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Tag: PASS
Transformer Hydranets and Multi-Task Learning with Hugging Face and PyTorch: Ensembling vs. Entwinement
The Lernaean Hydra, a many-headed serpentine water monster, has been living with us for over 2,700 years. Heracles is said to have used the Hydra’s poisonous blood to dip arrows later used to kill the centaur Nessus. Today the Hydra—reified in many forms—continues to augment our tools in the hunt…
python – Print intermediate gradient values during backward pass in Pytorch using hooks
I am trying to print the value of each of the intermediate gradients during backward pass of a model, using register backward hooks: class func_NN(torch.nn.Module): def __init__(self,) : super().__init__() self.a = torch.nn.Parameter(torch.rand(1)) self.b = torch.nn.Parameter(torch.rand(1)) def forward(self, inp): mul_x = torch.cos(self.a.view(-1,1)*inp) sum_x = mul_x – self.b return sum_x # hook…
Organ-specific characteristics govern the relationship between histone code dynamics and transcriptional reprogramming during nitrogen response in tomato
A supply of nitrate triggers organ-specific changes of histone modifications at specific gene loci To investigate the organ specificity of dynamic histone modifications in response to N changes, we treated 3-week-old tomato seedlings (Solanum lycopersicum, cultivar M82) with four days of N starvation, followed by N-supply (2.8 mM NO3−; +N) or…
How to Regulate Unsecured “Open-Source” AI: No Exemptions
Wes Cockx & Google DeepMind / Better Images of AI / AI large language models / CC-BY 4.0 Unsecured “open-source” AI systems pose a massive series of threats to society and democracy. They deserve no exemptions and should be regulated just like other high-risk AI systems. Their developers and deployers…
Function ‘SubBackward0’ returned nan values in its 1th output – autograd
I am trying to implement a model where the forward function calls to an external function that computes the values using the model’s parametes. class R_model(torch.nn.Module): def __init__(self,) : super().__init__() self.Kx = torch.nn.Parameter(torch.randint(-200, -100, (1,)).float()*0.0001) self.Ky = torch.nn.Parameter(torch.randint(-200, -100, (1,)).float()*0.0001) self.Kz = torch.nn.Parameter(torch.randint(-200, -100, (1,)).float()*0.0001) def forward(self): return generate_r(Kx=self.Kx, Ky=self.Ky,…
Investigating needle-free ultrasound vaccine delivery
Ultrasound pulses deliver vaccines through the skin without needles. This technique, which employs sound waves to create bubbles that forge a path for the vaccine, may be especially helpful for DNA vaccines. Credit: Darcy Dunn-Lawless An estimated quarter of adults and two-thirds of children have strong fears around needles, according…
Detecting the Language of a Person’s Name using a PyTorch RNN
In this tutorial, we’ll build a Recurrent Neural Network (RNN) in PyTorch that will classify people’s names by their languages. We assume that the reader has a basic understanding of PyTorch and machine learning in Python. At the end of this tutorial, we’ll be able to predict the language of…
Bam files generated with STAR cause a segmentation fault core dump error when used with another tool
I am mapping RNA-Seq data using STAR, using multi-sample two-pass mapping. I first mapped all samples with one-pass then concatenated their SJOut files and filtered junctions. I launched the second mapping by using this SJOut file. I used this command to generate genome : ` /home/STAR-2.7.10b/bin/Linux_x86_64/STAR \ –runThreadN 10 \…
TVM Monthly – November 2023 – Announcement
Note: This monthly report contains main branch only. As discussed by the TVM PMC, our goal is to provide a monthly summary of the project so users and developers can get a better understanding of the goings on of the TVM community. Feedback and suggestions are welcomed so that we…
PyTorch Tensor to Numpy array Conversion and Vice-Versa
Pytorch is a machine learning library that allows you to do projects based on computer vision and natural language processing. In this tutorial, I will show you how to convert PyTorch tensor to NumPy array and NumPy array to PyTorch tensor. Convert Pytorch Tensor to Numpy Array In this section,…
ASD jab: Chinese scientists reach milestone in revolutionary gene therapy for autism
Mice given the injection containing the editing system registered a decrease in ASD-associated behaviour. In a paper on their research, published in the journal Nature Neuroscience on November 27, the scientists said the potential treatment method could not just be used for patients with ASD, but also other genetic neurodevelopmental…
Senior Bioinformatics Scientist Job in Minnesota
We are seeking a highly motivated bioinformatician to join the Institute on the Biology of Aging and Metabolism (iBAM) and the Department of Genetics, Cell Biology, and Development at the University of Minnesota. Aging is a natural process throughout an entire life course. Focusing on health and well-being, in…
How does the new Honda Pilot stack up against the 2024 Toyota Grand Highlander? | Auto
The Honda Pilot is a popular midsize SUV for shoppers in need of a versatile family-oriented hauler. For years, buyers have enjoyed its three rows of seating, loads of storage, and clever features. Now, there is a new generation that debuted for 2023. It has fresh styling, more interior room,…
PyTorch Transformer for CIFAR Classification
