path: root/2021/captions/research.md

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# Transcript

[[!template new="1" text="Hello, everyone. My name is Ahmed" start="00:00:00.480" video="mainVideo" id=subtitle]]
[[!template text="and I am very happy to be here." start="00:00:02.639" video="mainVideo" id=subtitle]]
[[!template text="Today I'll talk about" start="00:00:05.279" video="mainVideo" id=subtitle]]
[[!template text="my academic workflow inside Emacs." start="00:00:07.359" video="mainVideo" id=subtitle]]
[[!template text="So the main needs that I have" start="00:00:12.160" video="mainVideo" id=subtitle]]
[[!template text="is to keep up with the current research" start="00:00:14.880" video="mainVideo" id=subtitle]]
[[!template text="in my field, and to be able" start="00:00:16.880" video="mainVideo" id=subtitle]]
[[!template text="to take notes, and write," start="00:00:19.760" video="mainVideo" id=subtitle]]
[[!template text="and use these notes later" start="00:00:23.920" video="mainVideo" id=subtitle]]
[[!template text="in writing my papers inside Emacs." start="00:00:25.359" video="mainVideo" id=subtitle]]
[[!template text="Emacs is a great program for this" start="00:00:29.439" video="mainVideo" id=subtitle]]
[[!template text="because it is very extendable" start="00:00:31.119" video="mainVideo" id=subtitle]]
[[!template text="and we can basically write" start="00:00:32.880" video="mainVideo" id=subtitle]]
[[!template text="whatever we are missing." start="00:00:36.960" video="mainVideo" id=subtitle]]
[[!template text="It replaced my earlier" start="00:00:39.440" video="mainVideo" id=subtitle]]
[[!template text="proprietary workflow" start="00:00:41.360" video="mainVideo" id=subtitle]]
[[!template text="that involved using Mendeley" start="00:00:42.559" video="mainVideo" id=subtitle]]
[[!template text="and Visual Studio Code" start="00:00:44.320" video="mainVideo" id=subtitle]]
[[!template text="and many other tools" start="00:00:46.320" video="mainVideo" id=subtitle]]
[[!template text="in order to do the things" start="00:00:47.760" video="mainVideo" id=subtitle]]
[[!template text="that I'll show today." start="00:00:49.760" video="mainVideo" id=subtitle]]
[[!template new="1" text="So the first concern that I have" start="00:00:51.760" video="mainVideo" id=subtitle]]
[[!template text="is to keep up with new papers." start="00:00:54.480" video="mainVideo" id=subtitle]]
[[!template text="To do that, I use this package called elfeed." start="00:00:57.280" video="mainVideo" id=subtitle]]
[[!template text="Elfeed is basically just an RSS reader," start="00:01:02.399" video="mainVideo" id=subtitle]]
[[!template text="and here I fetch all the papers that I need" start="00:01:05.760" video="mainVideo" id=subtitle]]
[[!template text="from arXiv, which is the main source" start="00:01:09.600" video="mainVideo" id=subtitle]]
[[!template text="of papers in my field" start="00:01:12.159" video="mainVideo" id=subtitle]]
[[!template text="and many other scientific fields." start="00:01:14.080" video="mainVideo" id=subtitle]]
[[!template text="It allows me to view these papers" start="00:01:16.720" video="mainVideo" id=subtitle]]
[[!template text="with the abstracts and so on." start="00:01:22.640" video="mainVideo" id=subtitle]]
[[!template text="In order to simplify viewing" start="00:01:27.680" video="mainVideo" id=subtitle]]
[[!template text="and searching for relevant papers," start="00:01:32.159" video="mainVideo" id=subtitle]]
[[!template text="I used this other package called" start="00:01:34.799" video="mainVideo" id=subtitle]]
[[!template text="elfeed-score, and elfeed-score enables me" start="00:01:36.400" video="mainVideo" id=subtitle]]
[[!template text="to assign a numerical score like this" start="00:01:41.600" video="mainVideo" id=subtitle]]
[[!template text="to each of the archive entries." start="00:01:44.560" video="mainVideo" id=subtitle]]
[[!template text="This numerical score is very simple." start="00:01:47.600" video="mainVideo" id=subtitle]]
[[!template text="It's just based on matching things." start="00:01:49.200" video="mainVideo" id=subtitle]]
[[!template text="So, for example, we can ask elfeed" start="00:01:52.560" video="mainVideo" id=subtitle]]
[[!template text="to explain this. So if we say = x," start="00:01:59.200" video="mainVideo" id=subtitle]]
[[!template text="then this just says that" start="00:02:05.040" video="mainVideo" id=subtitle]]
[[!template text="this matches three rules" start="00:02:08.720" video="mainVideo" id=subtitle]]
