Tag: CLIP

python – having problem with multi-gpu in pytorch transformer

I am currently trying to make a translation model with Trnasformer model through PyTorch. Since I have 2 GPUs (2080ti x 2) available for training, I want to train the model through multi-gpu. Currently, the gpu is assigned to 0 and 1 respectively. The way I use multi-gpu is to…

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Pregap4 – Table of Contents

Organisation of the Pregap4 Manual Introduction Summary of the Files used and the Processing Steps Introduction to the Pregap4 User Interface Introduction to the Files to Process Window Introduction to the Configure Modules Window Introduction to the Textual Output Window Introduction to Running Pregap4 Pregap4 Menus Pregap4 File menu Pregap4…

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Multiplex Chemical Imaging Based on Broadband Stimulated Raman Scattering Microscopy

We present a protocol to acquire chemical images with broadband stimulated Raman scattering (SRS) microscopy. Based on an SRS microscope that operates with differential multichannel-lock-in detection, the protocol describes the sample preparation, adjustment of the SRS apparatus, and chemometrics to disentangle different constituents of chemically heterogeneous samples. Our protocol describes…

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Language Modeling with LSTMs in PyTorch | by Essam Wisam | Sep, 2022

“Learning how to protect their affections at the genre, an assertive case of its own,” said the model. In the last three stories we discussed a lot about RNNs and LSTMs from a theoretical perspective. In this story, we will bridge the gap to practice by implementing an English language…

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r – How to plot in time series with ggplot, geom_line, with line group by ‘answer’

I have plotted this time series data that contains three variables: date, answer, and counts. I would like to plot in time series where the lines representing categories of the answers. I have tried this codes below, but result are not as expected: I did’t get any line. Could anyone…

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The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering

Retrosynthesis from target to chassis Typically, the target compound, also named “source compound” is the compound of interest one wishes to produce, while the precursors are usually compounds that are natively present in a chassis strain. In the present implementation, the target can be any chemical that could be described…

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Introduction to HybridNets using PyTorch

In deep learning and computer vision, models tackle a specific task. For example, we can find models for image classification, object detection, and image segmentation also. But there are very few models out there which perform end-to-end vision perception on both, object detection and semantic segmentation. But one of the…

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Efficient genome editing in wild strains of mice using the i-GONAD method

Mice A laboratory strain B6 was purchased from CLEA Japan Inc. (Tokyo, Japan), while nine wild strains (BFM/2, BLG2, CHD, HMI, KJR, MSM, NJL, PGN2, and SWN) were bred at NIG (Shizuoka, Japan) (Table 1). All mice were maintained at the animal facility in NIG, under specific-pathogen-free conditions and controlled…

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New instrument can be clipped on to a smartphone to rapidly test for Zika virus in blood

As seen with the COVID-19 pandemic, detection methods that are rapid, simple, accurate, and sensitive are vital for detecting viral pathogens and for controlling the spread of infectious diseases. Unfortunately, laboratory-based methods often require trained personnel and involve complex procedures. In a new study, researchers at the University of Illinois…

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Robotic Left Hepatectomy using Indocyanine Green Fluorescence Imaging for an Intrahepatic Complex Biliary Cyst

Robotic liver surgery has gained more acceptance as a feasible, safe, and effective procedure for the treatment of both benign and malignant indications. However, robotic left hepatectomy is still technically demanding. We describe our surgical technique of a robotic left hepatectomy using indocyanine green fluorescence imaging for a large biliary…

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Description, Programming Languages, Similar Projects of ggfx

ggfx is a (currently experimantal) package that allows the use of various filters and shaders on ggplot2 layers. Installation You can install ggfx from CRAN in the usual manner (install.packages(‘ggfx’)) or you can grab the development version directly from github using the devtools package: # install.packages(‘devtools’) devtools::install_github(‘thomasp85/ggfx’) Example The basic…

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Roles of circRNAs | CMAR

Introduction Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer, with an increasing global incidence, and a leading cause of cancer-related mortality.1 Although hepatitis B and C virus infections, cirrhosis, alcohol intake, and non-alcoholic fatty liver disease (NAFLD) are the main risk factors contributing to HCC.1,2 Approximately…

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Biogenesis, biology and characterization of circular RNAs

Biogenesis, biology and characterization of circular RNAs Kristensen LS et al. The biogenesis, biology and characterization of circular RNAs. Nat Rev Genet. (2019) Summary text Biogenesis and properties of circRNAs Biogenesis of cirRNA Characteristics of circRNAs Discover and analyze circRNAs circRNA genome-wide analysis CircRNA site-specific analysis circRNA visualization Biological functions…

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LinkedIn

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Frontiers | COMMD2 Upregulation Mediated by an ncRNA Axis Correlates With an Unfavorable Prognosis and Tumor Immune Infiltration in Liver Hepatocellular Carcinoma

