In this research, we extend the universal reinforcement learning agent models of artificial general intelligence to quantum environments. The utility function of a classical exploratory stochastic Knowledge Seeking Agent, KL-KSA, is generalized to distance measures from quantum information theory on density matrices. Quantum process tomography (QPT) algorithms form a tractable subset of programs for modeling environmental dynamics. The optimal QPT policy is selected based on a mutable cost function based on algorithmic complexity as well as computational resource complexity. The entire agent design is encapsulated in a self-replicating quine which mutates the cost function based on the predictive value of the optimal policy choosing scheme. Thus, multiple agents with pareto-optimal QPT policies evolve using genetic programming, mimicking the development of physical theories each with different resource trade-offs. This formal framework, termed Quantum Knowledge Seeking Agent (QKSA), is a resource-bounded participatory observer modification to the recently proposed algorithmic information-based reconstruction of quantum mechanics. A proof-of-concept is implemented and available as open-sourced software.

With the potential of quantum algorithms to solve intractable classical problems, quantum computing is rapidly evolving, and more algorithms are being developed and optimized. Expressing these quantum algorithms using a high-level language and making them executable on a quantum processor while abstracting away hardware details is a challenging task. First, a quantum programming language should provide an intuitive programming interface to describe those algorithms. Then a compiler has to transform the program into a quantum circuit, optimize it, and map it to the target quantum processor respecting the hardware constraints such as the supported quantum operations, the qubit connectivity, and the control electronics limitations. In this article, we propose a quantum programming framework named OpenQL, which includes a high-level quantum programming language and its associated quantum compiler. We present the programming interface of OpenQL, we describe the different layers of the compiler and how we can provide portability over different qubit technologies. Our experiments show that OpenQL allows the execution of the same high-level algorithm on two different qubit technologies, namely superconducting qubits and Si-Spin qubits. Besides the executable code, OpenQL also produces an intermediate quantum assembly code, which is technology independent and can be simulated using the QX simulator.

In this article, we present QuASeR, a reference-free DNA sequence reconstruction implementation via de novo assembly on both gate-based and quantum annealing platforms. This is the first time this important application in bioinformatics is modeled using quantum computation. Each one of the four steps of the implementation (TSP, QUBO, Hamiltonians and QAOA) is explained with a proof-of-concept example to target both the genomics research community and quantum application developers in a self-contained manner. The implementation and results on executing the algorithm from a set of DNA reads to a reconstructed sequence, on a gate-based quantum simulator, the D-Wave quantum annealing simulator and hardware are detailed. We also highlight the limitations of current classical simulation and available quantum hardware systems. The implementation is open-source and can be found on https://github.com/QE-Lab/QuASeR.

Memristor-based Computation-in-Memory (CIM) is one of the emerging architectures for next-generation Big Data problems. Its design requires a radically new synthesis flow as the memristor is a passive device that uses resistances to encode its logic values. This article proposes a synthesis flow for mapping parallel applications on memristor-based CIM architecture. First, it employs solution templates that contain scheduling, placement, and routing information to map multiple algorithms with similar data flow graphs to the memristor crossbar; this template is named skeleton. Complex algorithms that do not fit a single skeleton can be solved by nested skeletons. Therefore, this approach can be applied to a wide range of applications while using a limited number of skeletons only. Second, it further improves the design when spatial and temporal patterns exist in input data. To accelerate simulation of generated SystemC models, we integrate MPI in skeletons. The synthesis flow and its additional features are verified with multiple applications, and the results are compared against a multicore platform. These experiments demonstrate the feasibility and the potential of this approach.

BACKGROUND: In Overlap-Layout-Consensus (OLC) based de novo assembly, all reads must be compared with every other read to find overlaps. This makes the process rather slow and limits the practicality of using de novo assembly methods at a large scale in the field. Darwin is a fast and accurate read overlapper that can be used for de novo assembly of state-of-the-art third generation long DNA reads. Darwin is designed to be hardware-friendly and can be accelerated on specialized computer system hardware to achieve higher performance. RESULTS: This work accelerates Darwin on GPUs. Using real Pacbio data, our GPU implementation on Tesla K40 has shown a speedup of 109x vs 8 CPU threads of an Intel Xeon machine and 24x vs 64 threads of IBM Power8 machine. The GPU implementation supports both linear and affine gap, scoring model. The results show that the GPU implementation can achieve the same high speedup for different scoring schemes. CONCLUSIONS: The GPU implementation proposed in this work shows significant improvement in performance compared to the CPU version, thereby making it accessible for utilization as a practical read overlapper in a DNA assembly pipeline. Furthermore, our GPU acceleration can also be used for performing fast Smith-Waterman alignment between long DNA reads. GPU hardware has become commonly available in the field today, making the proposed acceleration accessible to a larger public. The implementation is available at https://github.com/Tongdongq/darwin-gpu .

Quantum computers hold great promise for accelerating computationally challenging algorithms on noisy intermediate-scale quantum (NISQ) devices in the upcoming years. Much attention of the current research is directed towards algorithmic research on artificial data that is disconnected from live systems, such as optimization of systems or training of learning algorithms. In this paper we investigate the integration of quantum systems into industry-grade system architectures. In this work we propose a system architecture for the integration of quantum accelerators. In order to evaluate our proposed system architecture we investigated various data-driven functions for various accelerators, including a classical system, a gate-based quantum accelerator and a quantum annealer. The data-driven function predict user preference and is trained on real-world data. This work also includes an evaluation of the quantum enhanced kernel, that previously was only evaluated on artificial data. In our evaluation, we showed that the quantum-enhanced kernel performs at least equally well to a classical state-of-The-Art kernel when simulated. We also showed a low reduction in accuracy and latency numbers within acceptable bounds when running on the gate-based IBM quantum accelerator. We therefore conclude it is feasible to integrate NISQ-era devices in industry-grade system architectures in preparation for future advancements in quantum hardware.