import torch import torch.nn as nn import torch.optim as optim import torchvision.datasets as datasets import torchvision.transforms as transforms from torch.utils.data import DataLoader # Define the Transformer model class TransformerModel(nn.Module): def __init__(self, embed_dim, num_heads): super(TransformerModel, self).__init__() self.transformer = nn.TransformerDecoder( nn.TransformerDecoderLayer(embed_dim, num_heads), num_layers=6 ) self.fc = nn.Linear(embed_dim, 10) def forward(self, x): x…
Sen. Gary Peters Protects CCP-Linked Biotech Firm Accused of DNA Theft
Sen. Gary Peters (D-MI) is reportedly protecting a CCP-linked biotech firm that Republicans appear ready to ban from operating in the United States after it was accused of stealing Americans’ DNA. Peters’ decision to hold up the legislation might permanently prevent lawmakers from passing legislation to cause Beijing Genomics Institute (BGI)…
Young talent Mumba soars from community to Red Arrows Premier
Zambia: Ackim Mumba is another young, talented player in the books of Red Arrows, rising through community and academy football to the top flight of the Zambian game. Born on a sunny day of October 4th, 1996, Ackim started his school at Kabanana Primary School before moving to El Elion…
Automating API Documentation: A Journey from TypeScript to OpenAPI and Schema Governence with Optic
In the previous blog post Documenting and Testing Schemas of Serverless Stacks with Optic & Cypress, we focused on the benefits of schema testing and governance. Briefly, some of the core problems addressed were: Effortless API Documentation: Automating the API documentation creation and update, ensuring that our API documentation evolves…
I need to know whether my implementation is correct or not
im working on generating ecg signals using a gan and i need to know if my model is implemented correctly or not as i seem to get signals but all of them seem same to me im fairly new on gans so yeah plz do help me import torchimport torch.nn…
Senior Bioinformatics Systems Analyst in Santa Cruz, CA for University of California Santa Cruz
Details Posted: 01-Dec-23 Location: Santa Cruz, California Salary: Open Categories: Information Technology Staff/Administrative Senior Bioinformatics Systems Analyst Location: Santa CruzJob ID: 61781 JOB POSTING NO VISA SPONSORSHIP IS AVAILABLE FOR THIS POSITION.THIS RECRUITMENT WILL REMAIN OPEN UNTIL FILLED. HOW TO APPLY For full consideration, applicants should attach their resume and…
Does GNOMAD use all LOFTEE LoF filters?
Does GNOMAD use all LOFTEE LoF filters? 0 Hi all, I have some lof variants and I want to know if they have already been detected in GNOMAD (I am essentially curious if my lof variants are novel). In order to make this comparison to GNOMAD I have run my…
A Guide to Automating Information Extraction with Vertex AI
In today’s fast-paced and competitive business landscape, quick, clear, and dependable customer service is essential. Modern businesses continually strive to enhance the customer experience by providing fast responses to customer inquiries. Think of a tool that can respond immediately to customer questions such as, “What is the size range for product…
systemd autopkgtest regression on arm64 and s390x on mantic
Is seems the container fails to boot. From a bad run: 9109s autopkgtest [10:39:17]: test tests-in-lxd: [———————– 9145s 2023-11-28T10:39:50Z INFO Waiting for automatic snapd restart… 9259s lxd 5.19-8635f82 from Canonical** installed 9288s Creating autopkgtest-prepare-jhI 9475s Retrieving image: metadata: 100% (323.81MB/s) Retrieving image: rootfs: 1% (3.53MB/s) <SNIP> Retrieving image: rootfs: 100%…
Entry Bioinformatics Professional Cancer Research job with University of Colorado Anschutz Medical Campus
Entry Bioinformatics Professional – Cancer Research – 31970 University Staff Description University of Colorado Anschutz Medical Campus Department: Pediatrics – Hematology, Oncology, and Bone Marrow Transplant Job Title: Entry Bioinformatics Professional – Cancer Research Position: # 00817933 – Requisition: # 31970 Job Summary: The Entry Bioinformatics Professional utilizes applied or…
Conservative groups call on Congress to pass amendment banning business with China firm stealing US DNA
Congress is feeling the heat from more than a dozen conservative groups that are calling for the passage of a National Defense Appropriations Act (NDAA) amendment to government contracts with a Chinese Communist Party (CCP)-linked biotech firm. Sixteen conservative groups sent a letter to senators and House lawmakers, calling on…
r – add additional labels to y-axis without tickmark using ggplot2
You could try df <- data.frame( x = c(1, 2.6, 3, 4, 5), y = c(2, 5, 3.6, 8.2, 10), y_ticks = c(2, 4, 5, 8, 10), y_labels = c(“Low”, “Mid-Low”, “Medium”, “Mid-High”, “High”) ) # Create a scatter plot with custom y-axis ticks and labels library (ggplot2) ggplot(df, aes(x,…
Testing an OpenAPI specification in PHP
Introduction OpenAPI has become the de facto standard for API specifications. According to its description, “It is a specification language for HTTP APIs that defines structure and syntax in a way that is not wedded to the programming language the API is created in”. The specification is independent of the…
python – Is my PyTorch code for fine-tuning a BERT model on a question-answering task correct? How do I save, load, and test the model in a different file?
