Tag: PASS

Loss.backward() error when using custom autograd function – vision

Hi All! I am facing the error:AttributeError: ‘CheckpointFunctionBackward’ object has no attribute ‘input_tensors’ Please find the implementation of my custom backward function. Hi @torch2.0, When sharing code, please copy and paste the code and wrap it within 3 backticks “`, rather than sharing a screenshot. Your issue is that you…

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Master Continuous Control with DDPG

Master Continuous Control with DDPG | PyTorch Tutorial Table of Contents: Introduction Understanding Deep Deterministic Policy Gradients (DDPG) The Lunar Lander Environment Implementing a Deterministic Policy Gradient Agent 4.1. Importing the Required Libraries 4.2. Initializing the Agent 4.3. Implementing the Actor Network 4.4. Implementing the Critic Network 4.5. Implementing the…

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Fedora 39 update for mbedtls

This security bulletin contains information about 2 vulnerabilities. EUVDB-ID: #VU86233 Risk: Medium CVSSv3.1: 5.1 [CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:C/C:L/I:N/A:N/E:U/RL:O/RC:C] CVE-ID: CVE-2024-23170 CWE-ID: CWE-385 – Covert Timing Channel Exploit availability: No Description The vulnerability allows a remote attacker to perform MitM attack. The vulnerability exists due to a timing side channel in RSA private operations….

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Ubuntu Manpage: samtools-quickcheck – a rapid sanity check on input files

Provided by: samtools_1.19-1_amd64 NAME samtools-quickcheck – a rapid sanity check on input files SYNOPSIS samtools quickcheck [options] in.sam|in.bam|in.cram [ … ] DESCRIPTION Quickly check that input files appear to be intact. Checks that beginning of the file contains a valid header (all formats) containing at least one target sequence and…

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Vertex AI docker in docker: Cannot connect to the Docker daemon

So I am using kubeflow Containerized Python Components to create a Vertex AI training pipeline. As the last step of the pipeline, I would like to build and push a custom prediction container using a Custom Prediction Routine, with the newly trained model baked in. In the Dockerfile that creates…

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Problems rendering a quarto qmd file through jupyter in VS Code – JupyterHub

bj631 January 19, 2024, 10:45pm 1 I’m trying to preview a .qmd file using quarto with jupyter in VS Code. There is a little banner in the bottom right corner that shows up when trying to render the .qmd that says ” command ‘quarto.preview’ not found “. It is a…

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Electroporation Instruments Market Insights, Market Players and Forecast Till 2031

In 2024, “Electroporation Instruments Market Size “, Status and Market Insights, forecast to 2031 “Electroporation Instruments Market” by Types (Total Electroporation System, Eukaryotic Electroporation System, Microbial Electroporation System), End User (Biotechnology and Pharmaceutical Company, Hospital Laboratories, Academic Research Institutions, Others), Global Electroporation Instruments Market Due to the COVID-19 pandemic, the…

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Compute Saliency Maps for Image Classification using PyTorch

import matplotlib.pyplot as plt import numpy as np import torch import torch import torchvision.models as models from PIL import Image from torch.autograd import Variable from tqdm import tqdm from helpers.data_utils import * from helpers.image_utils import * class SaliencyMap: def compute_saliency_maps(self, X, y, model): “”” Compute a class saliency map using…

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Solved What evidence suggests that a gene in the mtDNA is

What evidence suggests that a gene in the mtDNA is causing this disorder? Males are more often affected but do not pass on the trait. Males and females are both affected and both likely to pass on the trait. The disorder exhibits a high degree of penetrance from generation to…

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Using ColabFold to predict protein structures | by Natan Kramskiy | Jan, 2024

A few hours before the CASP14 (14th Critical Assessment of Structure Prediction) meeting, the latest biannual structure prediction experiment where participants build models of proteins given their amino acid sequences, this image went viral on twitter. Ranking of participants in CASP14, as per the sum of the Z-scores of their…

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Hyperspectral Line-Scanning VSFG Microscope Setup, Alignment, and Calibration

Begin by setting up the pulsed laser system, centered at 1025 nanometers. Guide the output of the seed laser into a commercial Optical Parametric Amplifier, or OPA, to generate a mid-infrared or mid-IR beam. Tune the mid-IR beam to the frequency of interest. Pass the residual 1025 nanometer beam from…

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From nucleotide or proteine sequences to EC number using biopython

From nucleotide or proteine sequences to EC number using biopython 0 Hi, if I have a fasta file containing nucleotide sequences or proteines sequences is it possible to get EC number using biopython for example 1.1.1.169 1.1.1.205 1.1.1.25 1.1.1.302 1.1.1.330 1.1.1.34 ps : I’m working on fungus so I need…

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python – OpenAPI: Return structured data from text input

Given a txt input which represents extracted resume (or “CV” outside of the US) data, pass the text to an AI model and return a JSON version of the original input. I have created the below script, which tries to prompt gpt3-turbo in order to process and return the JSON….