Introduction Liver hepatocellular carcinoma (LIHC) is the most common type of primary cancer in the liver and third leading cause of cancer-related mortality worldwide (1). Although substantial improvements have been made in LIHC therapy, particularly in molecular targeted therapy and immunotherapy (2, 3), the 5-year survival rate of LIHC is…

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Conducting Respiratory Oscillometry in an Outpatient Setting

Respiratory telemetry is a different modality of the pulmonary function testing that is now increasingly used in the clinical and research setting. Oscillometry is conducted through tighter breathing with three acceptable measurements, and can be performed with minimal contraindications. The main advantage of respiratory oscillometry is that it requires minimal…

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Establishment of a Mouse Severe Acute Pancreatitis Model using Retrograde Injection of Sodium Taurocholate into the Biliopancreatic Duct

A mouse model of severe acute pancreatitis is described herein. The procedure presented here is very rapid, simple, and accessible, thereby potentially allowing the study of the molecular mechanisms and different therapeutic interventions in acute pancreatitis in a convenient way. The overall goal of this video is to establish a…

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In Vivo Methods to Assess Retinal Ganglion Cell and Optic Nerve Function and Structure in Large Animals

Here we demostrate several in vivo tests (flash visual evoked potential, pattern electroretinogram and optic coherence tomography) in goat and rhesus macaque to understand the structure and function of the optic nerve and its neurons. Hi, everyone. This is Yikui Zhang from Wenzhou Eye Hospital. The upper nerve lacks Exxons…

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[MonashBioinformaticsPlatform/RSeQC] junction_saturation not suit for bam/sam file generated by minimap or pbmm2

because the CIGAR in bam/sam file generated by minimap2 contain “=” , represent right match with reference, and “X”, represent wrong match with reference. while the bam_cigar.py in ./lib/qcmodule/bam_cigar.py only suit for bam/sam generated such as BWA/bowtie, which CIGAR contain only “M” ,represent mis/match. So i modified the bam_cigar.py 77…

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Scikit Learn Minmaxscaler – January 2022

Sklearn Preprocessing Minmaxscaler – XpCourse Posted: (7 days ago) Scikit_Learn preprocessing.MinMaxScaler example. class sklearn.preprocessing.MinMaxScaler (feature_range=0, 1, *, copy=True, clip=False) [source] Transform features by scaling each feature to a given range. This estimator scales and translates each feature individually such that it is in the given range on the training set,…

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UMItools dedup deduplication taking too much time + RAM

I have some RNAseq data from miRNAs that I have processed with Bowtie2 (aligning to miRBase). Now, when doing the deduplication with umi_tools dedup I find that some of the files take a lot of time+RAM to finish (some files take around 3-4 minutes and 4-5GB of RAM and some…

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10 things we learned about microbes in 2021

Take a trip to the marvelous world of microbes, where bacteria breathe electricity, neon-yellow slime molds forage for snacks on the forest floor, and thousands of mysterious viruses hang out in your guts. This year, scientists made a slew of fascinating discoveries about the microscopic organisms living in and all…

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Multiple data points in one r ggplot2 plot ( R, Ggplot2 )

Problem : ( Scroll to solution ) I have two sets of data points that both relate to the same primary axis, but who differ in secondary axis. Is there some way to plot them on top of each other in R using ggplot2? What I am looking for is…

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RStudio AI Weblog: Picture segmentation with U-Internet

Certain, it’s good when I’ve an image of some object, and a neural community can inform me what sort of object that’s. Extra realistically, there is perhaps a number of salient objects in that image, and it tells me what they’re, and the place they’re. The latter process (referred to…

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Piranha Peak-Calling with multiple replicates

Piranha Peak-Calling with multiple replicates 0 I am trying to call RNA-Protein interation peaks by using Piranha software. I have multiple replicates for each experiment and the control data, and I can’t seem to understand how to combine them into one Piranha query. For example, if I was to call…

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Independent and minimal implementations of some reinforcement learning algorithms using PyTorch (including PPO, A3C, A2C, …).