[[!template text="for a score of 76. This paper." start="00:02:10.000" video="mainVideo" id=subtitle]]
[[!template text="This is simply because I am searching" start="00:02:12.720" video="mainVideo" id=subtitle]]
[[!template text="for these keywords" start="00:02:14.959" video="mainVideo" id=subtitle]]
[[!template text="that are very interesting to me," start="00:02:16.800" video="mainVideo" id=subtitle]]
[[!template text="such as neural networks" start="00:02:19.040" video="mainVideo" id=subtitle]]
[[!template text="or federated learning." start="00:02:20.879" video="mainVideo" id=subtitle]]
[[!template text="And now, if I see a paper here" start="00:02:22.879" video="mainVideo" id=subtitle]]
[[!template text="that I am interested in..." start="00:02:28.959" video="mainVideo" id=subtitle]]
[[!template new="1" text="Let's say I'm interested in this paper" start="00:02:30.239" video="mainVideo" id=subtitle]]
[[!template text="about Gaussian Process Inference," start="00:02:32.720" video="mainVideo" id=subtitle]]
[[!template text="then I want to store it" start="00:02:35.040" video="mainVideo" id=subtitle]]
[[!template text="in my local library. So I want the PDF" start="00:02:36.640" video="mainVideo" id=subtitle]]
[[!template text="and I want to be able to cite it" start="00:02:40.160" video="mainVideo" id=subtitle]]
[[!template text="in the future. To do that," start="00:02:41.920" video="mainVideo" id=subtitle]]
[[!template text="I use a package called org-ref" start="00:02:44.000" video="mainVideo" id=subtitle]]
[[!template text="that allows me to fetch papers from arXiv." start="00:02:46.080" video="mainVideo" id=subtitle]]
[[!template text="So here I wrote a helper function," start="00:02:54.640" video="mainVideo" id=subtitle]]
[[!template text="this elfeed-entry-to-arxiv" start="00:02:56.720" video="mainVideo" id=subtitle]]
[[!template text="that automatically gets this paper." start="00:02:59.200" video="mainVideo" id=subtitle]]
[[!template text="It asks me where to put it," start="00:03:02.480" video="mainVideo" id=subtitle]]
[[!template text="it completes with my default libraries," start="00:03:03.840" video="mainVideo" id=subtitle]]
[[!template text="and then it fetches the paper from arXiv" start="00:03:07.840" video="mainVideo" id=subtitle]]
[[!template text="and places it in this folder," start="00:03:13.360" video="mainVideo" id=subtitle]]
[[!template text="and also places it in my bibliography file" start="00:03:16.159" video="mainVideo" id=subtitle]]
[[!template text="which is written in BibLaTex." start="00:03:20.000" video="mainVideo" id=subtitle]]
[[!template text="So here, if we search for this paper now," start="00:03:23.280" video="mainVideo" id=subtitle]]
[[!template text="we find that it is in our library." start="00:03:30.239" video="mainVideo" id=subtitle]]
[[!template text="This library interface" start="00:03:35.200" video="mainVideo" id=subtitle]]
[[!template text="is from a package called citar," start="00:03:38.000" video="mainVideo" id=subtitle]]
[[!template text="and I have customized it quite a bit" start="00:03:41.280" video="mainVideo" id=subtitle]]
[[!template text="to display all of the papers in my library" start="00:03:44.000" video="mainVideo" id=subtitle]]
[[!template text="in this format." start="00:03:48.879" video="mainVideo" id=subtitle]]
[[!template new="1" text="This just reads from a BibLaTeX file." start="00:03:50.560" video="mainVideo" id=subtitle]]
[[!template text="So if we open it like this," start="00:03:55.439" video="mainVideo" id=subtitle]]
[[!template text="you'll see that this is the" start="00:03:59.519" video="mainVideo" id=subtitle]]
[[!template text="the entry that it placed." start="00:04:02.879" video="mainVideo" id=subtitle]]
[[!template text="One of the interesting things here is that" start="00:04:06.640" video="mainVideo" id=subtitle]]
[[!template text="org-ref actually doesn't really fetch" start="00:04:10.959" video="mainVideo" id=subtitle]]
[[!template text="all of the entries in this format." start="00:04:13.519" video="mainVideo" id=subtitle]]
[[!template text="Moreover, I want all the entries in my file" start="00:04:16.079" video="mainVideo" id=subtitle]]
[[!template text="to look quite similar," start="00:04:18.639" video="mainVideo" id=subtitle]]
[[!template text="and to have this very similar look," start="00:04:20.160" video="mainVideo" id=subtitle]]
[[!template text="and the way I accomplish that is by" start="00:04:23.520" video="mainVideo" id=subtitle]]