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Deep Learning with Python and PyTorch, Certificate Practice Exam

Deep Learning with Python and PyTorch, Certificate Practice Exam   About the Service: The Risk Management in Development Projects, Certificate Practice Exam provides professionals with a comprehensive understanding of risk management principles and strategies in the context of development projects. This certification program focuses on the utilization of Big Data…

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Unraveling the Mystery of Protein Knots: The Limitations of AlphaFold in Protein Topology Prediction | by Pawel Dabrowski | Dec, 2023

Be carefull when predicting the protein’s topology with AlphaFold Introduction AlphaFold, a deep learning tool, has taken the scientific world by storm, revolutionizing the way we predict protein structures. However, like all groundbreaking technologies, it’s not without its limitations. In this article, we delve into one such limitation: AlphaFold’s struggle…

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Will 2024 Be The Year Of The Anthropocene?

As we approach the end of the year, we may not only be saying goodbye to 2023, but also the geochronologic unit of time we have been living in to date. In 2024, scientists will be making a decision on whether we have entered the Anthropocene, a new epoch marked…

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European Mouse Mutant Cell Repository

The following list defines the different statuses that EUCOMM report on the constructs in their pipeline. Mice – Genotype confirmed (M-GC)The genotype of testcross offspring has been confirmed molecularly. Mice – Germline transmission (M-GLT)Test crosses of chimaeras indicate germline transmission of the ES cell mutation based on coat color. Mice…

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Pharmaceutics | Free Full-Text | Natural Biopolymer-Based Delivery of CRISPR/Cas9 for Cancer Treatment

Cancer is one of the leading causes of disease-associated mortality, with a rising incidence worldwide [1]. Although many therapeutic methods have been used in cancer treatment, such as chemotherapy, radiotherapy, surgery, and targeted therapy, the overall therapeutic outcome remains unsatisfactory. Therefore, developing new therapeutic means is urgently needed. With advances…

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mysql – Trying to Authenticate the Slurm User via Keys Instead of Password Using the pam Plugin on MariaDB

mysql – Trying to Authenticate the Slurm User via Keys Instead of Password Using the pam Plugin on MariaDB – Database Administrators Stack Exchange Stack Exchange Network Stack Exchange network consists of 183 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their…

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Neural Style Transfer with PyTorch

In this tutorial, we’ll cover how to implement the neural-style algorithm that’s based on this paper. What is neural style transfer? Neural style transfer is a technique used to generate images in the style of another image. The neural-style algorithm takes a content-image as input, a style image, and returns…

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Tonix Pharmaceuticals Announces Highly Statistically Significant and Clinically Meaningful Topline Results in Second Positive Phase 3 Clinical Trial of TNX-102 SL for the Management of Fibromyalgia

Phase 3 RESILIENT study of TNX-102 SL successfully demonstrated daily pain reduction over placebo (primary endpoint, p = 0.00005) All six key secondary endpoints, including patient global impression, fibromyalgia-specific symptoms and dysfunction, fatigue and sleep measures were significantly improved (all p ≤ 0.001) Positive results support planned New Drug Application…

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Tonix Pharmaceuticals Announces Highly Statistically

Phase 3 RESILIENT study of TNX-102 SL successfully demonstrated daily pain reduction over placebo (primary endpoint, p = 0.00005) All six key secondary endpoints, including patient global impression, fibromyalgia-specific symptoms and dysfunction, fatigue and sleep measures were significantly improved (all p ≤ 0.001) Positive results support planned New Drug Application…

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Tonix Pharma (TNXP) Announces Positive Topline Results in Second Positive Phase 3 Clinical Trial of TNX-102 SL for the Management of Fibromyalgia

Tonix Pharmaceuticals Holding Corp. (Nasdaq: TNXP) (Tonix or the Company), a biopharmaceutical company with marketed products and a pipeline of development candidates, today announced that the Phase 3 RESILIENT study evaluating TNX-102 SL (cyclobenzaprine HCl sublingual tablets) met its pre-specified primary endpoint in the second of two positive Phase 3…

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NM_000546.6(TP53):c.743G>A (p.Arg248Gln) AND Lymphoma – ClinVar

NM_000546.6(TP53):c.743G>A (p.Arg248Gln) AND Lymphoma Based on: 1 submission [Details] Record status: current Accession: RCV000790860.7 Allele description NM_000546.6(TP53):c.743G>A (p.Arg248Gln) Gene: TP53:tumor protein p53 [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 17p13.1 Genomic location: Preferred name: NM_000546.6(TP53):c.743G>A (p.Arg248Gln) Other names: p.R248Q:CGG>CAG HGVS: NC_000017.11:g.7674220C>T NG_017013.2:g.18331G>A NM_000546.6:c.743G>AMANE SELECT NM_001126112.3:c.743G>A…

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Sperm Cell Powerhouses Contain Almost No DNA

