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February, 2023

Text or image generating AIs

It's all the rage these days. Let's collect the ones we've heard about so far.

Text

Image

I'm well aware there are like a 100 more, will add to this list as I get time.
On a related note, it's too bad Shaarli does not allow others to edit or at least comment on posts (but see this post regarding developments).
But if you really want, I guess you could open the post on its own page (see permalink below) and annotate that page using Hypothes.is.

Links and notes

artificial_intelligence collection_post
Lecture notes on condensed matter physics (PDF)

A work in progress. Over 700 pages, encompassing band structure, symmetry and much more.
By Daniel Arovas, UC Santa Barbara.

lecture_notes physics internetz thesis
Tong's lecture notes on theoretical physics

Lectures on theoretical physics from Cambridge University professor David Tong.

David Tong at Cambridge is a gifted educator and communicator who has written lecture notes that span a wide swath of the physics curriculum, from introductory material on mechanics through advanced graduate-level treatments of quantum field theory. Truly, these are a fantastic resource, made freely available.

Link and quote thanks to Douglas Natelson (nanoscale views).

I particularly like his notes on solid state physics (which contains links to other resources).

physics lecture_notes internetz thesis
Explore the In Our Time archive | Braggoscope

This unofficial site let's you explore the In Our Time archive by topic and year.
Via kottke.org.

radio podcast internetz
A note on working with bib2df and bib2gls

A small wrinkle when using bib2df together with bib2gls: the latter does not tolerate empty cross-reference fields.

bib2df::df2bib() takes a tibble and generates the entries.bib file, and since the tibble by necessity contains one column for each field, any entries with empty see fields get converted by bib2df::df2bib() to see={}. The presence of any glossary entry with an empty see={} field causes bib2gls to fail:

Processing resource thesis-1.glstex.
Parsing fields for entry 'absorption_coefficient'
Checking field aliases for absorption_coefficient.
Value=>user1={}
>> name={{}\ensuremath{\alpha}}
=>> name={{}\ensuremath{\alpha}}
>> first={absorption coefficient, \ensuremath{\alpha}}
=>> first={absorption coefficient, \ensuremath{\alpha}}
>> text={absorption coefficient}
=>> text={absorption coefficient}
>> description={absorption coefficient}
=>> description={absorption coefficient}
>> user1={}
=>> user1={}
>> see={}
=>> see={}
Checking cross-references for: absorption_coefficient
Field alias not set.
Error: EOFException
com.dickimawbooks.texparserlib.TeXParser.popStack(TeXParser.java:2635)
com.dickimawbooks.texparserlib.TeXObjectList.popArg(TeXObjectList.java:1294)
com.dickimawbooks.texparserlib.TeXObjectList.popArg(TeXObjectList.java:1275)
com.dickimawbooks.bib2gls.Bib2GlsEntry.initSeeRef(Bib2GlsEntry.java:4710)
com.dickimawbooks.bib2gls.Bib2GlsEntry.initCrossRefs(Bib2GlsEntry.java:4694)
com.dickimawbooks.bib2gls.GlsResource.processBibList(GlsResource.java:6722)
com.dickimawbooks.bib2gls.Bib2Gls.process(Bib2Gls.java:2706)
com.dickimawbooks.bib2gls.Bib2Gls.main(Bib2Gls.java:6616)

As you can see, other fields may be empty, but not the see field.

This is not a bug in either bib2df:: or bib2gls, and I don't expect either project to "fix" this issue. The former is not meant for and has no notion of glossaries, and the latter is not really expecting us to be generating the .bib file, so why should there be empty see fields?

To work around this I suggest removing all lines with see={} fields from the entries.bib file, here an example using sed:

sed -i '"/[Ss]ee\s*=\s*{}/d" entries.bib

I simply added this sed command to the R chunk that calls bib2df::df2bib().
I should probably add that my reason for generating the glossary bib-file from R in the first place was to make use of the excellent constants library.

Notes and links

This behaviour was observed on Ubuntu 22.04, R 4.1.3, TeXLive 2022, glossaries-extra 1.50, bib2gls 3.2, bib2df 1.1.1.

LaTeX glossary bib2gls
Cross-reference figures or tables from outside the document using cleveref and friends

Could we cross-reference objects (tables, figures, etc.) that exist in the attached papers (whose code-base is foreign to the thesis) while also having these cross-references target the appropriate paper in the List of Papers, with the aid of the cleveref, caption and hyperref packages?

To clarify, for a compilation PhD thesis, where the thesis itself is created using LaTeX, but where the attached papers (hence the compilation part in the thesis) may or may not have been created using LaTeX (even if they were created using LaTeX, their codebase is not available to the thesis at runtime).

So we need to setup some sort of static list of manually created \label{}s, that should occupy a counter and namespace separate from the thesis' own figures, tables, etc.