[[!template text="using several tools and chaining them." start="00:04:25.440" video="mainVideo" id=subtitle]]
[[!template text="So in order to see this..." start="00:04:28.960" video="mainVideo" id=subtitle]]
[[!template text="So here, this is the function" start="00:04:37.280" video="mainVideo" id=subtitle]]
[[!template text="that I used to..." start="00:04:39.600" video="mainVideo" id=subtitle]]
[[!template text="This is basically run as a hook after each time" start="00:04:41.680" video="mainVideo" id=subtitle]]
[[!template text="Emacs modifies the bibliography file," start="00:04:46.720" video="mainVideo" id=subtitle]]
[[!template text="and it runs rebiber" start="00:04:49.680" video="mainVideo" id=subtitle]]
[[!template text="which gets the conference versions" start="00:04:52.320" video="mainVideo" id=subtitle]]
[[!template text="of papers that I fetch from arXiv," start="00:04:56.479" video="mainVideo" id=subtitle]]
[[!template text="because arXiv is a pre-print directory," start="00:04:58.320" video="mainVideo" id=subtitle]]
[[!template text="and then biber normalizes the arXiv file" start="00:05:00.800" video="mainVideo" id=subtitle]]
[[!template text="to have a consistent look," start="00:05:05.360" video="mainVideo" id=subtitle]]
[[!template text="and then I apply just some substitutions" start="00:05:07.919" video="mainVideo" id=subtitle]]
[[!template text="which I like more." start="00:05:10.320" video="mainVideo" id=subtitle]]
[[!template text="Finally, I have the whole thing" start="00:05:12.960" video="mainVideo" id=subtitle]]
[[!template text="under version control." start="00:05:14.560" video="mainVideo" id=subtitle]]
[[!template text="This function, reformat-bib-library," start="00:05:16.639" video="mainVideo" id=subtitle]]
[[!template text="I make it into a hook" start="00:05:20.000" video="mainVideo" id=subtitle]]
[[!template text="and I run it every time after I save." start="00:05:21.840" video="mainVideo" id=subtitle]]
[[!template text="It just checks if the current buffer" start="00:05:24.720" video="mainVideo" id=subtitle]]
[[!template text="is the main bib library." start="00:05:27.039" video="mainVideo" id=subtitle]]
[[!template text="We will just reformat the library." start="00:05:29.039" video="mainVideo" id=subtitle]]
[[!template text="This allows me to keep the library" start="00:05:31.840" video="mainVideo" id=subtitle]]
[[!template text="looking all consistent like this." start="00:05:33.680" video="mainVideo" id=subtitle]]
[[!template text="By the way, all of the code is available." start="00:05:37.199" video="mainVideo" id=subtitle]]
[[!template text="You don't have to get it from the video." start="00:05:39.120" video="mainVideo" id=subtitle]]
[[!template text="I will attach it as a GitHub gist." start="00:05:40.880" video="mainVideo" id=subtitle]]
[[!template new="1" text="One of the things" start="00:05:48.720" video="mainVideo" id=subtitle]]
[[!template text="that are really important" start="00:05:49.919" video="mainVideo" id=subtitle]]
[[!template text="is that I want to be able to keep notes" start="00:05:51.520" video="mainVideo" id=subtitle]]
[[!template text="on papers that I read." start="00:05:54.080" video="mainVideo" id=subtitle]]
[[!template text="For example, here are some of" start="00:05:56.160" video="mainVideo" id=subtitle]]
[[!template text="my existing notes." start="00:05:58.479" video="mainVideo" id=subtitle]]
[[!template text="Now, let's add a note to the paper" start="00:06:00.319" video="mainVideo" id=subtitle]]
[[!template text="that we just got." start="00:06:04.720" video="mainVideo" id=subtitle]]
[[!template text="So the the pipeline here is that" start="00:06:06.080" video="mainVideo" id=subtitle]]
[[!template text="I use citar with embark," start="00:06:08.800" video="mainVideo" id=subtitle]]
[[!template text="which is another library," start="00:06:12.080" video="mainVideo" id=subtitle]]
[[!template text="but you can use any other library" start="00:06:13.199" video="mainVideo" id=subtitle]]
[[!template text="just for completion" start="00:06:15.600" video="mainVideo" id=subtitle]]
[[!template text="and acting upon completion, like ivy," start="00:06:17.039" video="mainVideo" id=subtitle]]
[[!template text="and I ask it to open notes" start="00:06:19.600" video="mainVideo" id=subtitle]]
[[!template text="and then it asks me how to capture it." start="00:06:21.360" video="mainVideo" id=subtitle]]
[[!template text="So these capture templates" start="00:06:23.680" video="mainVideo" id=subtitle]]
[[!template text="are handled by the org-roam package," start="00:06:25.120" video="mainVideo" id=subtitle]]