January 1, 2024 2 min read Scientists discover why fathers usually don’t pass on their mitochondria’s genome By Sneha Khedkar Credit: Kateryna Kon/Science Source Almost every human cell is powered by mitochondria, bean-shaped organelles that use oxygen to synthesize usable energy. These structures evolved billions of years ago from free-swimming…

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Master Image Segmentation with PyTorch U-NET

Master Image Segmentation with PyTorch U-NET Introduction Building the Model Preprocessing the Data Loading the Data Training the Model Evaluating Model Performance Saving and Loading the Model Visualizing Predictions Conclusion Frequently Asked Questions In this article, we will learn how to perform image segmentation in PyTorch. We will start by…

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How the Illumina/Grail Opinion Updates Case Law on Vertical Mergers and “Litigating the Fix”

Steven C. Salop analyzes the Fifth Circuit Court’s opinion accepting the Federal Trade Commission’s suit to block Illumina’s acquisition of Grail. The ruling sheds light on how courts may approach vertical merger analysis and “litigating the fix” in the future, and what this may mean for the Merger Guidelines’ approach…

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Gemini Models with Google Vertex AI Integration for Haystack

In this article, we will introduce you to the new Google Vertex AI Integration for Haystack 2.0-Beta. While this integration introduces several new components to the Haystack eco-system (feel free to explore the full integration repo!), we’d like to start by showcasing two components in particular: the GeminiGenerator and the…

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Brace yourselves for these trends in clinical research in 2024

There’s an air of cautious optimism about 2024, after a difficult few years following the end of the pandemic when investment in pharma and biotech research dropped substantially. After this significant reset, there’s now hope that in 2024, in line with emerging trends, the funds will be there for the…

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neural networks – Reshaping 6d input for PyTorch Conv2d, ReLU, and BatchNorm2d

neural networks – Reshaping 6d input for PyTorch Conv2d, ReLU, and BatchNorm2d – Cross Validated Stack Exchange Network Stack Exchange network consists of 183 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. Visit Stack Exchange Log…

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python – Custom Loss Functions in PyTorch: A Comprehensive …

Introduction Loss functions are the driving force behind all machine learning algorithms. They quantify how well our models are performing by calculating the difference between the predicted and actual outcomes. The goal of every machine learning algorithm is to minimize this loss function, thereby improving the model’s accuracy. Various libraries,…

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Post Masters RA – Bioinformatics Data Scientist Job

Job Description The Earth and Biological Sciences Directorate (EBSD) leads novel and necessary research in three core areas: Atmospheric and Climate sciences, Biological Sciences, and Environmental Molecular Sciences. The contributions of EBSD staff are many as we continue to elevate the impact of PNNL’s science mission: to understand, predict, and…

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insideBIGDATA AI News Briefs Bulletin Board

Welcome insideBIGDATA AI News Briefs Bulletin Board, our timely new feature bringing you the latest industry insights and perspectives surrounding the field of AI including deep learning, large language models, generative AI, and transformers. We’re working tirelessly to dig up the most timely and curious tidbits underlying the day’s most…

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My Cancer Experience in Poems

In the fall of 2022, Dr. John Smelcer was diagnosed with stage 2 non-specific non-Hodgkins Lymphoma. Over the next six months, he was hospitalized one week of every month in order to receive chemotherapy and immunotherapy. On a sunny day in early February 2023, he rang the bell on the…

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Research Biologist (Computational/Bioinformatics)/Microbiologist (Research Associate) Job in Columbia, MO

Summary The Agricultural Research Service (ARS) is the United States Department of Agriculture’s chief scientific research agency and one of the world’s premiere scientific organizations. ARS Postdoctoral Research Associates are hired to supplement a lead scientist’s research on agricultural problems of high national priority affecting American agriculture. **ANNOUNCEMENT IS OPEN…

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Special Issue : Extracellular Vesicles and ncRNA

Dear Colleagues, Over the past two decades, the biological science arena has witnessed the emergence and rapid advancement of two distinct research domains: noncoding RNA (ncRNA) and extracellular vesicles. Presently, the significance of ncRNA in the biology of virtually all living organisms is beyond dispute, and our comprehension of its…

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r – looping over several columns to create ggplots

You must adapt the function to have the column names as argument, not the column vectors. The code comments explain how it is made. Then loop over names(df2). suppressPackageStartupMessages( library(tidyverse) ) # Create Vectors var1 <- c(‘A’,’A’,’B’,’B’) var2 <- c(1,2,2,1) var3 <- c(‘sam’,’sam’,’saul’,’saul’) # Create DataFrame df <- data.frame(var1,var2,var3) #…

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Understanding GPU Memory 1: Visualizing All Allocations over Time

by Aaron Shi, Zachary DeVito During your time with PyTorch on GPUs, you may be familiar with this common error message: torch.cuda.OutOfMemoryError: CUDA out of memory. Tried to allocate 512.00 MiB. GPU 0 has a total capacity of 79.32 GiB of which 401.56 MiB is free. In this series, we…

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Cloud Deep Learning: 3 Focus Areas & Key Things to Know