I’ve been working on a PyTorch code to fine-tune a BERT model for a question-answering task. Could you give it a quick look to see if it’s on the right track? Because, my test code (test.py) is giving me “[cls]” as the output, and I’m not sure why. Any help…
A dual-targeted drug inhibits cardiac ryanodine receptor Ca2+ leak but activates SERCA2a Ca2+ uptake
Introduction During each heartbeat, the intracellular calcium concentration ([Ca2+]i) cycles dynamically between low resting diastolic and high active systolic levels within cardiomyocytes (Bers, 2002; Eisner et al, 2017; Sankaranarayanan et al, 2017): upon electrical excitation, Ca2+ influx via voltage-gated CaV1.2 channels activates Ca2+-induced Ca2+ release via SR ryanodine receptor type…
EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2023 | Nucleic Acids Research
Abstract The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) is one of the world’s leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory (EMBL), Europe’s only intergovernmental life sciences organisation. This…
What Physical Traits Are Inherited From Mother?
Title: The Maternal Imprint: Deciphering the Physical Traits Passed Down from Mother to Child The intricate dance of genetics determines the unique tapestry of traits that each individual carries. While both parents contribute to the genetic makeup of their offspring, certain physical characteristics are more prominently inherited from the mother….
Shooting for the stars: The healthtech using cosmology and AI to try to cure cancer
Dubbed the “emperor of all maladies” by physician and Pulitzer Prize winner Siddhartha Mukherjee, cancer is the cause of one in six deaths worldwide. The disease blights the lives of millions because of its complexity and shape-shifting ability to elude the human immune system and adapt to treatments. But there…
The crucial role of tissue quality in precision oncology
In precision oncology, tissue quality plays a pivotal role in maintaining data integrity. We explore the impact of standardizing tissue collection and processing on data quality, and how this helps enhance patient outcomes as well as our understanding of cancer. Insights from tissue samples play an important role across the…
Genome haplarithmisis sheds light on complex genetic landscape of miscarriages
About 10-15% of pregnancies fail after conception has been recognized, amounting to 23 million losses a year. Chromosomal anomalies underlie many embryonic and fetal losses, but their exact frequency and localization to the embryo or placenta are still unclear. A new study published in Nature Medicine reports on a chromosomal…
Plots are objects too – by Diego Catalan Molina
👋 The Core Ideas series uses data and code that you can get from this GitHub repo. Feel free to copy, test, adapt, and expand the code for your own projects 👍 The idea of building plots or cleaning data in R was completely abstract to me when I started using the…
Tricorder Tech: Sequencing DNA in Space
NASA is not often known for making the best use of existing COTS (commercial off the shelf technology) aboard the ISS. Then again, sometimes they are. This is an example of when the agency really grabs cutting edge biotech and sends it into space. There’s usually quite a lag time….
Evolution Midterm 1 Cheat Sheet – DNA Markers: nuclear DNA SNPs, mtDNA, SNPs, DNA sequences,
DNA Markers: nuclear DNA SNPs, mtDNA, SNPs, DNA sequences, microsatellites Popular neutral markers: Mitochondrial gene sequences (COI: animal), SNPs (single nucleotide polymorphisms), nuclear sequence (RUBISCO, rDNA: plants) (show SNP heteros have 2 lower peaks), genome resequencing, microsatellites (STR) Microsatellites: tandem repeats of 10-30 copies of 2-4 base pairs (diff in…
CRISPR enhanced nanotweezers for ultra-precise DNA manipulation and detection
Nov 27, 2023 (Nanowerk News) Since the concept of optical trapping was first proposed in the 1960s and 1970s by Arthur Ashkin, researchers have pursued innovative techniques to precisely manipulate and analyze individual biomolecules like DNA. Such capabilities would revolutionize genetics, molecular biology, and medicine by enhancing our understanding of…
How to get a Single Image from PyTorch DataLoader?
