OpenPARF: An Open-Source Placement and Routing Framework for Large-Scale Heterogeneous FPGAs with Deep Learning Toolkit

This paper proposes OpenPARF, an open-source placement and routing framework for large-scale FPGA designs. OpenPARF is implemented with the deep learning toolkit PyTorch and supports massive parallelization on GPU. The framework proposes a novel asymmetric multi-electrostatic field system to solve FPGA placement. It considers fine-grained routing resources inside configurable logic blocks (CLBs) for FPGA routing and supports large-scale irregular routing resource graphs. Experimental results on ISPD 2016 and ISPD 2017 FPGA contest benchmarks and industrial benchmarks demonstrate that OpenPARF can achieve 0.4-12.7% improvement in routed wirelength and more than $2\times$ speedup in placement. We believe that OpenPARF can pave the road for developing FPGA physical design engines and stimulate further research on related topics

Comparative mapping of chalkiness components in rice using five populations across two environments

BACKGROUND: Chalkiness is a major constraint in rice production because it is one of the key factors determining grain quality (appearance, processing, milling, storing, eating, and cooking quality) and price. Its reduction is a major goal, and the primary purpose of this study was to dissect the genetic basis of grain chalkiness. Using five populations across two environments, we also sought to determine how many quantitative trait loci (QTL) can be consistently detected. We obtained an integrated genetic map using the data from five mapping populations and further confirmed the reliability of the identified QTL. RESULTS: A total of 79 QTL associated with six chalkiness traits (chalkiness rate, white core rate, white belly rate, chalkiness area, white core area, and white belly area) were mapped on 12 chromosomes using five populations (two doubled haploid lines and three recombinant inbred lines) across two environments (Hainan in 2004 and Wuhan in 2004). The final integrated map included 430 markers; 58.3% of the QTL clustered together (QTL clusters), 71.4% of the QTL clusters were identified in two or more populations, and 36.1% of the QTL were consistently detected in the two environments. The QTL could be detected again and showed dominance (qWBR1, qWBR8, qWBR12, and qCR5) or overdominance effects (qWCR7) for the rate of the white belly or white core, respectively, and all four QTL clusters derived from Zhenshan 97 controlling white belly rate were stably and reliably identified in an F(2) population. CONCLUSIONS: Our results identified 79 QTL associated with six chalkiness traits using five populations across two environments and yielded an integrated genetic map, indicating most of the QTL clustered together and could be detected in different backgrounds. The identified QTL were stable and reliable in the F(2) population, and they may facilitate our understanding of the QTL related to chalkiness traits in different populations and various environments, the relationships among the various chalkiness QTL, and the genetic basis for chalkiness. Thus, our results may be immediately used for map-based cloning of important QTL and in marker-assisted breeding to improve grain quality in rice breeding

Single channel based interference-free and self-powered human-machine interactive interface using eigenfrequency-dominant mechanism

The recent development of wearable devices is revolutionizing the way of human-machine interaction (HMI). Nowadays, an interactive interface that carries more embedded information is desired to fulfil the increasing demand in era of Internet of Things. However, present approach normally relies on sensor arrays for memory expansion, which inevitably brings the concern of wiring complexity, signal differentiation, power consumption, and miniaturization. Herein, a one-channel based self-powered HMI interface, which uses the eigenfrequency of magnetized micropillar (MMP) as identification mechanism, is reported. When manually vibrated, the inherent recovery of the MMP caused a damped oscillation that generates current signals because of Faraday's Law of induction. The time-to-frequency conversion explores the MMP-related eigenfrequency, which provides a specific solution to allocate diverse commands in an interference-free behavior even with one electric channel. A cylindrical cantilever model was built to regulate the MMP eigenfrequencies via precisely designing the dimensional parameters and material properties. We show that using one device and two electrodes, high-capacity HMI interface can be realized when the MMPs with different eigenfrequencies have been integrated. This study provides the reference value to design the future HMI system especially for situations that require a more intuitive and intelligent communication experience with high-memory demand.Comment: 35 pages, 6 figure

In Silico Syndrome Prediction for Coronary Artery Disease in Traditional Chinese Medicine

Coronary artery disease (CAD) is the leading causes of deaths in the world. The differentiation of syndrome (ZHENG) is the criterion of diagnosis and therapeutic in TCM. Therefore, syndrome prediction in silico can be improving the performance of treatment. In this paper, we present a Bayesian network framework to construct a high-confidence syndrome predictor based on the optimum subset, that is, collected by Support Vector Machine (SVM) feature selection. Syndrome of CAD can be divided into asthenia and sthenia syndromes. According to the hierarchical characteristics of syndrome, we firstly label every case three types of syndrome (asthenia, sthenia, or both) to solve several syndromes with some patients. On basis of the three syndromes' classes, we design SVM feature selection to achieve the optimum symptom subset and compare this subset with Markov blanket feature select using ROC. Using this subset, the six predictors of CAD's syndrome are constructed by the Bayesian network technique. We also design Naïve Bayes, C4.5 Logistic, Radial basis function (RBF) network compared with Bayesian network. In a conclusion, the Bayesian network method based on the optimum symptoms shows a practical method to predict six syndromes of CAD in TCM