Cloud deep learning is the integration of cloud computing and deep learning models that can process inputs through different layers. By developing deep learning, businesses can perform more complex tasks compared to classical algorithms. There are various facets of the process to achieve this goal. Choosing classical models can require…

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Variant calling using HaplotypeCaller does not show #FILTER information

Variant calling using HaplotypeCaller does not show #FILTER information 0 Hi All, I would like to ask for Variant Calling using HaplotypeCaller. It’s supposed that after doing the HaplotypeCaller, the #FILTER columns in gvcf files shall show the ‘PASS/LowQ’ however in my case, the output #FILTER only shows ‘.’ without…

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People, not the climate, caused the decline of the giant mammals

About 100,000 years ago, the first modern humans migrated out of Africa in large numbers. They were eminent at adapting to new habitats, and they settled in virtually every kind of landscape — from deserts to jungles to the icy taiga in the far north. Part of the success was…

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Confusion with passing reactive input to ggplot – shinyapps.io

Dear all, I’m trying to create an app that uses heirarchical dropdown menus to select infput for ggplot.The error lies in the “best_sellers” tab where the user first selects a category to filter by and then and sub category . I then pass these variables to ggplot and am getting…

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backend – openApi documenation to upload an image in swagger

There are two ways you can do this. First and simplest, you can upload files directly using the relevant media type. For example, requestBody: content: image/png: means: content is an image in a byte array. schema: type: string format: binary The reason this is simple is that it is very…

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[llvm-bugs] [Bug 75428] clang crash when build IPEX code.

Issue 75428 Summary clang crash when build IPEX code. Labels clang Assignees Reporter xuhancn The error msg: “`cmd Stack dump: 0. Program arguments: /usr/bin/clang++ -DAT_PARALLEL_OPENMP=1 -DUSE_C10D_GLOO -DUSE_DISTRIBUTED -DUSE_RPC -DUSE_TENSORPIPE -Dintel_ext_pt_cpu_EXPORTS -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/aten -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/utils -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/jit -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/jit -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/utils -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/ideep/mkl-dnn/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/csrc/cpu/tpp -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/libxsmm/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/build/Release/csrc/cpu/csrc/cpu/cpu_third_party/ideep/mkl-dnn/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/ideep/include -I/home/xu/anaconda3/envs/ipex_cpu/include/python3.12 -I/home/xu/anaconda3/envs/ipex_cpu/include -I/home/xu/anaconda3/envs/ipex_cpu/lib/python3.12/site-packages/torch/include/torch/csrc/api/include -I/home/xu/conda_spaces/ipex_cpu/frameworks.ai.pytorch.ipex-cpu/third_party/ideep/mkl-dnn/src/../include -isystem /home/xu/anaconda3/envs/ipex_cpu/lib/python3.12/site-packages/torch/include -fPIC…

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Now Access Google’s Gemini Pro Models in Kaggle Notebooks For Free

Good news folks! Google’s Gemini Pro and Gemini Pro Vision models are available on Kaggle for Free. That means you can perform several AI tasks in Kaggle Notebooks for free. Gemini models are top-of-the-line generative AI models right now from Google. Gemini models have exceptional image, audio, video, and text…

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Mastering Text Analysis with LSTM Networks Using PyTorch | by Wade | Dec, 2023

A Comprehensive Guide to Building Your Own Text Classifier Understanding language is a complex task, not just for computers, but even for us humans. How do we interpret sentences, categorize news, or even decide if a text is positive or negative? This is the realm of text classification, and today,…

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Navigating Single Cell RNA Seq Courses: A Researcher’s Odyssey | by Genetic Observer | Dec, 2023

Greetings to my fellow researchers! As we delve into the ever-evolving landscape of genomics, one frontier that has truly revolutionized our understanding of cellular heterogeneity is Single Cell RNA Sequencing (scRNASeq). In my quest for proficiency in this transformative field, I embarked on a fascinating journey exploring various scRNASeq analysis…

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Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking

Prediction with AlphaFold2 and AlphaFold-Multimer For each PDB the release date in the Protein Data Bank34 was recorded. AlphaFold 2 (2.2.2) was run setting the –max_template_date flag to be the day before the release date of the PDB and the –model_preset to be either monomer for AF or multimer for…

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Significant Slowdown in Training Speed After Using compile() in PyTorch 2.1.0 – torch.compile

Hello everyone, I’m currently experiencing a substantial decrease in training speed after using the compile() function in my PyTorch model. Before the inclusion of compile(), my training iterations were completed in approximately 1 second per iteration. However, after integrating compile(), the speed has drastically reduced to about 70 seconds per…

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autopkgtest regression on architectures where char is unsigned

Source: rust-rusqlite Version: 0.29.0-2 Severity: serious tracker.debian.org/pkg/rust-rusqlite Issues preventing migration: ∙ ∙ autopkgtest for rust-rusqlite/0.29.0-2: amd64: Pass, arm64: Regression or new test ♻ (reference ♻), armel: Regression or new test ♻ (reference ♻), armhf: Regression or new test ♻ (reference ♻), i386: Pass, ppc64el: Reference test in progress, but real…