There are implementations of some reinforcement learning algorithms, whose characteristics are as follow: Less packages-based: Only PyTorch and Gym, for building neural networks and testing algorithms’ performance respectively, are necessary to install. Independent implementation: All RL algorithms are implemented in separate files, which facilitates to understand their processes and modify…

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Independent and minimal implementations of some reinforcement learning algorithms using PyTorch

There are implementations of some reinforcement learning algorithms, whose characteristics are as follow: Less packages-based: Only PyTorch and Gym, for building neural networks and testing algorithms’ performance respectively, are necessary to install. Independent implementation: All RL algorithms are implemented in separate files, which facilitates to understand their processes and modify…

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ggplot, drawing multiple lines across facets

ggplot, drawing multiple lines across facets I drew two panels in a column using ggplot2 facet, and would like to add two vertical lines across the panels at x = 4 and 8. The following is the code: library(ggplot2) library(gtable) library(grid) dat <- data.frame(x=rep(1:10,2),y=1:20+rnorm(20),z=c(rep(“A”,10),rep(“B”,10))) P <- ggplot(dat,aes(x,y)) + geom_point() +…

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CLIP and CLASH data for miRNA-RNA interaction

CLIP and CLASH data for miRNA-RNA interaction 0 Hi everyone, I am working on a project which revolves around data analysis of miRNA-RNA interactions, while reviewing the literature, I came across CLIP and CLASH methods that can be used for the same. I am planning to work on publically available…

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converting Bam to fastq while removing clipping(hard/soft clip bases)

converting Bam to fastq while removing clipping(hard/soft clip bases) 0 Hello, I want to do some analysis and my raw data is paired-end reads fastq files. So far: I used BWA mem to convert them to Sam file then used samtools to convert to BAM file. My next step is…

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Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova

Significance Putatively ancient asexual species pose a challenge to theory because they appear to escape the predicted negative long-term consequences of asexuality. Although long-term asexuality is difficult to demonstrate, specific signatures of haplotype divergence, called the “Meselson effect,” are regarded as strong support for long-term asexuality. Here, we provide evidence…

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Primers trimming from Illumina paired-end reads by BBDuk software

Primers trimming from Illumina paired-end reads by BBDuk software 0 Hi, I’m dealing with Illumina amplicon data. I’d like to apply BBDuk to remove primers from the 5’end of my forward and reverse reads, but have a couple of questions. Could you help me please? How may i indicate in…

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The Best 1105 Python kaggle-ranzcr-clip-public Libraries

Athena is an open-source implementation of end-to-end speech processing engine. Athena is an open-source implementation of end-to-end speech processing engine. Our vision is to empower both industrial application and academic research on end-to-end models for speech processing. To make speech processing available to everyone, we’re also releasing example implementation and…

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Trimmomatic error

Trimmomatic error 1 Hi everyone. I’m trying to trim some read data but i’m getting an error message. This is my input: trimmomatic PE -threads 24 -phred 33 /home/tbeckett/lustre/practice/output_data/ Filtered2S1_L3_R1.fastq.gz /home/tbeckett/lustre/practice/output_data/ Filtered2S1_L3_R2.fastq.gz /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R1_p.fastq /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R1_un.fastq /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R2_p.fastq /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R2_un.fastq ILLUMINACLIP:NexteraPE-PE.fa LEADING:20 TRAILING:20 MINLEN:60 This is the error i’m getting:…

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The Point of Base Editors: Correcting Point Mutations

Some genome editing systems are highly conspicuous. They introduce double-strand breaks to DNA that attract the attention of cellular mechanisms such as nonhomologous end joining and homology-directed repair. If a genome editing system is so brash as to attempt a sizable insertion of new DNA, homology-directed repair must ensure that…

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removing adaptor

removing adaptor 1 I have two RNAseq datasets, from two different sequencing core facilities – the fastq files they provide already are demultiplexed and trimmed for adaptor. This is the Adaptor content following fastqc-> multiqc . According to the multiqc all files passed the qc for adapter content. So I…

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BSgenomes for HIV viruses

BSgenomes for HIV viruses 0 Dear Biostars users, I wonder if there are BSgenomes available for HIV viruses? I am trying to identify clusters from CLIP-seq data mapping to the HIV genome with wavClusteR. I stuck at one step as below: `require(BSgenome.Hsapiens.UCSC.hg19) wavclusters <- filterClusters( clusters = clusters, highConfSub =…

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getting paired end datasets from SRA

getting paired end datasets from SRA 0 I am searching SRA by keywords like “paired-end”, but the sra-toolkit seems to only download one file (single-end) about 90% of the time. I just want to make sure my commands are all correct: prefetch SRR13310323 fastq-dump -I –split-files –outdir fastq –gzip –skip-technical…

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What’s Wrong With Limiting Transformers To Just Language Models

Three years back, Google introduced Transformer, a novel neural network architecture. Modelled on the self-attention mechanism and best suited for language understanding, transformers could outperform both recurrent and convolutional neural network models.  Transformers perceive the entire input sequences simultaneously. The process depends on transforming one sequence into another, like the…

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Trimming of adapters and indexes

Trimming of adapters and indexes 0 I investigate a protein which binds small DNA (<30 nt) and have a library of these small DNA. I know that adapters and indexes are from this site (5′ adapter has T instead of U). [To reach the page I want to show click…

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