source view license Current browse context: quant-ph new | recent | 2026-09 References & Citations INSPIRE HEP NASA ADSGoogle Scholar Semantic Scholar export BibTeX citation Loading... BibTeX formatted citation × loading... Data provided by: Bookmark Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer (What is the Explorer?) Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Code, Data and Media Associated with this Article alphaXiv Toggle alphaXiv (What is alphaXiv?) Links to Code Toggle CatalyzeX Code Finder for Papers (What is CatalyzeX?) DagsHub Toggle DagsHub (What is DagsHub?) GotitPub Toggle Gotit.pub (What is GotitPub?) Huggingface Toggle Hugging Face (What is Huggingface?) ScienceCast Toggle ScienceCast (What is ScienceCast?) Demos Demos Replicate Toggle Replicate (What is Replicate?) Spaces Toggle Hugging Face Spaces (What is Spaces?) Spaces Toggle TXYZ.AI (What is TXYZ.AI?) Related Papers Recommenders and Search Tools Link to Influence Flower Influence Flower (What are Influence Flowers?) Core recommender toggle CORE Recommender (What is CORE?) Author Venue Institution Topic About arXivLabs 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. Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)