Search for: All records

Abstract MotivationConditional testing via the knockoff framework allows one to identify—among a large number of possible explanatory variables—those that carry unique information about an outcome of interest and also provides a false discovery rate guarantee on the selection. This approach is particularly well suited to the analysis of genome-wide association studies (GWAS), which have the goal of identifying genetic variants that influence traits of medical relevance. ResultsWhile conditional testing can be both more powerful and precise than traditional GWAS analysis methods, its vanilla implementation encounters a difficulty common to all multivariate analysis methods: it is challenging to distinguish among multiple, highly correlated regressors. This impasse can be overcome by shifting the object of inference from single variables to groups of correlated variables. To achieve this, it is necessary to construct “group knockoffs.” While successful examples are already documented in the literature, this paper substantially expands the set of algorithms and software for group knockoffs. We focus in particular on second-order knockoffs, for which we describe correlation matrix approximations that are appropriate for GWAS data and that result in considerable computational savings. We illustrate the effectiveness of the proposed methods with simulations and with the analysis of albuminuria data from the UK Biobank. Availability and implementationThe described algorithms are implemented in an open-source Julia package Knockoffs.jl. R and Python wrappers are available as knockoffsr and knockoffspy packages. 

The neutral atom array has gained prominence in quantum computing for its scalability and operation fidelity. Previous works focus on fixed atom arrays (FAAs) that require extensive SWAP operations for long-range interactions. This work explores a novel architecture reconfigurable atom arrays (RAAs), also known as field programmable qubit arrays (FPQAs), which allows for coherent atom movements during circuit execution under some constraints. Such atom movements, which are unique to this architecture, could reduce the cost of longrange interactions significantly if the atom movements could be scheduled strategically. In this work, we introduce Atomique, a compilation framework designed for qubit mapping, atom movement, and gate scheduling for RAA. Atomique contains a qubit-array mapper to decide the coarse-grained mapping of the qubits to arrays, leveraging MAX k-Cut on a constructed gate frequency graph to minimize SWAP overhead. Subsequently, a qubit-atom mapper determines the fine-grained mapping of qubits to specific atoms in the array and considers load balance to prevent hardware constraint violations. We further propose a router that identifies parallel gates, schedules them simultaneously, and reduces depth. We evaluate Atomique across 20+ diverse benchmarks, including generic circuits (arbitrary, QASMBench, SupermarQ), quantum simulation, and QAOA circuits. Atomique consistently outperforms IBM Superconducting, FAA with long-range gates, and FAA with rectangular and triangular topologies, achieving significant reductions in depth and the number of two-qubit gates. 

Parameterized Quantum Circuits (PQC) are promising towards quantum advantage on near-term quantum hardware. However, due to the large quantum noises (errors), the performance of PQC models has a severe degradation on real quantum devices. Take Quantum Neural Network (QNN) as an example, the accuracy gap between noise-free simulation and noisy results on IBMQ-Yorktown for MNIST-4 classification is over 60%. Existing noise mitigation methods are general ones without leveraging unique characteristics of PQC; on the other hand, existing PQC work does not consider noise effect. To this end, we present QuantumNAT, a PQC-specific framework to perform noise-aware optimizations in both training and inference stages to improve robustness. We experimentally observe that the effect of quantum noise to PQC measurement outcome is a linear map from noise-free outcome with a scaling and a shift factor. Motivated by that, we propose post-measurement normalization to mitigate the feature distribution differences between noise-free and noisy scenarios. Furthermore, to improve the robustness against noise, we propose noise injection to the training process by inserting quantum error gates to PQC according to realistic noise models of quantum hardware. Finally, post-measurement quantization is introduced to quantize the measurement outcomes to discrete values, achieving the denoising effect. Extensive experiments on 8 classification tasks using 6 quantum devices demonstrate that QuantumNAT improves accuracy by up to 43%, and achieves over 94% 2-class, 80% 4-class, and 34% 10-class classification accuracy measured on real quantum computers. The code for construction and noise-aware training of PQC is available in the TorchQuantum library. 

Quantum Computing has attracted much research attention because of its potential to achieve fundamental speed and efficiency improvements in various domains. Among different quantum algorithms, Parameterized Quantum Circuits (PQC) for Quantum Machine Learning (QML) show promises to realize quantum advantages on the current Noisy Intermediate-Scale Quantum (NISQ) Machines. Therefore, to facilitate the QML and PQC research, a recent python library called TorchQuantum has been released. It can construct, simulate, and train PQC for machine learning tasks with high speed and convenient debugging supports. Besides quantum for ML, we want to raise the community's attention on the reversed direction: ML for quantum. Specifically, the TorchQuantum library also supports using data-driven ML models to solve problems in quantum system research, such as predicting the impact of quantum noise on circuit fidelity and improving the quantum circuit compilation efficiency. This paper presents a case study of the ML for quantum part in TorchQuantum. Since estimating the noise impact on circuit reliability is an essential step toward understanding and mitigating noise, we propose to leverage classical ML to predict noise impact on circuit fidelity. Inspired by the natural graph representation of quantum circuits, we propose to leverage a graph transformer model to predict the noisy circuit fidelity. We firstly collect a large dataset with a variety of quantum circuits and obtain their fidelity on noisy simulators and real machines. Then we embed each circuit into a graph with gate and noise properties as node features, and adopt a graph transformer to predict the fidelity. We can avoid exponential classical simulation cost and efficiently estimate fidelity with polynomial complexity. Evaluated on 5 thousand random and algorithm circuits, the graph transformer predictor can provide accurate fidelity estimation with RMSE error 0.04 and outperform a simple neural network-based model by 0.02 on average. It can achieve 0.99 and 0.95 R2 scores for random and algorithm circuits, respectively. Compared with circuit simulators, the predictor has over 200× speedup for estimating the fidelity. The datasets and predictors can be accessed in the TorchQuantum library.