Exploring dimension-reduced embeddings

Related tags

Text Data & NLPsleepwalk
Overview

Travis Build Status CRAN_Status_Badge Downloads

sleepwalk

Exploring dimension-reduced embeddings

This is the code repository. See here for the Sleepwalk web page.

License and disclaimer

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.

Comments
  • Error running sleepwalk: cannot open the connection

    Error running sleepwalk: cannot open the connection

    Dear sleepwalk developers, Thanks a lot for providing such nice method. I could install the package but I get the following error when I tried to run:

    > sleepwalk([email protected][email protected], [email protected][email protected])
Estimating 'maxdist' for feature matrix 1
Server has been stopped.
Server has been stopped.
Error in app$openPage(useViewer, browser) : 
  Timeout waiting for websocket.
In addition: Warning messages:
1: In file(con, "r") :
  cannot open file 'sleepwalk_canvas.html': No such file or directory
2: In func(req) : File '/favicon.ico' is not found

    I know this is probably not a sleepwalk specific error, but I couldn't find a solution for this. Any hints/help on how to fix this issue?

    Also, I have a question about the output. Besides using the interactive mode to manually inspect cells that might be "misplaced" on the reduced-dimension space, I would like to systematically find the cells that don't quite fit to the clusters they were originally assigned to. In other words, how would you suggest to use sleepwalk to refine my clustering since I suspect that many of my cells were wrongly assigned to their clusters. I am using Seurat package to reduce dimension and clustering.

    Thank you very much, Gustavo

    opened by gufranca 2
  • Error: 'browser' must be a non-empty character string

    Error: 'browser' must be a non-empty character string

    Hello,

    After calling the sleepwalk function on a Seurat object, I got this error:

    > sleepwalk( as.matrix([email protected][email protected]), as.matrix([email protected][email protected]) )

Estimating 'maxdist' for feature matrix 1
Error in browseURL(str_c("http://localhost:", port, "/", pageobj$startPage),  :
  'browser' must be a non-empty character string

    I have loaded the stringr library (containing the function str_c()), and I cannot find the file originating this error. Can I ask if someone had this problem at some point?

    Thank you

    opened by PedroRaposo 2
  • slw_on_selection error when sleepwalk is not attached

    slw_on_selection error when sleepwalk is not attached

    Running sleepwalk without attaching the package (i.e., NOT specifying library(sleepwalk)) like this works fine:

    sleepwalk::sleepwalk(se[email protected][email protected], t([email protected][[email protected],]))

    But the moment you select cells with your mouse, it crashed (browser tab closes) and R gives this error:

    Error in slw_on_selection(selPoints, 1) : could not find function "slw_on_selection"

    Loading the package using library(sleepwalk) solves the issue, but it'd be nice if it weren't necessary.

    opened by FelixTheStudent 0
  • doc for comparison

    doc for comparison

    The example on the web page for comparing two embeddings still uses the old version where both distances are used concurrently. We also need to change the explanation below to say that the same cell always has the same colour in all embeddings

    opened by simon-anders 0
  • Suggestion: Link embeddings from transposed table

    Suggestion: Link embeddings from transposed table

    Let say I have e.g. a matrix where I have individuals (cells e.g.) as rows and features as columns, and then run a UMAP on both the ordinary matrix, and the transposed one. Then it would be natural to want to look at the individual UMAP with the default usage (the distances to other individuals), but it would also be interesting to see the features for that individual (and vice versa).

    Is it clear what I mean?

    opened by StaffanBetner 2
Releases(v0.3.2)

  • v0.3.2(Sep 17, 2021)

    • jrc now (v.0.5.0) uses setLimits function for all the security restriction. This update fixes the dependency problem caused by that change.
    Source code(tar.gz)
    Source code(zip)

  • v0.3.1(Sep 30, 2020)

  • v.0.3.0(Feb 27, 2020)

    • New argument metric allows to use angular distance (metric = "cosine") as an alternative to default Euclidean distance (meric = "euclid").

    • If compare = "distances", it is no longer required to provide several embeddings. If only one embedding is given, it will be used for all the distances.

    Source code(tar.gz)
    Source code(zip)

  • v0.2.1(Oct 2, 2019)

    • Changes due to an update of the jrc package.

    • Indices of selected points are no longer stored in a variable and can be accessed only via the callback function. Thus, no changes to the global environment are made, unless user specifies them his- or herself.

    • Added the possibility to pass arguments to jrc::openPage (such as port number or browser in which to open the app.)

    Source code(tar.gz)
    Source code(zip)

  • v0.2.0(Sep 27, 2019)

    • Now HTML Canvas is used to plot the embedding. It makes Sleepwalk faster and allows to simultaneously display more points.

    • New parameter mode = c("canvas", "svg") is added, that allows user to go back to the old SVG-based version of Sleepwalk app.

    • Bug in slw_snapshot is fixed. The function no longer returns a list of identical plots, when used with several different embeddings.