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Step-by-Step Guide to Your First Machine Learning Model with PyTorch | by Tristin | Dec, 2023

Mastering the Basics of Linear Regression in PyTorch Have you ever wondered how to create a machine learning model that can predict outcomes based on data? If you’re new to the world of machine learning, or if you’re familiar with it but haven’t yet dabbled in PyTorch, then you’re in…

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Scientist (Postdoc) in the field of Bioinformatics/Artificial Intelligence, Leipzig, Sachsen

The Fraunhofer-Gesellschaft () currently operates 76 institutes and research institutions throughout Germany and is the world’s leading applied research organization. Around employees work with an annual research budget of 2.9 billion euros. Its Fraunhofer Institute for Cell Therapy and Immunology IZI researches and develops special problem solutions at the interfaces…

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Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain

Mouse brain tissues All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee under protocol number 18-00006. Adult (P56) C57BL/6J male mice were purchased from the Jackson Laboratory at 7 weeks of age and maintained in the Salk animal barrier facility on 12-h dark–light…

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How Does PyTorch Backprop Through Argmax?

Backpropagation is a fundamental algorithm in training neural networks, allowing them to learn from data. Backpropagation involves iteratively updating the weights of a neural network to minimize the difference between predicted and actual outputs. It relies on the chain rule to calculate gradients, determining how much each parameter should be…

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Help me confirm if my reads are properly normalized and transformed or do I need to re-do

Help me confirm if my reads are properly normalized and transformed or do I need to re-do 0 Hello, can you help me confirm whether or not my reads dataset were normalized properly prior to my work on them? The data source is 40 florets from Arabidopsis for 3 replicates…

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Eels Can Genetically Modify Nearby Fish With Their Electrical Pulses | Smart News

Electric eels can discharge up to 860 volts of electricity. Mark Newman via Getty Images In the lab, researchers regularly use electricity to deposit medicine, DNA, bacteria or other substances into cells. This process is known as electroporation, and it works by creating temporary openings, or pores, in cell membranes…

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New Theory Claims that Identity Resides in the Human Genome and is Compatible with Cognitive Perspectives of ‘Self’

Newswise — One of the greatest philosophical thought exercises that has challenged the concept of identity, is the Ship of Theseus paradox. It poses the question: Are we the same person over time? The original meaning of ‘Identity’ is derived from Medieval Latin identitas or idem meaning ‘sameness’ or ‘same’….

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hardware acceleration – Very low GPU usage of Pytorch (slow training) in comparison to Tensorflow

When I train my model (a simple MLP) using pytorch and DataLoader using large batches of data (128000) with the whole dataset which contain 18.515.415 observations, the GPU (NVIDIA A40) memory occupation is only about 500Mb and the frequency does not go beyond 10% during a very short interval and…

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Short RStudio homework help – deadline 18.12.23 and I am willing to pay for the help so I can finish my Master’s studies! – General

Hello! I would really need help with a short Rstudio homework. I’m about to finish my Master’s degree, and in my last semester we currently have a research methods class where we need to do homework. If I don’t pass the homework, unfortunately I won’t be able to start writing…

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JetBrains Launches AI Assistant Integrated in its 2023.3 Release IDEs

JetBrains refreshes all of its IDEs in the last release of the year and promotes its integrated AI Assistant out of preview into general availability for paying customers. Besides its strong integration with the IDEs, JetBrains AI Assistant tries to stand out thanks to its support for multiple LLMs. According…

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GAN with PyTorch on CelebA Dataset

import torch from torchvision import datasets, transforms from torch.utils.data import DataLoader def train_model(): “”” Trains a PyTorch model on the CelebA dataset. This function uses the PyTorch framework to train a model on the CelebA dataset. It applies necessary transformations to the dataset, creates a data loader, defines the model…

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From the Desk of Thom Golab: ACSH and Sickle Cell Disease

When I worked for another think tank 40 years ago (dang, I am old), the president used to say books with new ideas are great, but people (by that, he meant journalists and policymakers) don’t have time to read books. So, those potential new policies aren’t discussed. His solution was…

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Meet EAGLE: A New Machine Learning Method for Fast LLM Decoding based on Compression

Large Language Models (LLMs) like ChatGPT have revolutionized natural language processing, showcasing their prowess in various language-related tasks. However, these models grapple with a critical issue – the auto-regressive decoding process, wherein each token requires a full forward pass. This computational bottleneck is especially pronounced in LLMs with expansive parameter…

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ubuntu – Medaka: unrecognized command ‘tools’ and samtools not found

When trying to run medaka_consensus in ubuntu, I am getting the following error. I installed into a virtualenv to run on ubuntu. (medaka) ubuntu:~/medaka$ medaka_consensus -i combined.fastq -d curated.fasta -t -o ~/medaka 10 -m r941_sup_plant_g610 TF_CPP_MIN_LOG_LEVEL is set to ‘3’ [main] unrecognized command ‘tools’ Attempting to automatically select model version….