[[!template text="which is a very, very interesting package" start="00:06:27.440" video="mainVideo" id=subtitle]]
[[!template text="for note-taking." start="00:06:30.400" video="mainVideo" id=subtitle]]
[[!template text="org-roam, among other things, allows us" start="00:06:32.560" video="mainVideo" id=subtitle]]
[[!template text="to write linkable notes in Org mode," start="00:06:36.160" video="mainVideo" id=subtitle]]
[[!template text="and moreover, it is very extensible." start="00:06:38.800" video="mainVideo" id=subtitle]]
[[!template text="There is another package called org-roam-bibtex" start="00:06:42.400" video="mainVideo" id=subtitle]]
[[!template text="that allows us to attach these nodes" start="00:06:45.600" video="mainVideo" id=subtitle]]
[[!template text="to bibliography files," start="00:06:47.840" video="mainVideo" id=subtitle]]
[[!template text="which is what I'm doing right now." start="00:06:50.000" video="mainVideo" id=subtitle]]
[[!template text="For example, I set up the capture template" start="00:06:51.919" video="mainVideo" id=subtitle]]
[[!template text="such that when I press s" start="00:06:54.800" video="mainVideo" id=subtitle]]
[[!template text="for short bibliography reference," start="00:06:57.680" video="mainVideo" id=subtitle]]
[[!template text="it will make a new headline" start="00:07:01.440" video="mainVideo" id=subtitle]]
[[!template text="in my &quot;Reference Notes&quot; note," start="00:07:04.800" video="mainVideo" id=subtitle]]
[[!template text="and I can write things here" start="00:07:08.479" video="mainVideo" id=subtitle]]
[[!template text="(so, for example, &quot;seems interesting&quot;)" start="00:07:10.479" video="mainVideo" id=subtitle]]
[[!template text="and then note here that it added this paper" start="00:07:14.960" video="mainVideo" id=subtitle]]
[[!template text="to ROAM_REFS, so this means that" start="00:07:18.000" video="mainVideo" id=subtitle]]
[[!template text="when I look at these papers using citar," start="00:07:24.319" video="mainVideo" id=subtitle]]
[[!template text="it will be able to find this note." start="00:07:26.720" video="mainVideo" id=subtitle]]
[[!template text="Similarly, we can also add long-form notes." start="00:07:30.319" video="mainVideo" id=subtitle]]
[[!template text="For example, if I do this and I add r," start="00:07:34.000" video="mainVideo" id=subtitle]]
[[!template text="it will create an entirely new file" start="00:07:37.199" video="mainVideo" id=subtitle]]
[[!template text="that I can take detailed notes in." start="00:07:39.840" video="mainVideo" id=subtitle]]
[[!template text="The strengths of org-roam is that" start="00:07:48.000" video="mainVideo" id=subtitle]]
[[!template text="I can do things like linking papers." start="00:07:50.639" video="mainVideo" id=subtitle]]
[[!template text="For example, here are several books" start="00:07:53.520" video="mainVideo" id=subtitle]]
[[!template text="that I am reading. This file just collects" start="00:07:55.360" video="mainVideo" id=subtitle]]
[[!template text="these books so that I can find them" start="00:08:00.000" video="mainVideo" id=subtitle]]
[[!template text="for easy reference." start="00:08:02.319" video="mainVideo" id=subtitle]]
[[!template text="Of course, I can link these files from inside." start="00:08:03.919" video="mainVideo" id=subtitle]]
[[!template text="You can see here that I also use org-cite" start="00:08:07.599" video="mainVideo" id=subtitle]]
[[!template text="to cite other files, and I can act upon this" start="00:08:13.759" video="mainVideo" id=subtitle]]
[[!template text="and open the notes corresponding to" start="00:08:18.720" video="mainVideo" id=subtitle]]
[[!template text="this other book." start="00:08:21.199" video="mainVideo" id=subtitle]]
[[!template text="So I'm a little short on time." start="00:08:28.240" video="mainVideo" id=subtitle]]
[[!template text="I cannot go into detail on everything," start="00:08:30.319" video="mainVideo" id=subtitle]]
[[!template text="but I will share my configuration," start="00:08:32.719" video="mainVideo" id=subtitle]]
[[!template text="and I hope that this will inspire other people" start="00:08:34.560" video="mainVideo" id=subtitle]]
[[!template text="to also use Emacs for their academic workflows." start="00:08:37.919" video="mainVideo" id=subtitle]]
[[!template text="Thank you so much." start="00:08:43.919" video="mainVideo" id=subtitle]]
[[!template text="captions by sachac" start="00:08:44.919" video="mainVideo" id=subtitle]]