Per-RMAP: Feasibility-Seeking and Superiorization Methods for Floorplanning with I/O Assignment

The feasibility-seeking approach provides a systematic scheme to manage and solve complex constraints for continuous problems, and we explore it for the floorplanning problems with increasingly heterogeneous constraints. The classic legality constraints can be formulated as the union of convex sets. However, the convergence of conventional projection-based algorithms is not guaranteed as the constrain sets are non-convex. In this work, we propose a resetting strategy to greatly eliminate the the divergence issue of the projection-based algorithm for the feasibility-seeking formulation. Furthermore, the superiorization methodology (SM), which lies between feasibility-seeking and constrained optimization, is firstly applied to floorplanning. The SM uses perturbations to steer the feasibility-seeking algorithm to a feasible solution with shorter total wirelength. The proposed flow is extendable to tackle various constraints and variants of floorplanning problems, e.g., floorplanning with I/O assignment problems. We have evaluated the proposed algorithm on the MCNC benchmarks. We can obtain legal floorplans only two times slower than the branch-and-bound method in its current prototype using MATLAB, with only 3% wirelength inferior to the optimal results. We evaluate the effectiveness of the flow by considering the constraints of I/O assignment, and our algorithm achieve 8% improvement on wirelength.Comment: Accepted for presentation at the International Symposium of EDA (Electronics Design Automation) ISEDA-2023, Nanjing, China, May 8-11, 202

Effectiveness of triple inhalation therapy and non-invasive ventilation in the treatment of acute exacerbated chronic obstructive pulmonary disease

Purpose: To determine the clinical effectiveness of combining triple inhalation therapy with noninvasive ventilation in treating acute exacerbated chronic obstructive pulmonary disease (AECOPD).Methods: A total of 128 AECOPD patients admitted in the Department of Respiratory Medicine of our Hospital were involved in the study. Two groups of patients were used (64 patients per group). The study group was given triple inhalation therapy and non-invasive ventilation, while only non-invasive ventilation was given to the control group. The curative effects of the two treatments and their effects on arterial PaCO2 (partial pressure of carbon dioxide), pH and PaO2 (partial pressure of oxygen) were determined.Results: The study group showed significantly higher treatment effectiveness than the control group (p < 0.05). Post-treatment PaCO2, pH, PaO2, respiratory rate and heart rate differed significantly between the two groups (p < 0.05). Improvements in the five indices were more in the study group than in the control group (p < 0.05).Conclusion: Combining triple inhalation therapy with non-invasive ventilation in the treatment of AECOPD enhances therapeutic effect, improves pulmonary ventilation, and reduces side effects.Keywords: Chronic obstructive pulmonary disease, Acute exacerbation, Triple inhalation, Non-invasive ventilatio

Fast Exact NPN Classification with Influence-aided Canonical Form

NPN classification has many applications in the synthesis and verification of digital circuits. The canonical-form-based method is the most common approach, designing a canonical form as representative for the NPN equivalence class first and then computing the transformation function according to the canonical form. Most works use variable symmetries and several signatures, mainly based on the cofactor, to simplify the canonical form construction and computation. This paper describes a novel canonical form and its computation algorithm by introducing Boolean influence to NPN classification, which is a basic concept in analysis of Boolean functions. We show that influence is input-negation-independent, input-permutation-dependent, and has other structural information than previous signatures for NPN classification. Therefore, it is a significant ingredient in speeding up NPN classification. Experimental results prove that influence plays an important role in reducing the transformation enumeration in computing the canonical form. Compared with the state-of-the-art algorithm implemented in ABC, our influence-aided canonical form for exact NPN classification gains up to 5.5x speedup.Comment: To be appeared in ICCAD'2

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

Memory partitioning and scheduling co-optimization in behavioral synthesis

Abstract—Achieving optimal throughput by extracting parallel-ism in behavioral synthesis often exaggerates memory bottleneck issues. Data partitioning is an important technique for increasing memory bandwidth by scheduling multiple simultaneous memory accesses to different memory banks. In this paper we present a vertical memory partitioning and scheduling algorithm that can generate a valid partition scheme for arbitrary affine memory inputs. It does this by arranging non-conflicting memory accesses across the border of loop iterations. A mixed memory partitioning and scheduling algorithm is also proposed to com-bine the advantages of the vertical and other state-of-art algo-rithms. A set of theorems is provided as criteria for selecting a valid partitioning scheme. This is followed by an optimal and scalable memory scheduling algorithm. By utilizing the property of constant strides between memory addresses in successive loop iterations, an address translation optimization technique for an arbitrary partition factor is proposed to improve performance, area and energy efficiency. Experimental results show that on a set of real-world medical image processing kernels, the proposed mixed algorithm with address translation optimization can gain speed-up, area reduction and power savings of 15.8%, 36 % and 32.4 % respectively, compared to the state-of-art memory parti-tioning algorithm

Responses of sequential and hierarchical phenological events to warming and cooling in alpine meadows

Organisms' life cycles consist of hierarchical stages, from a single phenological stage (for example, flowering within a season), to vegetative and reproductive phases, to the total lifespan of the individual. Yet phenological events are typically studied in isolation, limiting our understanding of life history responses to climate change. Here, we reciprocally transfer plant communities along an elevation gradient to investigate plastic changes in the duration of sequential phenological events for six alpine species. We show that prolonged flowering leads to longer reproductive phases and activity periods when plants are moved to warmer locations. In contrast, shorter post-fruiting leaf and flowering stages led to shorter vegetative and reproductive phases, respectively, which resulted in shorter activity periods when plants were moved to cooler conditions. Therefore, phenological responses to warming and cooling do not simply mirror one another in the opposite direction, and low temperature may limit reproductive allocation in the alpine region

The oyster genome reveals stress adaptation and complexity of shell formation

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa. © 2012 Macmillan Publishers Limited. All rights reserved

Comparative genomics reveals the hybrid origin of a macaque group

Although species can arise through hybridization, compelling evidence for hybrid speciation has been reported only rarely in animals. Here, we present phylogenomic analyses on genomes from 12 macaque species and show that the fascicularis group originated from an ancient hybridization between the sinica and silenus groups ~3.45 to 3.56 million years ago. The X chromosomes and low-recombination regions exhibited equal contributions from each parental lineage, suggesting that they were less affected by subsequent backcrossing and hence could have played an important role in maintaining hybrid integrity. We identified many reproduction-associated genes that could have contributed to the development of the mixed sexual phenotypes characteristic of the fascicularis group. The phylogeny within the silenus group was also resolved, and functional experimentation confirmed that all extant Western silenus species are susceptible to HIV-1 infection. Our study provides novel insights into macaque evolution and reveals a hybrid speciation event that has occurred only very rarely in primates

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another