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Exclusive interview: Florida Surgeon General Joseph Ladapo asks FDA for data on risks of DNA contaminants in COVID-19 vaccines

Florida Surgeon General Joseph Ladapo | Photo courtesy of FDOH BY JENNIFER CABRERA TALLAHASSEE, Fla. – On December 6, Florida Surgeon General Joseph Ladapo sent a letter to the U.S. Food and Drug Administration (FDA), asking questions about a recent preprint documenting the detection of billions of DNA fragments per…

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how to enter a bug in the future for sagemath in github with no github account?

Dear Nasser, On 11 December 2023 21:18:18 GMT, “‘Nasser M. Abbasi’ via sage-devel” <sage-…@googlegroups.com> wrote: > >I got email today that my github account will be terminated if I do not do >that 2FA (two factor authentication) each time to login. > >I am not interested in 2FA, I do…

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VSCode python terminal crashes after trying to train a PyTorch model

I’m using scanpy to train a scRNA model, however, whenever I pass my dataset (AnnData), it simply crashes the terminal: if train: sc_model = RNAStereoscope(sc_adata) sc_model.train(max_epochs=2) sc_model.history[“elbo_train”][10:].plot() sc_model.save(“scmodel”, overwrite=True) else: sc_model = RNAStereoscope.load( r”.\scmodel”, sc_adata, ) Has anyone had this issue before? It doesn’t even give a proper error, it…

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Early Diagnosis of High-Grade Serous Ovarian Cancer Feasible

MONDAY, Dec. 11, 2023 (HealthDay News) — Early diagnosis of high-grade serous ovarian cancer (HGSOC) seems feasible through analysis of genomic alterations in DNA from Papanicolaou (Pap) test smears, according to a study published online Dec. 6 in Science Translational Medicine. Lara Paracchini, Ph.D., from Humanitas University in Milan, and…

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AI Is Pushing Science Into an Age of Uncertainty

This summer, a pill intended to treat a chronic, incurable lung disease entered mid-phase human trials. Previous studies have demonstrated that the drug is safe to swallow, although whether it will improve symptoms of the painful fibrosis that it targets remains unknown; this is what the current trial will determine,…

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Electroporation Instruments Market 2031: Tomorrow’s Trends and Opportunities Unveiled

Latest Research Report On “Electroporation Instruments Market” 2024 Analysis, Future Projection, Forecast By 2031 Global “Electroporation Instruments Market” Report for the years 2024-2031 stands out as a comprehensive analysis, detailed examination delves into the present and prospective state of the Electroporation Instruments industry. Elevating its significance, this report not only offers…

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How to create a Chat-GPT clone starter | by Hamza ELJAOUHARI | Dec, 2023

Creating a Chat-GPT clone is a complex task, but I can guide you through the main steps, providing code snippets to illustrate the process. This guide assumes familiarity with Python, machine learning libraries like TensorFlow or PyTorch, and basic concepts of neural networks. Ensure you have Python installed. You will…

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Genentech: Press Releases | Sunday, Dec 10, 2023

Sunday, Dec 10, 2023 New Data for Genentech’s Columvi and Lunsumio Presented at ASH 2023 Support Continued Benefit for People With Lymphoma Longer-term data from pivotal studies of fixed-duration Columvi and Lunsumio continue to show durable responses in people with heavily pre-treated lymphomas   New data reinforce the potential of…

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Influence of pneumatic transportation on the stability of monoclonal antibodies

Characteristics of the PTS The PTS from the Institut de Cancérologie Strasbourg Europe (ICANS) is an Aerocom AC4000 160 mm, 1000 m long and includes approx. 20 curves (Fig. 1A,B). The cartridge used to transport the mAbs along the different departments from the institution undergoes an acceleration profile of 4.06 ± 1.75 g per…

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Electric Eels Can Shock DNA into Other Animals

Help keep One Green Planet free and independent! Together we can ensure our platform remains a hub for empowering ideas committed to fighting for a sustainable, healthy, and compassionate world. Please support us in keeping our mission strong. Electric eels, known for their ability to generate powerful electric shocks, may…

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Multiple Object Detection from scratch – vision

0fByte December 9, 2023, 10:15am 1 Hello all,I am looking to create a model to do multiple object detection from scratch. I understand the basics of how to create a (CNN) model for single object classification and localization but I wasn’t able to found a tutorial on how to model…

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Generating high-quality plant and fish reference genomes from field-collected specimens by optimizing preservation

Sample collection A total of nine species of marine fish were collected across three different sampling days (September 7th, 9th, and 12th 2022) under IACUC Animal Use Protocol S12219 (Supplementary Data 1). Six species were collected using a speargun donated by a local fisher. Fish were transported back to shore, euthanized,…

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Holiday Merriment and Sharing the Microbiome

