ShortcutFusion: From Tensorflow to FPGA-based accelerator with reuse-aware memory allocation for shortcut data

Residual block is a very common component in recent state-of-the art CNNs such as EfficientNet or EfficientDet. Shortcut data accounts for nearly 40% of feature-maps access in ResNet152 [8]. Most of the previous DNN compilers, accelerators ignore the shortcut data optimization. This paper presents ShortcutFusion, an optimization tool for FPGA-based accelerator with a reuse-aware static memory allocation for shortcut data, to maximize on-chip data reuse given resource constraints. From TensorFlow DNN models, the proposed design generates instruction sets for a group of nodes which uses an optimized data reuse for each residual block. The accelerator design implemented on the Xilinx KCU1500 FPGA card significantly outperforms NVIDIA RTX 2080 Ti, Titan Xp, and GTX 1080 Ti for the EfficientNet inference. Compared to RTX 2080 Ti, the proposed design is 1.35-2.33x faster and 6.7-7.9x more power efficient. Compared to the result from baseline, in which the weights, inputs, and outputs are accessed from the off-chip memory exactly once per each layer, ShortcutFusion reduces the DRAM access by 47.8-84.8% for RetinaNet, Yolov3, ResNet152, and EfficientNet. Given a similar buffer size to ShortcutMining [8], which also mine the shortcut data in hardware, the proposed work reduces off-chip access for feature-maps 5.27x while accessing weight from off-chip memory exactly once.Comment: 12 page

Rosetta Brains: A Strategy for Molecularly-Annotated Connectomics

We propose a neural connectomics strategy called Fluorescent In-Situ Sequencing of Barcoded Individual Neuronal Connections (FISSEQ-BOINC), leveraging fluorescent in situ nucleic acid sequencing in fixed tissue (FISSEQ). FISSEQ-BOINC exhibits different properties from BOINC, which relies on bulk nucleic acid sequencing. FISSEQ-BOINC could become a scalable approach for mapping whole-mammalian-brain connectomes with rich molecular annotations

Targeted and Genome-Scale Methylomics Reveals Gene Body Signatures in Human Cell Lines

Cytosine methylation, an epigenetic modification of DNA, is a target of growing interest for developing high throughput profiling technologies. Here we introduce two new, complementary techniques for cytosine methylation profiling utilizing next generation sequencing technology: bisulfite padlock probes (BSPPs) and methyl sensitive cut counting (MSCC). In the first method, we designed a set of ~10,000 BSPPs distributed over the ENCODE pilot project regions to take advantage of existing expression and chromatin immunoprecipitation data. We observed a pattern of low promoter methylation coupled with high gene body methylation in highly expressed genes. Using the second method, MSCC, we gathered genome-scale data for 1.4 million HpaII sites and confirmed that gene body methylation in highly expressed genes is a consistent phenomenon over the entire genome. Our observations highlight the usefulness of techniques which are not inherently or intentionally biased in favor of only profiling particular subsets like CpG islands or promoter regions

Staged Surgery for Chronic Primary Aortoduodenal Fistula in a Septic Patient

Aortoenteric fistula is one of the most challenging problems that confront the vascular surgeons. Controversy remains over the optimal treatment because of the continued publication of series with high mortality, amputation, and aortic disruption rates. A positive preoperative blood culture is the best predictor of mortality with increased amputation rates due to infection of the extra-anatomic bypass. Therefore, in selected cases with sepsis, a prudent management protocol is required. We report a 68-yr-old male presenting with a chronic primary aortoduodenal fistula extensively involving the duodenum and Gram-negative sepsis. We planned a staged operation. Initially, an emergency laparotomy and control of the aorta allowed stabilization of the patient, identification of the fistula, and direct in situ placement of the prosthetic graft followed by an en bloc resection of the aneurysm and the surrounding structures. After he recovered from sepsis and had been stabilized, a staged extra-anatomic bypass followed by transabdominal removal of the temporarily placed graft was done. This management plan will allow the highest success rate and may be a prudent management protocol for these difficult cases

The Outcomes of Hypertransfusion in Major ABO Incompatible Allogeneic Stem Cell Transplantation