Establishment of UPLC-Q-TOF-MS Fingerprints and Antioxidant Spectroscopic Relationship of Ethanol-eluting Sites of Tetrastigma hemsleyanum Macroporous Resin

Objective: To study the spectrum-effect relationship between the extracts of Tetrastigma hemsleyanum and its antioxidant activity, and to clarify the quality markers of its antioxidant activity. Methods: The extract was prepared and separated by macroporous resin elution, six different elution sites were obtained using ethanol at concentrations of 10%, 30%, 50%, 70%, 90% and 100%. The fingerprints of the Tetrastigma hemsleyanum extract and each elution site were established by UPLC-Q-TOF-MS and the characteristic peaks were screened. The free radical scavenging rate of 1,1-diphenyl-2-trinitrophenylhydrazine (DPPH) was used as an antioxidant index to investigate the antioxidant activity of the extract and each elution site of Tetrastigma hemsleyanum. The Pearson correlation coefficient method and orthogonal partial least squares (OPLS) method were combined to analyze and study the spectrum-effect relationship between the characteristic peaks and the antioxidant activity, to screen the quality markers, and to analyze and identify the chemical compositions. Results: Under the positive and negative ion modes, 57 and 92 characteristic peaks were identified in the extract and each elution site of Tetrastigma hemsleyanum, respectively. The combined results of Pearson correlation coefficient and OPLS analysis showed that 14 ion peaks contributed more to the antioxidant activity, which was vanillin (P2), catechin (P13, N19), rutin (P27, N54), and isoquercitrin (P28), kaempferol-3-O-rutinoside (P33, N61), proanthocyanidin B (N18), proanthocyanidin C (N22), and ion peaks N23, N25, N26, and N29, respectively. Conclusion: UPLC-Q-TOF-MS fingerprints of Tetrastigma hemsleyanum extract and each elution site were established, and the quality markers of Tetrastigma hemsleyanum antioxidant activity were revealed to provide technical support for the formulation of quality standards and resource development and utilization of Tetrastigma hemsleyanum

Computational cytometer based on magnetically modulated coherent imaging and deep learning.

Detecting rare cells within blood has numerous applications in disease diagnostics. Existing rare cell detection techniques are typically hindered by their high cost and low throughput. Here, we present a computational cytometer based on magnetically modulated lensless speckle imaging, which introduces oscillatory motion to the magnetic-bead-conjugated rare cells of interest through a periodic magnetic force and uses lensless time-resolved holographic speckle imaging to rapidly detect the target cells in three dimensions (3D). In addition to using cell-specific antibodies to magnetically label target cells, detection specificity is further enhanced through a deep-learning-based classifier that is based on a densely connected pseudo-3D convolutional neural network (P3D CNN), which automatically detects rare cells of interest based on their spatio-temporal features under a controlled magnetic force. To demonstrate the performance of this technique, we built a high-throughput, compact and cost-effective prototype for detecting MCF7 cancer cells spiked in whole blood samples. Through serial dilution experiments, we quantified the limit of detection (LoD) as 10 cells per millilitre of whole blood, which could be further improved through multiplexing parallel imaging channels within the same instrument. This compact, cost-effective and high-throughput computational cytometer can potentially be used for rare cell detection and quantification in bodily fluids for a variety of biomedical applications

Deep learning-based holographic polarization microscopy

Polarized light microscopy provides high contrast to birefringent specimen and is widely used as a diagnostic tool in pathology. However, polarization microscopy systems typically operate by analyzing images collected from two or more light paths in different states of polarization, which lead to relatively complex optical designs, high system costs or experienced technicians being required. Here, we present a deep learning-based holographic polarization microscope that is capable of obtaining quantitative birefringence retardance and orientation information of specimen from a phase recovered hologram, while only requiring the addition of one polarizer/analyzer pair to an existing holographic imaging system. Using a deep neural network, the reconstructed holographic images from a single state of polarization can be transformed into images equivalent to those captured using a single-shot computational polarized light microscope (SCPLM). Our analysis shows that a trained deep neural network can extract the birefringence information using both the sample specific morphological features as well as the holographic amplitude and phase distribution. To demonstrate the efficacy of this method, we tested it by imaging various birefringent samples including e.g., monosodium urate (MSU) and triamcinolone acetonide (TCA) crystals. Our method achieves similar results to SCPLM both qualitatively and quantitatively, and due to its simpler optical design and significantly larger field-of-view, this method has the potential to expand the access to polarization microscopy and its use for medical diagnosis in resource limited settings.Comment: 20 pages, 8 figure