Kirsten D/peopleimages.com/Adobe Stock The holidays are upon us, with many opportunities to visit with extended family members, renew old friendships, and spread cheer to neighbors and workmates. It is a wonderful time of year for human gatherings, providing a chance to share updated activities from the past year, exchange ideas,…

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How to group atoms as molecules in reax – LAMMPS General Discussion

Using Aug 2023 version of Lammps This is a rather basic issue. I am following the paper by Kim to model , water, ethahol and phosphoric acid adsorbed to TiO2 using their ff.Reactive MD-force field: Kim, S.-Y., van Duin, A. C. T., and Kubicki, J. D., 2012, Molecular dynamics simulations…

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sparklyr – Databricks Connect v2

Last updated: Thu Dec 7 16:28:19 2023 Intro Databricks Connect enables the interaction with Spark clusters remotely. It is based on Spark Connect, which enables remote connectivity thanks to its new decoupled client-server architecture. This allows users to interact with the Spark cluster without having to run the jobs from…

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Fully Automated NGS Sample Preparation Using a Digital Microfluidics Platform

Hello everyone, and thank you for attending Lab Managers Automation Digital Summit. My name is Mary Beth DiDonna and I’ll be moderating this discussion. Welcome to this session, fully automated NGS sample preparation using a digital microfluidics platform. The Miro NGS Prep System is a compact digital microfluidics platform, which…

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Why claims of a new ‘genetic vaccine’ being given to Australian children don’t align with reality

CheckMate December 8, 2023 This week, we debunk viral social media posts that claim a new “genetic vaccine” has been added to the national vaccine schedule for children aged 2-6 months. We also show why the “mother of all revelations” was more fizzer than Pfizer, and identify some of the…

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Illumina RNA Sequencing – SeqCenter, LLC

RNA, the intermediate stage in the flow of genetic information from DNA to protein, contains many systems of expression and regulation that can be studied through RNA sequencing. While whole genome sequencing reveals information at the DNA level, next generation RNA sequencing (RNA-seq) characterizes the transcriptome and provides additional context…

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Electric Eels Can Zap DNA Into Nearby Animals, Shocking Study Finds

In something straight out of a comic book, electric eels may be able to shoot DNA into other animals when they zap them with electricity. The electric eel can release up to 860 volts of electricity, enough to genetically modify nearby fish larvae via a process known as electroporation, according…

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Jams To Trim The Tree To, And Watch Some Hockey Too

My family isn’t huge on Christmas music, but we all have our favorites that get played around the holidays. We are huge Caniacs, and we have a favorite Hurricane. Why not pair these up and see what happens? Seth Jarvis- Merry Christmas From The Family by Robery Earl Keen. REK…

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c – MBEDTLS_ERR_NET_INVALID_CONTEXT Error in mbedtls. Epoll gives EPOLLIN event notification when no data is available to read with TLS

I made a epoll HTTPS server with mbedtls. It listens on two ports: one for HTTP and the other is for HTTPS. The HTTP one works perfectly well. But for HTTPS I seem to get EPOLLIN notification when no data is available to read with mbedtls_ssl_read(). It could be that…

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Google Releases Gemini Generative AI Model Designed to Match and Exceed OpenAI’s GPT-4 and ChatGPT

on December 6, 2023 at 12:30 pm Google has officially unveiled its new Gemini generative AI model after nearly a year of anticipation. Gemini comes in three sizes and is officially multimodal out of the gate, though with limited availability for many of the features showcased by Google in an…

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Genomic Workstation Market Dynamics 2023-2030: Also about Its Market Trends, Projections, and Opportunities

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Opportunities”}],”lineInfo”:{“truncatedLoc”:”76″,”truncatedSloc”:”76″},”mode”:”file”},”image”:false,”isCodeownersFile”:null,”isPlain”:false,”isValidLegacyIssueTemplate”:false,”issueTemplateHelpUrl”:”docs.github.com/articles/about-issue-and-pull-request-templates&#8221;,”issueTemplate”:null,”discussionTemplate”:null,”language”:”Markdown”,”languageID”:222,”large”:false,”loggedIn”:false,”newDiscussionPath”:”/melchekhinf/Market-Research-Report-List-1/discussions/new”,”newIssuePath”:”/melchekhinf/Market-Research-Report-List-1/issues/new”,”planSupportInfo”:{“repoIsFork”:null,”repoOwnedByCurrentUser”:null,”requestFullPath”:”/melchekhinf/Market-Research-Report-List-1/blob/main/genomic-workstation-market.md”,”showFreeOrgGatedFeatureMessage”:null,”showPlanSupportBanner”:null,”upgradeDataAttributes”:null,”upgradePath”:null},”publishBannersInfo”:{“dismissActionNoticePath”:”/settings/dismiss-notice/publish_action_from_dockerfile”,”dismissStackNoticePath”:”/settings/dismiss-notice/publish_stack_from_file”,”releasePath”:”/melchekhinf/Market-Research-Report-List-1/releases/new?marketplace=true”,”showPublishActionBanner”:false,”showPublishStackBanner”:false},”rawBlobUrl”:”github.com/melchekhinf/Market-Research-Report-List-1/raw/main/genomic-workstation-market.md&#8221;,”renderImageOrRaw”:false,”richText”:” Market Overview and Report Coverage \n…