This paper presents the definition and implementation of a quantum computer architecture to enable creating a new computational device - a quantum computer as an accelerator. A key question addressed is what such a quantum computer is and how it relates to the classical processor that controls the entire execution process. In this paper, we present explicitly the idea of a quantum accelerator which contains the full stack of the layers of an accelerator. Such a stack starts at the highest level describing the target application of the accelerator. The next layer abstracts the quantum logic outlining the algorithm that is to be executed on the quantum accelerator. In our case, the logic is expressed in the universal quantum-classical hybrid computation language developed in the group, called OpenQL, which visualised the quantum processor as a computational accelerator. The OpenQL compiler translates the program to a common assembly language, called cQASM, which can be executed on a quantum simulator. The cQASM represents the instruction set that can be executed by the micro-architecture implemented in the quantum accelerator. We propose that the industrial and societal application developers use perfect qubits that have no decoherence or error-rates. The perfect qubits offers facilities to the quantum application developer and they are not blocked by issues such as decoherence.

Matching algorithms can be used for identifying errors in quantum systems, being the most famous the Blossom algorithm. Recent works have shown that small distance quantum error correction codes can be efficiently decoded by employing machine learning techniques based on neural networks (NN). Various NN-based decoders have been proposed to enhance the decoding performance and the decoding time. Their implementation differs in how the decoding is performed, at logical or physical level, as well as in several neural network related parameters. In this work, we implement and compare two NN-based decoders, a low level decoder and a high level decoder, and study how different NN parameters affect their decoding performance and execution time. Crucial parameters such as the size of the training dataset, the structure and the type of the neural network, and the learning rate used during training are discussed. After performing this comparison, we conclude that the high level decoder based on a Recurrent NN shows a better balance between decoding performance and execution time and it is much easier to train. We then test its decoding performance for different code distances, probability datasets and under the depolarizing and circuit error models.

The implementation and practicality of quantum algorithms hinge largely on the quality of operations within a quantum processor. Therefore, including realistic error models in quantum computing simulation platforms is crucial for testing these algorithms. Existing classical simulation techniques of quantum information processing devices exhibit a tradeoff between scalability (the number of qubits that can be simulated) and accuracy (how close the simulation is to the target error model). In this paper, we introduce a simulation approach that relies on approximating the density matrix evolution with a stochastic sum of unitary and measurement channels within a pure-state simulation environment. This model shows an improvement of at least one order of magnitude in terms of accuracy compared to the best known stochastic approaches while allowing us to simulate a larger number of qubits compared to the exact density matrix simulation. Furthermore, we used this approach to realistically simulate Grover's algorithm and the surface code 17 using a gate set tomography characterization of quantum operations as a noise model.

Following publication of the original article [1], the author requested changes to the figures 4, 7, 8, 9, 12 and 14 to align these with the text. The corrected figures are supplied below. The original article [1] has been corrected. [Typesetter, please insert new supplied figure in package].

BACKGROUND: Due the computational complexity of sequence alignment algorithms, various accelerated solutions have been proposed to speedup this analysis. NVBIO is the only available GPU library that accelerates sequence alignment of high-throughput NGS data, but has limited performance. In this article we present GASAL2, a GPU library for aligning DNA and RNA sequences that outperforms existing CPU and GPU libraries. RESULTS: The GASAL2 library provides specialized, accelerated kernels for local, global and all types of semi-global alignment. Pairwise sequence alignment can be performed with and without traceback. GASAL2 outperforms the fastest CPU-optimized SIMD implementations such as SeqAn and Parasail, as well as NVIDIA's own GPU-based library known as NVBIO. GASAL2 is unique in performing sequence packing on GPU, which is up to 750x faster than NVBIO. Overall on Geforce GTX 1080 Ti GPU, GASAL2 is up to 21x faster than Parasail on a dual socket hyper-threaded Intel Xeon system with 28 cores and up to 13x faster than NVBIO with a query length of up to 300 bases and 100 bases, respectively. GASAL2 alignment functions are asynchronous/non-blocking and allow full overlap of CPU and GPU execution. The paper shows how to use GASAL2 to accelerate BWA-MEM, speeding up the local alignment by 20x, which gives an overall application speedup of 1.3x vs. CPU with up to 12 threads. CONCLUSIONS: The library provides high performance APIs for local, global and semi-global alignment that can be easily integrated into various bioinformatics tools.

Modern computer applications usually consist of a variety of components that often require quite different computational co-processors. Some examples of such co-processors are TPUs, GPUs or FPGAs. A more recent and promising technology that is being investigated is quantum co-processors. In this paper, we present a modern computer architecture where a quantum co-processor is included as an additional accelerator. In such an environment, the idea is to execute the application on a heterogeneous architecture where the classic processor will execute the host part, but certain components will be mapped, in our case, on the quantum accelerator. To this purpose, we define the distinct layers for the quantum computer architecture where there is a clear boundary between the host program and quantum kernel(s). We also discuss the opportunities and challenges of mapping hybrid algorithms to such a heterogeneous quantum computer architecture.