Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes.

Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequencers and have resulted in a mix of contigs that derive from plasmids or chromosomes. New tools that accurately identify plasmids are needed to elucidate new plasmid-borne genes of high biological importance. We have developed Deeplasmid, a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data. It requires as input only assembled sequences generated by any sequencing platform and assembly algorithm and its runtime scales linearly with the number of assembled sequences. Deeplasmid achieves an AUC-ROC of over 89%, and it was more accurate than five other plasmid classification methods. Finally, as a proof of concept, we used Deeplasmid to predict new plasmids in the fish pathogen Yersinia ruckeri ATCC 29473 that has no annotated plasmids. Deeplasmid predicted with high reliability that a long assembled contig is part of a plasmid. Using long read sequencing we indeed validated the existence of a 102 kb long plasmid, demonstrating Deeplasmid's ability to detect novel plasmids.

Quantum-parallel vectorized data encodings and computations on trapped-ion and transmon QPUs.

Compact data representations in quantum systems are crucial for the development of quantum algorithms for data analysis. In this study, we present two innovative data encoding techniques, known as QCrank and QBArt, which exhibit significant quantum parallelism via uniformly controlled rotation gates. The QCrank method encodes a series of real-valued data as rotations on data qubits, resulting in increased storage capacity. On the other hand, QBArt directly incorporates a binary representation of the data within the computational basis, requiring fewer quantum measurements and enabling well-established arithmetic operations on binary data. We showcase various applications of the proposed encoding methods for various data types. Notably, we demonstrate quantum algorithms for tasks such as DNA pattern matching, Hamming weight computation, complex value conjugation, and the retrieval of a binary image with 384 pixels, all executed on the Quantinuum trapped-ion QPU. Furthermore, we employ several cloud-accessible QPUs, including those from IBMQ and IonQ, to conduct supplementary benchmarking experiments.

Quantum Computing and Visualization: A Disruptive Technological Change Ahead.

The focus of this Visualization Viewpoints article is to provide some background on quantum computing (QC), to explore ideas related to how visualization helps in understanding QC, and examine how QC might be useful for visualization with the growth and maturation of both technologies in the future. In a quickly evolving technology landscape, QC is emerging as a promising pathway to overcome the growth limits in classical computing. In some cases, QC platforms offer the potential to vastly outperform the familiar classical computer by solving problems more quickly or that may be intractable on any known classical platform. As further performance gains for classical computing platforms are limited by diminishing Moore's Law scaling, QC platforms might be viewed as a potential successor to the current field of exascale-class platforms. While present-day QC hardware platforms are still limited in scale, the field of quantum computing is robust and rapidly advancing in terms of hardware capabilities, software environments for developing quantum algorithms, and educational programs for training the next generation of scientists and engineers. After a brief introduction to QC concepts, the focus of this article is to explore the interplay between the fields of visualization and QC. First, visualization has played a role in QC by providing the means to show representations of the quantum state of single-qubits in superposition states and multiple-qubits in entangled states. Second, there are a number of ways in which the field of visual data exploration and analysis may potentially benefit from this disruptive new technology though there are challenges going forward.

Scaling and Benchmarking an Evolutionary Algorithm for Constructing Biophysical Neuronal Models.

Single neuron models are fundamental for computational modeling of the brain's neuronal networks, and understanding how ion channel dynamics mediate neural function. A challenge in defining such models is determining biophysically realistic channel distributions. Here, we present an efficient, highly parallel evolutionary algorithm for developing such models, named NeuroGPU-EA. NeuroGPU-EA uses CPUs and GPUs concurrently to simulate and evaluate neuron membrane potentials with respect to multiple stimuli. We demonstrate a logarithmic cost for scaling the stimuli used in the fitting procedure. NeuroGPU-EA outperforms the typically used CPU based evolutionary algorithm by a factor of 10 on a series of scaling benchmarks. We report observed performance bottlenecks and propose mitigation strategies. Finally, we also discuss the potential of this method for efficient simulation and evaluation of electrophysiological waveforms.