From 36e7964b31787ffeb6064f3a424c2e131eab1cf6 Mon Sep 17 00:00:00 2001 From: mikelove Date: Mon, 12 Nov 2018 13:41:23 -0500 Subject: [PATCH 1/2] first hack at abstract, 251 words --- content/01.abstract.md | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/content/01.abstract.md b/content/01.abstract.md index c6ebbc4..c5a9289 100644 --- a/content/01.abstract.md +++ b/content/01.abstract.md @@ -1,3 +1,33 @@ ## Abstract {.page_break_before} **Instructions**: Describe your collaborative project, highlighting key achievements of the project; limited to 250 words. + + +The HCA provides a reference atlas to human cell types, states, and +the biological processes in which they engage. The utility of the +reference therefore requires that one can easily compare references to +each other, or a new sample to the compendium of reference +samples. Low-dimensional representations, because they compress the +space, provide the building blocks for search approaches that can be +practically applied across very large datasets such as the HCA. +Our seed network proposes to compress HCA data +into fewer dimensions that preserve the important attributes of the +original high dimensional data and yield interpretable, searchable +features. +We hypothesize that building an ensemble of low +dimensional representations across latent space methods will provide a +reduced dimensional space that captures biological sources of +variability and is robust to measurement noise. +We will identify techniques that learn interpretable, +biologically-aligned representations, improve techniques for fast and +accurate quantification, and implement these base enabling +technologies and methods for search, analysis, and latent space +transformations as freely available, open source software tools. +By using and extending our base enabling technologies, we will provide +three principle tools and resources for the HCA. These include 1) +software to enable fast and accurate search and annotation using +low-dimensional representations of cellular features, 2) a versioned +and annotated catalog of latent spaces corresponding to signatures of +cell types, states, and biological attributes across the the HCA, and +3) short course and educational materials that will increase the use +and impact of low-dimensional representations and the HCA in general. From 12cbac962b36c1205e7dccbe1fff9879f4228dec Mon Sep 17 00:00:00 2001 From: mikelove Date: Mon, 12 Nov 2018 13:45:34 -0500 Subject: [PATCH 2/2] 249 word abstract --- content/01.abstract.md | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/content/01.abstract.md b/content/01.abstract.md index c5a9289..8a2b4df 100644 --- a/content/01.abstract.md +++ b/content/01.abstract.md @@ -1,7 +1,7 @@ ## Abstract {.page_break_before} -**Instructions**: Describe your collaborative project, highlighting key achievements of the project; limited to 250 words. - +**Instructions**: Describe your collaborative project, highlighting +key achievements of the project; limited to 250 words. The HCA provides a reference atlas to human cell types, states, and the biological processes in which they engage. The utility of the @@ -24,10 +24,11 @@ accurate quantification, and implement these base enabling technologies and methods for search, analysis, and latent space transformations as freely available, open source software tools. By using and extending our base enabling technologies, we will provide -three principle tools and resources for the HCA. These include 1) -software to enable fast and accurate search and annotation using -low-dimensional representations of cellular features, 2) a versioned -and annotated catalog of latent spaces corresponding to signatures of -cell types, states, and biological attributes across the the HCA, and +three principle tools and resources for the HCA: +1) software to enable fast and accurate search and annotation using +low-dimensional representations of cellular features, +2) a versioned and annotated catalog of latent spaces corresponding to +signatures of cell types, states, and biological attributes across the +the HCA, and 3) short course and educational materials that will increase the use -and impact of low-dimensional representations and the HCA in general. +and impact of low-dimensional representations and the HCA in general.