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/
🤗 Transformers: State-of-the-art Natural Language Processing for Pytorch, TensorFlow, and JAX.

English | 简体中文 | 繁體中文 State-of-the-art Natural Language Processing for Jax, PyTorch and TensorFlow 🤗 Transformers provides thousands of pretrained mo

Hugging Face 77.2k Jan 03, 2023
Codename generator using WordNet parts of speech database

codenames Codename generator using WordNet parts of speech database References: https://possiblywrong.wordpress.com/2021/09/13/code-name-generator/ ht

possiblywrong 27 Oct 30, 2022
Cải thiện Elasticsearch trong bài toán semantic search sử dụng phương pháp Sentence Embeddings

Cải thiện Elasticsearch trong bài toán semantic search sử dụng phương pháp Sentence Embeddings Trong bài viết này mình sẽ sử dụng pretrain model SimCS

Vo Van Phuc 18 Nov 25, 2022
This is the 25 + 1 year anniversary version of the 1995 Rachford-Rice contest

Rachford-Rice Contest This is the 25 + 1 year anniversary version of the 1995 Rachford-Rice contest. Can you solve the Rachford-Rice problem for all t

13 Sep 20, 2022
Ongoing research training transformer language models at scale, including: BERT & GPT-2

What is this fork of Megatron-LM and Megatron-DeepSpeed This is a detached fork of https://github.com/microsoft/Megatron-DeepSpeed, which in itself is

BigScience Workshop 316 Jan 03, 2023
문장단위로 분절된 나무위키 데이터셋. Releases에서 다운로드 받거나, tfds-korean을 통해 다운로드 받으세요.

Namuwiki corpus 문장단위로 미리 분절된 나무위키 코퍼스. 목적이 LM등에서 사용하기 위한 데이터셋이라, 링크/이미지/테이블 등등이 잘려있습니다. 문장 단위 분절은 kss를 활용하였습니다. 라이선스는 나무위키에 명시된 바와 같이 CC BY-NC-SA 2.0

Jeong Ukjae 16 Apr 02, 2022
kochat

Kochat 챗봇 빌더는 성에 안차고, 자신만의 딥러닝 챗봇 애플리케이션을 만드시고 싶으신가요? Kochat을 이용하면 손쉽게 자신만의 딥러닝 챗봇 애플리케이션을 빌드할 수 있습니다. # 1. 데이터셋 객체 생성 dataset = Dataset(ood=True) #

1 Oct 25, 2021
glow-speak is a fast, local, neural text to speech system that uses eSpeak-ng as a text/phoneme front-end.

Glow-Speak glow-speak is a fast, local, neural text to speech system that uses eSpeak-ng as a text/phoneme front-end. Installation git clone https://g

Rhasspy 8 Dec 25, 2022
Code for CodeT5: a new code-aware pre-trained encoder-decoder model.

CodeT5: Identifier-aware Unified Pre-trained Encoder-Decoder Models for Code Understanding and Generation This is the official PyTorch implementation

Salesforce 564 Jan 08, 2023
An implementation of the Pay Attention when Required transformer

Pay Attention when Required (PAR) Transformer-XL An implementation of the Pay Attention when Required transformer from the paper: https://arxiv.org/pd

7 Aug 11, 2022
Trex is a tool to match semantically similar functions based on transfer learning.

Trex is a tool to match semantically similar functions based on transfer learning.

62 Dec 28, 2022
ConvBERT-Prod

ConvBERT 目录 0. 仓库结构 1. 简介 2. 数据集和复现精度 3. 准备数据与环境 3.1 准备环境 3.2 准备数据 3.3 准备模型 4. 开始使用 4.1 模型训练 4.2 模型评估 4.3 模型预测 5. 模型推理部署 5.1 基于Inference的推理 5.2 基于Serv

yujun 7 Apr 08, 2022
Conversational-AI-ChatBot - Intelligent ChatBot built with Microsoft's DialoGPT transformer to make conversations with human users!

Conversational AI ChatBot Intelligent ChatBot built with Microsoft's DialoGPT transformer to make conversations with human users! In this project? Thi

Rajkumar Lakshmanamoorthy 6 Nov 30, 2022
A fast hierarchical dimensionality reduction algorithm.

h-NNE: Hierarchical Nearest Neighbor Embedding A fast hierarchical dimensionality reduction algorithm. h-NNE is a general purpose dimensionality reduc

Marios Koulakis 35 Dec 12, 2022
In this project, we aim to achieve the task of predicting emojis from tweets. We aim to investigate the relationship between words and emojis.

Making Emojis More Predictable by Karan Abrol, Karanjot Singh and Pritish Wadhwa, Natural Language Processing (CSE546) under the guidance of Dr. Shad

Karanjot Singh 2 Jan 17, 2022
edge-SR: Super-Resolution For The Masses

edge-SR: Super Resolution For The Masses Citation Pablo Navarrete Michelini, Yunhua Lu and Xingqun Jiang. "edge-SR: Super-Resolution For The Masses",

Pablo 40 Nov 10, 2022
BERN2: an advanced neural biomedical namedentity recognition and normalization tool

BERN2 We present BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by

DMIS Laboratory - Korea University 99 Jan 06, 2023
This Project is based on NLTK It generates a RANDOM WORD from a predefined list of words, From that random word it read out the word, its meaning with parts of speech , its antonyms, its synonyms

This Project is based on NLTK(Natural Language Toolkit) It generates a RANDOM WORD from a predefined list of words, From that random word it read out the word, its meaning with parts of speech , its

SaiVenkatDhulipudi 2 Nov 17, 2021
An open source framework for seq2seq models in PyTorch.

pytorch-seq2seq Documentation This is a framework for sequence-to-sequence (seq2seq) models implemented in PyTorch. The framework has modularized and

International Business Machines 1.4k Jan 02, 2023
Code Generation using a large neural network called GPT-J

CodeGenX is a Code Generation system powered by Artificial Intelligence! It is delivered to you in the form of a Visual Studio Code Extension and is Free and Open-source!

DeepGenX 389 Dec 31, 2022