In order to train a PyTorch model you must read training data into memory, convert the data to PyTorch tensors, and serve the data in batches. This task is not trivial. In this tutorial, We will use PyTorch Dataset and DataLoader interfaces to serve up training data from the folder….
Implementing Soft Nearest Neighbor Loss in PyTorch | by Abien Fred Agarap | Nov, 2023
Representation learning is the task of learning the most salient features in a given dataset by a deep neural network. It is usually an implicit task done in a supervised learning paradigm, and it is a crucial factor in the success of deep learning (Krizhevsky et al., 2012; He et…
RF & EMS: Top 10 Best | Radio Electroporation Face Beauty Machine in 2021
2021 Top Rated and Reviewed RF&EMS Radio Mesotherapy Electroporation Beauty Machine. ——————————————————— References to the goods: ——————————————————— 1)► 7in1 RF & EMS Radio Mesotherapy Electroporation Beauty Machine ● Buy on AliExpress: s.click.aliexpress.com/e/_99uLid ——————————————————— 2)► 5in1 RF& EMS Mesotherapy Electroporation Face Beauty Machine ● Buy on AliExpress: s.click.aliexpress.com/e/_A1PDxX ——————————————————— 3)► iebilif…
NOT REAL NEWS: A look at what didn’t happen this week | The Verde Independent
To view this content you must be logged in as a subscriber. 4 WEEKS $3 UNLIMITED DIGITAL ACCESS 4 WEEKS 1 YEAR $39 UNLIMITED DIGITAL ACCESS FOR 12 MONTHS DAY PASS $0.99 UNLIMITED DIGITAL ACCESS FOR 24 HOURS Plans include full website access, e-Edition and exclusive online extras. Print and…
PyTorch and NumPy in AI Applications
import torch import numpy as np def ai_with_pytorch_and_numpy(): “”” Function to demonstrate the usage of PyTorch and NumPy in AI applications. This function creates a simple neural network using PyTorch and performs basic operations using NumPy. Returns: – torch.Tensor: Returns a PyTorch tensor representing the output of the neural network….
Certificate in Deep Learning with PyTorch Practice Course
Certificate in Deep Learning with PyTorch Practice Course About the Service: Enhance your expertise in deep learning and master the PyTorch framework with our comprehensive Certificate in Deep Learning with PyTorch Practice Course. Designed for professionals seeking hands-on experience, this course equips you with the practical skills required to…
Israel-based Fungit has a mission to feed billions of people around the world
“The global population is growing by a staggering 100 million per year,” explained Fungit Biosolutions. “By the year 2050, the world population is expected to grow by more than 3 billion and exceed 10 billion people. An increase in population directly translates into an immediate increase in demand for food.”…
How to Fix “RuntimeError: CUDA out of Memory”?
In the research and development community, PyTorch has become a popular deep-learning framework. In the case of large models or datasets, users may encounter the frustrating “RuntimeError: CUDA out of Memory” error. This error indicates that the GPU’s memory has been exhausted, preventing deep learning from being completed. In this…
From Pixels to Patterns Exploring CNN Architectures using PyTorch
Created with DALL-E 3 Welcome back to our journey through the fascinating world of Convolutional Neural Networks (CNNs)! Last week, in Part 1, we laid the foundation by exploring the basic concepts and components of CNNs. We jumped into the essence of convolutional layers, understood the significance of filters or…
How to build a forward pass of a network in PyTorch based on a string expression?