Preamble, literally

Uppsala university has a thesis template (my version, LuaLaTeX-based) that defines a listofpapers environment (the details of which are not important right now) that allows us to create a List of Papers and easily assign a label for each paper, like this:

\begin{listofpapers}
   \item\label{P1}
   Li, C.; Ahmed, T.; Ma, M.; Edvinsson, T.; Zhu, J. %
   Photocatalytic properties of ZnO/CdS nanoarrays\\%
   \item \label{P2}
   Ahmed, T.; Edvinsson, T. %
   Photocatalytic activity of ultrasmall ZnO\\%
\end{listofpapers}

The above works in conjunction with the following definitions in the preamble:

\usepackage{cleveref}
\crefname{listofpapersc}{\textbf{\textsc{paper}}}{\textbf{\textsc{papers}}}
\Crefname{listofpapersc}{\textbf{\textsc{paper}}}{\textbf{\textsc{papers}}}
\creflabelformat{listofpapersc}{#2\textbf{\textsc{#1}}#3}

to give a nicely formatted Paper 1 (in small-caps in this case) in the text when we issue \cref{P1}.

Solution: new floating environment and a custom cleveref format per paper

I have limited time to type this up, so here goes.

\usepackage{newfloat} % for the DeclareFloatingEnvironment cmd
\usepackage[nameinlink]{cleveref}
\crefname{listofpapersc}{\textbf{\textsc{paper}}}{\textbf{\textsc{papers}}}
\Crefname{listofpapersc}{\textbf{\textsc{paper}}}{\textbf{\textsc{papers}}}
\creflabelformat{listofpapersc}{#2\textbf{\textsc{#1}}#3}

\DeclareFloatingEnvironment[within=none]{tableP1}
\crefformat{tableP1}{\textsc{#2tab.~#1#3}~of\space\cref{P1}}
\Crefformat{tableP1}{\textsc{#2Tab.~#1#3}~of\space\cref{P1}}
\crefrangeformat{tableP1}{\textsc{tabs.~#3#1#4--#5#2#6}~of\space\cref{P1}}
\Crefrangeformat{tableP1}{\textsc{Tabs.~#3#1#4--#5#2#6}~of\space\cref{P1}}
\crefmultiformat{tableP1}{%
   \scshape tabs.~#2#1#3}{%
   \:\&\:#2#1#3~\textnormal{of\space}\cref{P1}}{%
   , #2#1#3}{%
   \:\&\:#2#1#3~\textnormal{of\space}\cref{P1}}
\Crefmultiformat{tableP1}{%
   \scshape Tabs.~#2#1#3}{%
   \:\&\:#2#1#3~\textnormal{of\space}\cref{P1}}{%
   , #2#1#3}{%
   \:\&\:#2#1#3~\textnormal{of\space}\cref{P1}}
\crefrangemultiformat{tableP1}{%
   \scshape tabs.~#3#1#4--#5#2#6}{%
   \:\&\:#3#1#4--#5#2#6~\textnormal{of\space}\cref{P1}}{%
   , #3#1#4--#5#2#6}{%
   \:\&\:#3#1#4--#5#2#6~\textnormal{of\space}\cref{P1}}
\Crefrangemultiformat{tableP1}{%
   \scshape Tabs.~#3#1#4--#5#2#6}{%
   \:\&\:#3#1#4--#5#2#6~\textnormal{of\space}\cref{P1}}{%
   , #3#1#4--#5#2#6}{%
   \:\&\:#3#1#4--#5#2#6~\textnormal{of\space}\cref{P1}}

and repeat the last block (everything down from DeclareFloatingEnvironment) for figureP1, and for tableP2, figureP2, etc.

And then, for the pièce de résistance, in one fell swoop we abuse both the listofpapers environment and the phantomcaption command to create the labels that our cross-references will target:

\begin{listofpapers}
   \item\label{P1}
   Li, C.; Ahmed, T.; Ma, M.; Edvinsson, T.; Zhu, J. %
   Photocatalytic properties of ZnO/CdS nanoarrays\\%
      \bgroup
      \captionsetup{type=figureP2}
      \phantomcaption\label{fig:P1-schematic}
      \phantomcaption\label{fig:P1-mechanism}
      [... more figure labels as necessary ...]
      \egroup
      \bgroup
      \captionsetup{type=tableP2}
      \phantomcaption\label{tab:P1-parameters}
      \phantomcaption\label{tab:P1-rates}
      [... more table labels as necessary ...]
      \egroup
   \item \label{P2}
   Ahmed, T.; Edvinsson, T. %
   Photocatalytic activity of ultrasmall ZnO\\%
\end{listofpapers}

captionsetup needs to be constrained by an environment (the manual suggests a minipage, which works fine but occupies a little bit of vertical space on the page), and it turns out group works in this context and has the added benefit of occupying no space in the List of Papers.

With that, we can simply type \cref{fig:P1-schematic} in the source to produce a nicely formatted cross-reference in the output document. The use of small-caps, abbreviated label names, and the trailing of paper X is my way to make these references contrast with the normal, in-thesis cross-references.

Here's an example of how the typeset cross-references look like:

Links and notes

LaTeX thesis