arXiv subjects

Fabio Cumbo

Publications and source records attributed to Fabio Cumbo.

7 recordsLinked to original sources

arXiv2026

Logarithmic-scale variational quantum eigensolver for off-lattice protein structure prediction in continuous torsional angle space

Classical and current quantum approaches to protein structure prediction (QPSP) face limitations, notably massive qubit requirements restricting near-term models to simplistic on-lattice simulations. We propose a logarithmic-scale variational quantum eigensolver (VQE) that reduces qubit requirements for N torsional degrees of freedom to O(log2N), enabling off-lattice, all-atom simulations. Our architecture extracts molecular torsions from relative phases in statevector simulations. On quantum hardware, a decoder maps the empirical cumulative distribution function (CDF) from basis-state probabilities to bounded torsional variables. These feed a classical algorithm to build heavy-atom coordinates. We use an EfficientSU2 ansatz and multi-stage relaxation to mitigate barren plateaus. Structures are evaluated via a custom hybrid quantum-classical Hamiltonian, alongside Rosetta and OpenMM benchmarks. Evaluation on chignolin and Trp-cage yielded native-like conformations. Chignolin reached a 0.623 {\AA} C{\alpha} RMSD in retained snapshots and 1.199 {\AA} in final models; Trp-cage achieved a 2.501 {\AA} RMSD among snapshots (3.512 {\AA} in final models). Execution on IBM processors (ibm_cleveland, ibm_miami) successfully recovered native-like structures with a best RMSD of 1.758 {\AA}. The custom energy function performed best overall, though energy-ranking imbalances persisted across sampled landscapes for all functions. This introduces the first all-atom, continuous-space quantum algorithm for QPSP. By converting physical qubit constraints into circuit depth constraints, it proves high-resolution prediction is feasible with exponentially fewer qubits. Despite current limits like computational overhead and energy function sensitivity, it establishes a scalable foundation for hybrid quantum biophysics.

quant-ph↗

arXiv2026

An Automatic Pipeline for the Integration of Python-Based Tools into the Galaxy Platform: Application to the anvi'o Framework

The integration of command-line tools into the Galaxy platform is crucial for making complex computational methods accessible to a broader audience and ensuring reproducible research. However, the manual development of tool wrappers is a time-consuming, error-prone, and knowledge-intensive process. This bottleneck significantly affects the rapid deployment of new and updated tools, creating a gap between tool development and its availability to the scientific community. We have developed a novel, automated approach that directly translates Python tool interfaces into Galaxy-compliant tool wrappers. Our method leverages the argparse library, a standard for command-line argument parsing in Python. By embedding structured metadata within the metavar attribute of input and output arguments, our system programmatically parses the tool's interface to extract all necessary information. This includes parameter types, data formats, help text, and input/output definitions. The system then uses this information to automatically generate a complete and valid Galaxy tool XML wrapper, requiring no manual intervention. To validate the scalability and effectiveness of our approach, we applied it to the anvi'o framework, a comprehensive and complex bioinformatics platform comprising hundreds of individual programs. Our method successfully parsed the argparse definitions for the entire anvi'o suite and generated functional Galaxy tool wrappers. The resulting integration allows for the seamless execution of anvi'o workflows within the Galaxy environment. This work presents a significant advancement in the automation of tool integration for scientific workflow systems. By establishing a convention-based approach using Python's argparse library, we have created a scalable and generalizable solution that dramatically reduces the effort required to make command-line tools available in Galaxy.

cs.SC↗

arXiv2026

hdlib 2.0: Extending Machine Learning Capabilities of Vector-Symbolic Architectures

Following the initial publication of hdlib, a Python library for designing Vector-Symbolic Architectures (VSA), we introduce a major extension that significantly enhances its machine learning capabilities. VSA, also known as Hyperdimensional Computing, is a computing paradigm that represents and processes information using high-dimensional vectors. While the first version of hdlib established a robust foundation for creating and manipulating these vectors, this update addresses the growing need for more advanced, data-driven modeling within the VSA framework. Here, we present four extensions: significant enhancements to the existing supervised classification model also enabling feature selection, and a new regression model for predicting continuous variables, a clustering model for unsupervised learning, and a graph-based learning model. Furthermore, we propose the first implementation ever of Quantum Hyperdimensional Computing with quantum-powered arithmetic operations and a new Quantum Machine Learning model for supervised learning. hdlib remains open-source and available on GitHub at https://github.com/cumbof/hdlib under the MIT license, and distributed through the Python Package Index (pip install hdlib) and Conda (conda install -c conda-forge hdlib). Documentation and examples of these new features are available on the official Wiki at https://github.com/cumbof/hdlib/wiki.

cs.LG↗

arXiv2025

Quantum Hyperdimensional Computing: a foundational paradigm for quantum neuromorphic architectures