I have a string expression like “self.w0torch.sin(x)+self.w1torch.exp(x)”. How can I use this expression as the forward pass of a model in PyTorch? The class for instantiate a model is as follows: class MyModule(nn.Module): def init(self,vector): super().init() self.s=”self.w0torch.sin(x)+self.w1torch.exp(x)” w0=0.01*torch.rand(1,dtype=torch.float,requires_grad=True) self.w0 = nn.Parameter(w0) w1=0.01*torch.rand(1,dtype=torch.float,requires_grad=True) self.w1 = nn.Parameter(w1) def forward(self,x): return ???? For…
Setting CORS when creating a user server on Kubernetes via REST API – JupyterHub
Hi, I am having trouble setting up CORS options on a single user server that are being spun up. The error I am seeing: Access to fetch at ‘<URL>’ from origin ‘http://localhost:3000’ has been blocked by CORS policy: Response to preflight request doesn’t pass access control check: No ‘Access-Control-Allow-Origin’ header…
Different learning rates for different parameters
Hello! How can I specify a different learning rate for each parameter of my model. In my case I have something of the form: x_index = torch.tensor([14.,15.,8.,9.,10.,11.,13.,12.,5.,4.,3.,2.,0.,1.]) wavenumber_vals = torch.tensor([284829.132,284829.132,284840.730,284840.730,284854.732,284854.132,284864.420,284864.920,284884.170,284884.620,284898.434,284898.814,284910.218,284910.218],dtype=torch.float64) params = torch.tensor([B_0, D_0, gamma_0, b1_0, c1_0, b2_0,eqQ_0],dtype=torch.float64, requires_grad=True) opt = optim.Adam([params], lr=1e-3) for i in range(10): opt.zero_grad() loss =…
How To Create Dashboards In R: A Step-By-Step Approach
Dashboards are essential tools for visualizing data effectively, and R offers robust capabilities to build them. This guide provides a step-by-step approach to creating interactive, user-friendly dashboards in R, tailored to meet the specific needs of developers and programmers. Setting Up The Environment Designing The Dashboard Layout Adding Interactive Elements…
python – Adapting PyTorch GRU Model for Variable Number of Detected Objects
I’m currently grappling with an issue while working with a PyTorch GRU model in a dynamic scenario where the number of detected objects can vary. The model is specifically designed to process bounding box features using an attention mechanism. Here’s a architecture : Here’s a condensed version of the relevant…
Reactions to the UK’s Approval of a CRISPR Medicine
Last week, the UK’s MHRA conditionally approved the world’s first CRISPR-Cas9 therapy: Casgevy for sickle cell disease and transfusion dependent beta thalassemia. The therapy has been developed by Vertex and CRISPR Therapeutics. A decision in the US is not expected until December 8. It’s a remarkable moment for the CRISPR…
Pruning with –indep-pairwise with plink 1.9
I’m new to PLINK and I would like to obtain a file with SNPs in approximate linkage equilibrium. Here is my script and the outputs of each step. If someone could tell me if there is an error in the script because at…
Company exits stealth to launch molecular gates
On this week’s podcast we have a conversation with Jordi Mata-Fink, co-founder and chief executive officer of Gate Bioscience. Gate Bioscience is a U.S.-based biotechnology company creating a new class of medicines called Molecular Gates. Founded in 2021, Gate is emerging from stealth with a novel scientific platform and $60…
SNPs of a specific mouse strain
Hi, I wonder how can I get SNPs for a particular mouse strain like C57BL6. I have downloaded a mouse reference vcf from ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.rsID.vcf.gz Its header is #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 129P2_OlaHsd 129S1_SvImJ 129S5SvEvBrd A_J AKR_J B10.RIII BALB_cByJ BALB_cJ BTBR_T+_Itpr3tf_J BUB_BnC3H_HeH C3H_HeJ C57BL_10J C57BL_10SnJ C57BL_6NJ…
How to do the MD simulation of a metalloenzyme with ligand? – User discussions
GROMACS version: 2023GROMACS modification: YesHere post your question : Recently, I want to make the simulation of a metalloenzyme with ligand. The metalloenzyme has two Mn ions in its active site. When producing the topol file for this metalloenzyme, gromacs cannot find the Mn ion in the rtp file. I…
Empowering optical tweezers with ‘biometric eyes’
a, The diagrammatic sketch of the three components in the solution: DNA@AuNS conjugate, CRISPR/Cas12a complex, and target ssDNA. b, Optical setup, the BS, SPF, and TL are beam splitter, short pass filter, and tube lens (f=200 mm), respectively. Additional details of the setup are provided in the Materials and Methods…
CRISPR-powered optothermal nanotweezers allow targeted manipulation of single DNA molecules
Nov 22, 2023 (Nanowerk News) For decades, researchers have sought ways to precisely manipulate and identify individual molecules like DNA in liquid environments. Such capabilities could revolutionize areas ranging from disease diagnosis to drug development. However, the randomness of molecular movements in fluids has hindered progress. Now, scientists from Shenzhen…
Building a Neural Network with PyTorch
Building your first neural network could seem like a formidable undertaking, but deep learning frameworks like PyTorch have made the task more accessible than ever. In this article, I’ll explain how to build a neural network using PyTorch—even if you’re brand new to neural networks. We at Gcore recently developed…
Pass reads file form host to container
Docker: Pass reads file form host to container 0 Hello, I need your help please. I want to create docker container to analyse my reads, to run it via nextflow or wdl worflow. I have a python script, and I would like to pass my reads as argument something like…
How to Calculate the Norm of a Vector or Matrix in PyTorch?
The norm of a matrix or vector is a computation of its length/magnitude. In PyTorch, a vector is simply a 1D tensor that has only one dimension whereas a matrix is a 2D tensor that has two dimensions i.e. rows and columns. Sometimes, users may want to calculate the norm…
python – Why does pytorch treat network classes like functions?