    Source code(tar.gz)
    Source code(zip)
Owner
S. Anders's research group at ZMBH
S. Anders's research group at ZMBH
GitHub Repository https://anders-biostat.github.io/sleepwalk/
Pretty-doc - Composable text objects with python

pretty-doc from __future__ import annotations from dataclasses import dataclass

Taine Zhao 2 Jan 17, 2022
Phrase-BERT: Improved Phrase Embeddings from BERT with an Application to Corpus Exploration

Phrase-BERT: Improved Phrase Embeddings from BERT with an Application to Corpus Exploration This is the official repository for the EMNLP 2021 long pa

70 Dec 11, 2022
Rhythm-Finder is a unsupervised ML driven python powered web-application that can find the songs that suits you.

ML-powered Music Recommendation Engine

Google Developer Student Clubs - JGEC 23 Oct 09, 2022
RoNER is a Named Entity Recognition model based on a pre-trained BERT transformer model trained on RONECv2

RoNER RoNER is a Named Entity Recognition model based on a pre-trained BERT transformer model trained on RONECv2. It is meant to be an easy to use, hi

Stefan Dumitrescu 9 Nov 07, 2022
A simple word search made in python

Word Search Puzzle A simple word search made in python Usage $ python3 main.py -h usage: main.py [-h] [-c] [-f FILE] Generates a word s

Magoninho 16 Mar 10, 2022
Write Python in Urdu - اردو میں کوڈ لکھیں

UrduPython Write simple Python in Urdu. How to Use Write Urdu code in سامپل۔پے The mappings are as following: "۔": ".", "،":

Saad A. Bazaz 26 Nov 27, 2022
This is the Alpha of Nutte language, she is not complete yet / Essa é a Alpha da Nutte language, não está completa ainda

nutte-language This is the Alpha of Nutte language, it is not complete yet / Essa é a Alpha da Nutte language, não está completa ainda My language was

catdochrome 2 Dec 18, 2021
Higher quality textures for the Metal Gear Solid series.

Metal Gear Solid: HD Textures Higher quality textures for the Metal Gear Solid series. The goal is to maximize the quality of assets that the engine w

Samantha 6 Dec 06, 2022
Unifying Cross-Lingual Semantic Role Labeling with Heterogeneous Linguistic Resources (NAACL-2021).

Unifying Cross-Lingual Semantic Role Labeling with Heterogeneous Linguistic Resources Description This is the repository for the paper Unifying Cross-

Sapienza NLP group 16 Sep 09, 2022
:hot_pepper: R²SQL: "Dynamic Hybrid Relation Network for Cross-Domain Context-Dependent Semantic Parsing." (AAAI 2021)

R²SQL The PyTorch implementation of paper Dynamic Hybrid Relation Network for Cross-Domain Context-Dependent Semantic Parsing. (AAAI 2021) Requirement

huybery 60 Dec 31, 2022
Client library to download and publish models and other files on the huggingface.co hub

huggingface_hub Client library to download and publish models and other files on the huggingface.co hub Do you have an open source ML library? We're l

Hugging Face 644 Jan 01, 2023
Crowd sourced training data for Rasa NLU models

NLU Training Data Crowd-sourced training data for the development and testing of Rasa NLU models. If you're interested in grabbing some data feel free

Rasa 169 Dec 26, 2022
PIZZA - a task-oriented semantic parsing dataset

The PIZZA dataset continues the exploration of task-oriented parsing by introducing a new dataset for parsing pizza and drink orders, whose semantics cannot be captured by flat slots and intents.

17 Dec 14, 2022
Code and data accompanying Natural Language Processing with PyTorch

Natural Language Processing with PyTorch Build Intelligent Language Applications Using Deep Learning By Delip Rao and Brian McMahan Welcome. This is a

Joostware 1.8k Jan 01, 2023
Large-scale Self-supervised Pre-training Across Tasks, Languages, and Modalities

Hiring We are hiring at all levels (including FTE researchers and interns)! If you are interested in working with us on NLP and large-scale pre-traine

Microsoft 7.8k Jan 09, 2023
Code repository of the paper Neural circuit policies enabling auditable autonomy published in Nature Machine Intelligence

Code repository of the paper Neural circuit policies enabling auditable autonomy published in Nature Machine Intelligence

9 Jan 08, 2023
A framework for implementing federated learning

This is partly the reproduction of the paper of [Privacy-Preserving Federated Learning in Fog Computing](DOI: 10.1109/JIOT.2020.2987958. 2020)

DavidChen 46 Sep 23, 2022
KakaoBrain KoGPT (Korean Generative Pre-trained Transformer)

KoGPT KoGPT (Korean Generative Pre-trained Transformer) https://github.com/kakaobrain/kogpt https://huggingface.co/kakaobrain/kogpt Model Descriptions

Kakao Brain 797 Dec 26, 2022
LUKE -- Language Understanding with Knowledge-based Embeddings

LUKE (Language Understanding with Knowledge-based Embeddings) is a new pre-trained contextualized representation of words and entities based on transf

Studio Ousia 587 Dec 30, 2022
code for "AttentiveNAS Improving Neural Architecture Search via Attentive Sampling"

AttentiveNAS: Improving Neural Architecture Search via Attentive Sampling This repository contains PyTorch evaluation code, training code and pretrain

Facebook Research 94 Oct 26, 2022