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ProPicks: 6 AI-Curated Stock-Picking Strategies Proven to Beat the Market

ProPicks, an AI-powered investment tool, consistently outperforms benchmarks like the S&P 500 with meticulously analyzed high-performing stocks, offering refined long-term investment strategies. With six robust strategies, ProPicks caters to diverse investor preferences, ensuring superior performance through continuous updates and evaluations. Subscribe now for up to a 60% discount during the…

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eciboadaptech/finapi-webform – Packagist

The following pages give you some general information on how to use our APIs.The actual API services documentation then follows further below. You can use the menu to jump between API sections. This page has a built-in HTTP(S) client, so you can test the services directly from within this page,…

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Is there a way to compute weight gradients in Pytorch with no_grad – autograd

I know the question seems like it answers itself (compute weight gradients without gradients?). But the issue I am trying to resolve is that I will need to change leaf variables before computing the backwards pass. Without no_grad pytorch will complain about in-place modifications. Define the model (it is split…

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How to use Nextflow to call scripts from different environments?

How to use Nextflow to call scripts from different environments? 0 I have the following conda environments: wf-preprocess_env wf-assembly_env Each environment has unique dependencies installed. I have 3 scripts: preprocess.py which I use with wf-preprocess_env environment assembly.py and assembly-long.py which I use with wf-assembly_env How can I use Nextflow to…

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Post Masters RA – Bioinformatics Data Scientist – Richland

**Overview** The Earth and Biological Sciences Directorate (EBSD) leads novel and necessary research in three core areas: Atmospheric and Climate sciences, Biological Sciences, and Environmental Molecular Sciences. The contributions of EBSD staff are many as we continue to elevate the impact of PNNL’s science mission: to understand, predict, and control…

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Snoqualmie River in phase 3 flood alert, road closures possible

Snoqualmie River in phase 3 flood alert, road closures possible Heavy rainfall over the last 24 hours has pushed the Snoqualmie River into a phase 3 flood level. Heavy rainfall over the last 24 hours has pushed the Snoqualmie River into a phase 3 flood alert, the King County Department…

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Converting sklearn Classifier to PyTorch

Hi, Due to certain system requirements, our team is looking at converting our use of an SGD classifier from sklearn over to PyTorch. So far, I’ve been able to take the transformed data from a Column Transformer and pass that into PyTorch tensors which seem like I can pass them…

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Broadway Curve project on Interstate 10 enters Phase 3

PHOENIX — Phase three is now underway for the Interstate 10 Broadway Curve Improvement Project after two-and-a-half years since the project began. There are a number of tasks the project will incorporate. Included among them by the Arizona Department of Transportation are: Also included are the widening of bridges and…

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NM_000391.4(TPP1):c.379C>T (p.Arg127Ter) AND Angelman syndrome – ClinVar

NM_000391.4(TPP1):c.379C>T (p.Arg127Ter) AND Angelman syndrome Based on: 1 submission [Details] Record status: current Accession: RCV001804926.2 Allele description [Variation Report for NM_000391.4(TPP1):c.379C>T (p.Arg127Ter)] NM_000391.4(TPP1):c.379C>T (p.Arg127Ter) Gene: TPP1:tripeptidyl peptidase 1 [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 11p15.4 Genomic location: Preferred name: NM_000391.4(TPP1):c.379C>T (p.Arg127Ter) Other names: p.R127*:CGA>TGA…

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FDA Shuts Down Enquiries About DNA Contamination In COVID Vaccines

Authored by Maryanne Demasi via The Brownstone Institute, The recent findings of DNA fragments in the Pfizer and Moderna Covid-19 vaccines has led many to question why the FDA, which is responsible for monitoring the quality and safety of the vaccines, has failed to sound the alarm. For years, the FDA has…

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Needle-free ultrasound vaccine delivery | ScienceDaily

An estimated quarter of adults and two-thirds of children have strong fears around needles, according to the U.S. Centers for Disease Control and Prevention. Yet, public health depends on people being willing to receive vaccines, which are often administered by a jab. Darcy Dunn-Lawless, a doctoral student at the University…

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K-fold Cross Validation with PyTorch | by Francesco Franco | Dec, 2023

Machine learning models must be evaluated with a test set after they have been trained. We do this to ensure that models have not overfit and to ensure that they work with real-life datasets, which may have slightly deviating distributions compared to the training set. But in order to make…

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Kaggle TPU roberta Finetuning – xla

I have pretrained roberta-base on dna promoter sequences of plants (working on a project). I am currently trying to finetune it on a downstream task of predicting gene expression values, basically a list of 8 values (corresponding to various tissues) from a single promoter sequence. This wasn’t possible on kaggle’s…

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