There’s a few layers to this. First, the pure python layer: Python objects have various dunder methods (double underscore) such as __init__, __repr__, and others. One such method is __call__. If you call a python object like a function, it invokes the __call__ method of the object class. class MyClass…
The OpenAI meltdown: Winners and losers in the battle for AI supremacy
Conventional wisdom says Microsoft Corp. is the big winner in the recent OpenAI saga. We don’t quite see it that way. Both Microsoft and OpenAI are in a worse position today than it was last Thursday, prior to the firing of OpenAI Chief Executive Sam Altman and the ongoing public…
Possible inclusion of PLUMED interface – Developers discussions
Dear GROMACS developers, we (PLUMED developers) noticed that GROMACS now makes it possible to easily add plugins modifying forces. We would like to investigate if it makes sense for us to implement an interface for PLUMED in the spirit of the one introduced for the Colvars package in this commit:…
Congress charges forward with proposed BAN on Chinese Communist Party-linked biotech company believed to be stealing DNA from Americans
Congress is closing in on an effective ban of a China-based genomics company accused of stealing Americans’ DNA and exploiting Covid to collect genetic data. The Beijing Genomics Institute, now known as BGI Group, is one of the largest genomic sequencing companies in the world and is listed by the Pentagon as…
javascript – Use Ajv to validate OpenAPI component schemas
no reason to use anyOf for a single schema, just pass that schema as the reference API.yaml openapi: 3.0.3 info: title: Demo version: 1.0.0 paths: /carousel: get: responses: “200”: description: Successful operation content: application/json: schema: type: array items: $ref: “#/components/schemas/test” components: schemas: other: type: object properties: component: type: object test:…
Watch rare footage of 2 mini mola swimming together off Canada’s Pacific coast
Divers spotted two juvenile ocean sunfish (Mola mola) swimming together off the coast of British Columbia. (Image credit: Timothy Manuelides) A scuba diver has captured rare footage of two “very young” sunfish swimming in emerald waters off the coast of British Columbia in Canada. Experts identified the pair as ocean…
msn/fastcve-openapi – Packagist
fast, rich and API-based search for CVE and more (CPE, CWE, CAPEC) Installation & Usage Requirements PHP 7.4 and later. Should also work with PHP 8.0. Composer To install the bindings via Composer, add the following to composer.json: { “repositories”: [ { “type”: “vcs”, “url”: “https://github.com/msn/fastcve-openapi.git” } ], “require”: {…
Only 1 OpenAPI scan found.
I’m trying to scan openapi with the docker version of ZAP from localhost. Here is the command. docker run -t ghcr.io/zaproxy/zaproxy:stable zap-api-scan.py -t 10.231.232.31:3000 -f openapi -z “-addoninstall OpenAPI Support -openapifile /Users/(my_app_path)/swagger.json” Here is the log after execution. 2023-11-21 00:47:52,648 Number of Imported URLs: 1 Total of 79 URLs PASS:…
All variants in a VCF register as “invalid genotype records in input file”
ANNOVAR Error: All variants in a VCF register as “invalid genotype records in input file” 0 Hello, I am running into an error with convert2annovar.pl where it is registering all of the variants in my VCF as invalid. My VCF is 1925 variants plus the header with the following format:…
A Step-by-Step Guide to building a BERT model with PyTorch (Part 2c) | by Tahir Rauf | Nov, 2023
So far in the series, we have accomplished several tasks: In Part 1, we prepared our dataset for BERT training. In Part 2a, we prepared fixed input embeddings for the BERT. Following that, in Part 2b, we implemented multi-head attention and the feedforward block. However, we still need to implement…
Bayer study halts, Carmot to IPO, and more
Want to stay on top of the science and politics driving biotech today? Sign up to get our biotech newsletter in your inbox. Today, we explore the future of obesity drugs and how they’re named, we chat with CRISPR pioneers about what it’s like to see the technology approved for human use,…
Predicting Forest Fires Using PyTorch
In this article, I use transfer learning with PyTorch* to classify aerial photos according to the fire danger they convey using only image details. The MODIS fire dataset establishes known fires in California from 2018 to 2020. The MODIS (Moderate Resolution Imaging Spectroradiometer) dataset contains high-resolution imagery and labeled map…
Accuracy and depth evaluation of clinical low pass genome sequencing in the detection of mosaic aneuploidies and CNVs
Background: Low-pass genome sequencing (LP GS) has shown distinct advantages over traditional methods for the detection of mosaicism. However, no study has systematically evaluated the accuracy of LP GS in the detection of mosaic aneuploidies and copy number variants (CNVs) in prenatal diagnosis. Moreover, the influence of sequencing depth on…
How long does sequencing take?