A significant challenge in quantum computing (QC) is developing learning models that truly align with quantum principles, as many current approaches are complex adaptations of classical frameworks. In this work, we introduce Quantum Hyperdimensional Computing (QHDC), a fundamentally new paradigm. We demonstrate that the core operations of its classical counterpart, Hyperdimensional Computing (HDC), a brain-inspired model, map with remarkable elegance and direct correspondence onto the native operations of a QC. This suggests HDC is exceptionally well-suited for a quantum-native implementation. We establish a direct, resource-efficient mapping: (i) hypervectors are mapped to quantum states, (ii) the bundling operation is implemented as a quantum-native averaging process using a Linear Combination of Unitaries (LCU) and Oblivious Amplitude Amplification (OAA), (iii) the binding operation is realized via quantum phase oracles, (iv) the permutation operation is implemented using the Quantum Fourier Transform (QFT), and (v) vector similarity is calculated using quantum state fidelity measurements based on the Hadamard Test. We present the first-ever implementation of this framework, validated through symbolic analogical reasoning and supervised classification tasks. The viability of QHDC is rigorously assessed via a comparative analysis of results from classical computation, ideal quantum simulation, and execution of a 156-qubit IBM Heron r3 quantum processor. Our results validate the proposed mappings and demonstrate the versatility of the framework, establishing QHDC as a physically realizable technology. This work lays the foundation for a new class of quantum neuromorphic algorithms and opens a promising avenue for tackling complex cognitive and biomedical problems intractable for classical systems.

quant-ph↗

arXiv2025

Quantum Algorithm for Protein Structure Prediction Using the Face-Centered Cubic Lattice

In this work, we present the first implementation of the face-centered cubic (FCC) lattice model for protein structure prediction with a quantum algorithm. Our motivation to encode the FCC lattice stems from our observation that the FCC lattice is more capable in terms of modeling realistic secondary structures in proteins compared to other lattices, as demonstrated using root mean square deviation (RMSD). We utilize two quantum methods to solve this problem: a polynomial fitting approach (PolyFit) and the Variational Quantum Eigensolver with constraints (VQEC) based on the Lagrangian duality principle. Both methods are successfully deployed on Eagle R3 (ibm_cleveland) and Heron R2 (ibm_kingston) quantum computers, where we are able to recover ground state configurations for the 6-amino acid sequence KLVFFA under noise. A comparative analysis of the outcomes generated by the two QPUs reveals a significant enhancement (reaching nearly a two-fold improvement for PolyFit and a three-fold improvement for VQEC) in the prediction and sampling of the optimal solution (ground state conformations) on the newer Heron R2 architecture, highlighting the impact of quantum hardware advancements for this application.

quant-ph↗

arXiv2023

A perspective on protein structure prediction using quantum computers

Despite the recent advancements by deep learning methods such as AlphaFold2, \textit{in silico} protein structure prediction remains a challenging problem in biomedical research. With the rapid evolution of quantum computing, it is natural to ask whether quantum computers can offer some meaningful benefits for approaching this problem. Yet, identifying specific problem instances amenable to quantum advantage, and estimating quantum resources required are equally challenging tasks. Here, we share our perspective on how to create a framework for systematically selecting protein structure prediction problems that are amenable for quantum advantage, and estimate quantum resources for such problems on a utility-scale quantum computer. As a proof-of-concept, we validate our problem selection framework by accurately predicting the structure of a catalytic loop of the Zika Virus NS3 Helicase, on quantum hardware.

quant-ph↗

arXiv2018

Classification of large DNA methylation datasets for identifying cancer drivers

DNA methylation is a well-studied genetic modification crucial to regulate the functioning of the genome. Its alterations play an important role in tumorigenesis and tumor-suppression. Thus, studying DNA methylation data may help biomarker discovery in cancer. Since public data on DNA methylation become abundant, and considering the high number of methylated sites (features) present in the genome, it is important to have a method for efficiently processing such large datasets. Relying on big data technologies, we propose BIGBIOCL an algorithm that can apply supervised classification methods to datasets with hundreds of thousands of features. It is designed for the extraction of alternative and equivalent classification models through iterative deletion of selected features. We run experiments on DNA methylation datasets extracted from The Cancer Genome Atlas, focusing on three tumor types: breast, kidney, and thyroid carcinomas. We perform classifications extracting several methylated sites and their associated genes with accurate performance. Results suggest that BIGBIOCL can perform hundreds of classification iterations on hundreds of thousands of features in few hours. Moreover, we compare the performance of our method with other state-of-the-art classifiers and with a wide-spread DNA methylation analysis method based on network analysis. Finally, we are able to efficiently compute multiple alternative classification models and extract, from DNA-methylation large datasets, a set of candidate genes to be further investigated to determine their active role in cancer. BIGBIOCL, results of experiments, and a guide to carry on new experiments are freely available on GitHub.

q-bio.GN↗