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  1. Abstract

    Due to its specificity, fluorescence microscopy has become a quintessential imaging tool in cell biology. However, photobleaching, phototoxicity, and related artifacts continue to limit fluorescence microscopy’s utility. Recently, it has been shown that artificial intelligence (AI) can transform one form of contrast into another. We present phase imaging with computational specificity (PICS), a combination of quantitative phase imaging and AI, which provides information about unlabeled live cells with high specificity. Our imaging system allows for automatic training, while inference is built into the acquisition software and runs in real-time. Applying the computed fluorescence maps back to the quantitative phase imaging (QPI) data, we measured the growth of both nuclei and cytoplasm independently, over many days, without loss of viability. Using a QPI method that suppresses multiple scattering, we measured the dry mass content of individual cell nuclei within spheroids. In its current implementation, PICS offers a versatile quantitative technique for continuous simultaneous monitoring of individual cellular components in biological applications where long-term label-free imaging is desirable.

  2. Abstract

    Significant investments to upgrade and construct large-scale scientific facilities demand commensurate investments in R&D to design algorithms and computing approaches to enable scientific and engineering breakthroughs in the big data era. Innovative Artificial Intelligence (AI) applications have powered transformational solutions for big data challenges in industry and technology that now drive a multi-billion dollar industry, and which play an ever increasing role shaping human social patterns. As AI continues to evolve into a computing paradigm endowed with statistical and mathematical rigor, it has become apparent that single-GPU solutions for training, validation, and testing are no longer sufficient for computational grand challenges brought about by scientific facilities that produce data at a rate and volume that outstrip the computing capabilities of available cyberinfrastructure platforms. This realization has been driving the confluence of AI and high performance computing (HPC) to reduce time-to-insight, and to enable a systematic study of domain-inspired AI architectures and optimization schemes to enable data-driven discovery. In this article we present a summary of recent developments in this field, and describe specific advances that authors in this article are spearheading to accelerate and streamline the use of HPC platforms to design and apply accelerated AI algorithms in academiamore »and industry.

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  3. Abstract Background Modern Next Generation- and Third Generation- Sequencing methods such as Illumina and PacBio Circular Consensus Sequencing platforms provide accurate sequencing data. Parallel developments in Deep Learning have enabled the application of Deep Neural Networks to variant calling, surpassing the accuracy of classical approaches in many settings. DeepVariant, arguably the most popular among such methods, transforms the problem of variant calling into one of image recognition where a Deep Neural Network analyzes sequencing data that is formatted as images, achieving high accuracy. In this paper, we explore an alternative approach to designing Deep Neural Networks for variant calling, where we use meticulously designed Deep Neural Network architectures and customized variant inference functions that account for the underlying nature of sequencing data instead of converting the problem to one of image recognition. Results Results from 27 whole-genome variant calling experiments spanning Illumina, PacBio and hybrid Illumina-PacBio settings suggest that our method allows vastly smaller Deep Neural Networks to outperform the Inception-v3 architecture used in DeepVariant for indel and substitution-type variant calls. For example, our method reduces the number of indel call errors by up to 18%, 55% and 65% for Illumina, PacBio and hybrid Illumina-PacBio variant calling respectively, compared tomore »a similarly trained DeepVariant pipeline. In these cases, our models are between 7 and 14 times smaller. Conclusions We believe that the improved accuracy and problem-specific customization of our models will enable more accurate pipelines and further method development in the field. HELLO is available at https://github.com/anands-repo/hello« less
  4. Abstract Seismograms are convolution results between seismic sources and the media that seismic waves propagate through, and, therefore, the primary observations for studying seismic source parameters and the Earth interior. The routine earthquake location and travel-time tomography rely on accurate seismic phase picks (e.g., P and S arrivals). As data increase, reliable automated seismic phase-picking methods are needed to analyze data and provide timely earthquake information. However, most traditional autopickers suffer from low signal-to-noise ratio and usually require additional efforts to tune hyperparameters for each case. In this study, we proposed a deep-learning approach that adapted soft attention gates (AGs) and recurrent-residual convolution units (RRCUs) into the backbone U-Net for seismic phase picking. The attention mechanism was implemented to suppress responses from waveforms irrelevant to seismic phases, and the cooperating RRCUs further enhanced temporal connections of seismograms at multiple scales. We used numerous earthquake recordings in Taiwan with diverse focal mechanisms, wide depth, and magnitude distributions, to train and test our model. Setting the picking errors within 0.1 s and predicted probability over 0.5, the AG with recurrent-residual convolution unit (ARRU) phase picker achieved the F1 score of 98.62% for P arrivals and 95.16% for S arrivals, and picking rates weremore »96.72% for P waves and 90.07% for S waves. The ARRU phase picker also shown a great generalization capability, when handling unseen data. When applied the model trained with Taiwan data to the southern California data, the ARRU phase picker shown no cognitive downgrade. Comparing with manual picks, the arrival times determined by the ARRU phase picker shown a higher consistency, which had been evaluated by a set of repeating earthquakes. The arrival picks with less human error could benefit studies, such as earthquake location and seismic tomography.« less
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