The turnaround time for HLA and genome sequencing varies based on the sequencing type, sample quality, and number of samples. We typically estimate turnaround between 10-15 business days for smaller projects, from the time your samples arrive in the lab to when we deliver results. Important Notes DNA extraction is…
R scale_type — EndMemo
R scale_type You will need to define a method for this method if you want to extend ggplot2 to handle new types of data. If you simply want to pass the vector through as an additional aesthetic, return “identity”. scale_type is located in package ggplot2. Please install and load package…
[Kernel-packages] [Bug 2007050] Autopkgtest regression report (initramfs-tools/0.142ubuntu15.1)
All autopkgtests for the newly accepted initramfs-tools (0.142ubuntu15.1) for mantic have finished running. The following regressions have been reported in tests triggered by the package: initramfs-tools/0.142ubuntu15.1 (armhf) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1]. people.canonical.com/~ubuntu-archive/proposed-…
Accuracy and depth evaluation of clinical low pass genome sequencing in the detection of mosaic aneuploidies and CNVs | BMC Medical Genomics
Study design and sample collection To evaluate the accuracy and benchmark the optimal DP of LP GS in the detection of mosaicism, evaluation strategies were designed using simulated data and virtual samples, respectively (Fig. 1). The DNA of a total of 28 clinical samples (S1 ~ S28) (aborted fetal tissue, whole blood, chorionic…
IDG-SW3 Cell Culture in a Three-Dimensional Extracellular Matrix
Here, we present a protocol for culturing IDG-SW3 cells in a three-dimensional (3D) extracellular matrix. We detailed a protocol to establish a 3D system using an extracellular metrics along with collagen one for analyzing formation and gene expression through osteogenesis. Extracellular metrics can increase the transparency of the collagen one…
R ggplot2-scales-binned — EndMemo
R ggplot2-scales-binned These functions provide the option to use binned palettes along with the ggplot2 package. It goes without saying that it requires ggplot2 to work. ggplot2-scales-binned is located in package paletteer. Please install and load package paletteer before use. scale_colour_paletteer_binned(palette, direction = 1, …) scale_color_paletteer_binned(palette, direction = 1, …)…
pytorch – Neural Net not able to learn simple analytical equation
I am currently making my first attempts with Pytorch. I am trying to solve a simple equation with a neural net. Analytically solved, the result of my neural net shall look like this: $$ y = \frac{x_5}{x_2} – \frac{x_1-x_2}{2 x_3 x_4}\frac{x_2}{x_1} $$ while I am randomly generating input data with…
University Positions – Postdoc in GPU algorithms for molecular dynamics with GROMACS
Job description We are looking for an HPC expert to contribute to one or multiple projects related to the GROMACS molecular simulation software. GROMACS is one of the most important HPC applications in the world and runs on all modern CPU and GPU architectures. GROMACS uses a hierarchical parallelization with…
OIDC RBAC – possible to map users to groups and groups to roles, where users and groups are defined by OIDC? – JupyterHub
jrouly November 16, 2023, 2:16pm 1 Hello! Is it possible to leverage both OIDC (via GenericOAuthenticator) and RBAC at the same time? And, specifically, is it possible to use RBAC to map groups to roles, and then OIDC (GenericOAuthenticator) to map users to groups? Here’s what I would expect to…
RNA star taking more than 24h to complete 2nd pass
RNA star taking more than 24h to complete 2nd pass 0 Hello all, I am very new to star alignment and rna seq in general. I have 20 mouse rna bulk samples which I am trying to align to a reference genome, after performing QC filtering and trimming. To align,…
Optimizing PyTorch for Efficient AI Model Training and Inferencing
Optimizing PyTorch for Efficient AI Model Training and Inferencing Introduction Scaling Neural Networks Adding More Layers Capturing More Nuance in Data Performing Complex Tasks Increased Memory and Compute Requirements Distributed Data Parallel (DDP) Three Steps of DDP Training Computation and Communication Overlap Bucket Division and Gradients Synchronization Full Utilization of…
Tonix Pharmaceuticals Completes Clinical Stage of Phase 3 RESILIENT Study of TNX-102 SL for the Management of Fibromyalgia
Topline results expected late December 2023 RESILIENT is expected to be the final efficacy trial required for submission of a New Drug Application to FDA; first successful Phase 3 trial, RELIEF, achieved statistical significance (p=0.010) Preliminary unaudited rate of adverse-event (AE) related discontinuations in the RESILIENT study was 4.8% which…
Tonix Pharmaceuticals Completes Clinical Stage of Phase 3 RESILIENT Study of TNX-102 SL for the Management of Fibromyalgia -November 15, 2023 at 07:01 am EST
Topline results expected late December 2023 RESILIENT is expected to be the final efficacy trial required for submission of a New Drug Application to FDA; first successful Phase 3 trial, RELIEF, achieved statistical significance (p=0.010) Preliminary unaudited rate of adverse-event (AE) related discontinuations in the RESILIENT study was 4.8% which…
r – Create a function to change the margin of a ggplot based on the labels
I want to create a funciton called gg_format_width() which automatically formats the width of a plot based on the length of the labels on the y-axis. Ideally I would want to add gg_format_width to an existing plot much like I would add the theme or a geom. So for example…
Tonix Pharmaceuticals Completes Clinical Stage of Phase 3
Topline results expected late December 2023 RESILIENT is expected to be the final efficacy trial required for submission of a New Drug Application to FDA; first successful Phase 3 trial, RELIEF, achieved statistical significance (p=0.010) Preliminary unaudited rate of adverse-event (AE) related discontinuations in the RESILIENT study was 4.8% which…
How To Install R Packages: Steps For Efficient Integration
Installing R packages is a fundamental skill for every programmer and developer working with R. This guide provides straightforward steps to ensure a smooth installation process. Whether you’re a beginner or an experienced user, these instructions will help you efficiently integrate new packages into your R environment. Understanding R Package…
R geom_spatial_segment — EndMemo
R geom_spatial_segment While the implementation is slightly differrent, this function is intended to behave identically to ggplot2::geom_segment(). Use great_circle = FALSE and detail = NULL if you wish ignore the fact that the earth is round. geom_spatial_segment is located in package ggspatial. Please install and load package ggspatial before use….