Major ABO incompatibility may be potentially associated with immediate or delayed hemolysis and delayed onset of erythropoiesis in patients receiving allogeneic hematopoietic stem cell transplantation (HSCT). To determine if hemolysis can be prevented by the inhibition of graft erythropoiesis, we performed hypertransfusion and assessed red cell transfusion requirement and independence. Between October 1995 and December 2001, 28 consecutive patients receiving major ABO incompatible HSCT at Samsung Medical Center were hypertransfused to maintain their hemoglobin levels at 15 g/dL or more. We retrospectively compared the outcomes of these patients with those of 47 patients at Asan Medical Center whose target hemoglobin levels were 10 g/dL. Reticulocyte engraftment was significantly delayed in hypertransfused group (51 days vs. 23 days; p=.001). There was no significant difference in the total amount of red cells transfused within 90 days post-HSCT (25 units vs. 26 units; p=.631). No significant difference in the time to red cell transfusion independence was observed between the two groups (63 days vs. 56 days; p=.165). In conclusion, we failed to improve red cell transfusion requirement and independence in major ABO incompatible HSCT with hypertransfusion

Subarachnoid Hemorrhage Misdiagnosed as an Acute ST Elevation Myocardial Infarction

Without significant coronary artery stenosis, ischemic electrocardiographic change including ST segment elevation, segmental wall motion abnormality and elevated serum cardiac-specific markers (creatine kinase-MB, Troponin-T) may develop after central nervous system injuries such as subarachnoid, intracranial or subdural hemorrhage. Misdiagnosing these patients as acute myocardial infarction may result in catastrophic outcomes. By reporting a case of a 55-year old female with subarachnoid hemorrhage mimicking acute ST elevation myocardial infarction, we hope to underline that careful attention of neurologic abnormality is critical in making better prognosis

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

RNA sequencing measures the quantitative change in gene expression over the whole transcriptome, but it lacks spatial context. On the other hand, in situ hybridization provides the location of gene expression, but only for a small number of genes. Here we detail a protocol for genome-wide profiling of gene expression in situ in fixed cells and tissues, in which RNA is converted into cross-linked cDNA amplicons and sequenced manually on a confocal microscope. Unlike traditional RNA-seq our method enriches for context-specific transcripts over house-keeping and/or structural RNA, and it preserves the tissue architecture for RNA localization studies. Our protocol is written for researchers experienced in cell microscopy with minimal computing skills. Library construction and sequencing can be completed within 14 d, with image analysis requiring an additional 2 d

An Antireflective Nanostructure Array Fabricated by Nanosilver Colloidal Lithography on a Silicon Substrate

An alternative method is presented for fabricating an antireflective nanostructure array using nanosilver colloidal lithography. Spin coating was used to produce the multilayered silver nanoparticles, which grew by self-assembly and were transformed into randomly distributed nanosilver islands through the thermodynamic action of dewetting and Oswald ripening. The average size and coverage rate of the islands increased with concentration in the range of 50–90 nm and 40–65%, respectively. The nanosilver islands were critically affected by concentration and spin speed. The effects of these two parameters were investigated, after etching and wet removal of nanosilver residues. The reflection nearly disappeared in the ultraviolet wavelength range and was 17% of the reflection of a bare silicon wafer in the visible range

Nanosilver Colloids-Filled Photonic Crystal Arrays for Photoluminescence Enhancement

For the improved surface plasmon-coupled photoluminescence emission, a more accessible fabrication method of a controlled nanosilver pattern array was developed by effectively filling the predefined hole array with nanosilver colloid in a UV-curable resin via direct nanoimprinting. When applied to a glass substrate for light emittance with an oxide spacer layer on top of the nanosilver pattern, hybrid emission enhancements were produced from both the localized surface plasmon resonance-coupled emission enhancement and the guided light extraction from the photonic crystal array. When CdSe/ZnS nanocrystal quantum dots were deposited as an active emitter, a total photoluminescence intensity improvement of 84% was observed. This was attributed to contributions from both the silver nanoparticle filling and the nanoimprinted photonic crystal array