How to include a lookup table in a function for R ggplot graph and/or pass certain strings into graph?
I am trying to write a function in R for re-creating a ggplot graph. The graph is using climate data, and I want to be easily able to remake it for 3 different climate scenarios (rcp column) and multiple different percentiles/smooths. Code to generate an example dataframe: df_hist <- data.frame(rcp…
Safer P-CARE intravenous needle softens once inserted into body
While intravenous needles need to be rigid in order to pierce the skin, that rigidity sometimes causes damage to the veins. A new needle addresses that issue by softening upon insertion into the patient’s body – plus it reduces the likelihood of needle-poke injuries. One of the problems with conventional…
Scientists from Australia and the US team up on African swine fever vaccine
African swine fever virus. Credit: Ben Clark, Plum Island Animal Disease Center, Department of Homeland Security Scientists from Australia and the United States are teaming up to tackle one of animal science’s biggest challenges: a safe and effective vaccine against African swine fever, a viral pandemic devastating the world’s pig…
python – How to use tensorboard Embedding Projector using Pytorch with custom dataset and custom model
Currently im doing image embedding visualisation and I want to use Tensorboard Projector PCA and T-SNE to see the image embedding similarity. I follow a website code to do the visualisation but I am unable to make the expected visualisation where the same images should clump together but it just…
Astria Therapeutics shares Q3 results, positive phase 1a data, and pipeline expansion By Investing.com
© Reuters. Astria Therapeutics recently reported its third-quarter financial results and provided a corporate update, highlighting its promising Phase 1a data for STAR-0215, a potential preventative treatment for Hereditary Angioedema (HAE). The company also announced the expansion of its pipeline with STAR-0310, a potential therapy for atopic dermatitis. Key takeaways…
Intel 5th Gen Emerald Rapids 64-Core & Granite Rapids Xeon CPUs Performance Unveiled
Intel has unveiled the latest performance and internal projections of its upcoming 5th Gen Emerald Rapids & next-gen Granite Rapids Xeon CPUs. Intel 5th Gen Emerald Rapids Xeon 64-Core CPU Offers Up To 40% Better Performance Than 56-Core Sapphire Rapids Talking about its Xeon CPUs during SC23, Intel unveiled new…
Implicit Models and Neural Numerical Methods in PyTorch
Abstract: Computation in traditional deep learning models is directly determined by the explicit linking of select primitives e.g. layers or blocks arranged in a computational graph. Implicit neural models follow instead a declarative approach; a desiderata is encoded into constraints and a numerical method is applied to solve the resulting…
AI-900: Conversational AI Workloads: Examples and Benefits
Learn what conversational AI workloads are and how they can improve customer experience and satisfaction. Find out how Azure AI can help you build, connect, and manage conversational AI applications. Question Which two scenarios can be used as examples of conversational Al workloads? Select all options that apply. A. Assembly…
python – Docker with Rstudio & conda virtual env – unable to load R packages
I have this dockerfile: # Use the rocker/rstudio image with R version 4.1.2 FROM rocker/rstudio:4.1.2 # Install deps RUN apt-get update && apt-get install -y \ wget \ bzip2 \ bash-completion \ libxml2-dev \ zlib1g-dev \ libxtst6 \ libxt6 \ libhdf5-dev \ libcurl4-openssl-dev \ libssl-dev \ libfontconfig1-dev \ libcairo2-dev \…