Tag Archives: Reading List

Use Paperpile’s Annotation System

Reading scientific papers as PDFs is a major part of being an academic. Professors, postdocs, grad students and undergraduates end up working with PDFs, making notes, and then using those notes to write a manuscript or paper. Although there are lots of great PDF viewers and reference managers, I use Paperpile, which is cloud-based PDF manager and was originally designed to be a reference manager for Google Docs. It can sync all your PDFs with your Google Drive (so you can read them offline) and neatly integrates with Google Scholar and Chrome so that you can import references and PDFs from anywhere. It handles citations in Docs and in Word and has a beta app for iPad that is brilliant.

We use this in my lab all the time. It’s a paid app, but it is not very expensive, they have education pricing and as the lab PI, I just pay for a site license for all my trainees.

Making Notes

One of the best features is the notes-taking and annotation system. Like most PDF viewers, the built in PDF viewers lets you highlight, markup, and annotate PDFs with sticky notes. These annotations stay with the PDF and will sync across devices because it’s cloud based. Just like in Adobe or Apple Preview, you can highlight, add notes, use strike-thru, or even draw with a pencil. Paperpile organizes these well and makes it easy to navigate. And if you use the iPad app you can make notes there that will show up in the browser and notes in the browser will show up on the iPad. The icon on the upper right hides your notes.

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Exporting and Sharing

If you’re reading along, taking notes and making highlights, you may want to share these with someone or use them in a manuscript (or even a manuscript review). There are several ways to do this.

Export the PDF

The File menu lets you print with or without annotations. If you want to send the PDF to someone as a clean PDF without your notes, that’s easy to do. Or it will save your notes in the new PDF.

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The exported PDF opens in other PDF viewers with your notes intact and editable (Apple Preview is shown below). This is great to share with someone who does not use Paperpile. Of course, you can print a clean PDF without the annotations.

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Export the annotations only

If you planning to write an an annotated bibliography, a critical review, a meta analysis, a paper for class or even a manuscript review for a journal, the ability is export the notes is invaluable. Using the same File menu, you will see the “export” option. This lets you export just your notes and highlights in several formats. If you want it to share on line, for examples, try the HTML option. This is great if you are writing a blog and wanted to include screen shots and notes. Notice that this keeps the annotations (notes, images, highlights) on the right and data about who made the notes on the left. Helpful if more than one person are making notes.

Screen Shot 2020-01-18 at 7.10.12 AM And of course, if you’re using this annotation tool to make notes for your own paper or a manuscript review, you can export just your notes as text or markdown and open in Google Docs, Word, or any editor and use those to help frame your draft. You have the contents of the notes as text and can quote highlighted text. Images are not saved, of course.

Conclusion

In my opinion, Paperpile is the best reference manager and PDF manager on the scene. Others, like Zotero, Mendeley, and Endnote are also good (and Zotero is free, of course). Each has things they do really well, but if you already use Paperpile, or are curious about it, I strongly suggest you spend some time with the PDF viewer and annotations. It’s really changed my workflow for the better. It’s just such well designed software.

 

Comments, corrections, and suggestion are always welcome.

August Reading List

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Will I get though all of these in a month?

August is one of two times during the year (the other being the stretch of time between Christmas and the new year) that I try to back away from email, social media, and work reading and try to catch up on reading for pleasure.

Reading for pleasure!  Is there any greater luxury than being able to read a few books on various topics, just because you have the time? I don’t think there is.

August is ideal for this. It begins with a long weekend in Canada (civic day) and often we spend a week at a vacation rental in the Bruce Peninsula at some point in the month, and the reality of Fall term has yet to hit. Our kids’ sports are over. There’s time to relax a bit.

Past August Reads

Over the years, I’ve tackled many things, and found some books and authors that I have greatly enjoyed. So here’s some recommendations from past year. One year, about a decade ago, I grabbed a copy of David Copperfield by Charles Dickens that was at a rental cottage and was immediately taken with how entertaining it was and the strength of the characters. I couldn’t finish it in a week, though, and I did not want to take the book from the cottage, so I bought the book from Amazon when I got back. So glad I finished and that led to me quickly reading Great Expectations, Hard Times, and Bleak House. At some point, I hope to finish the rest of Dickens’s books.

I also got caught up in the excellent police procedurals by Peter Robinson (Inspector Banks series), again because I came across one at a rental home and was hooked. I’ve since worked my way though about 7 of these since then. Very well written crime books.

Other recommendations from summer reads: The Caine Mutiny by Herman Wouk, probably the best fictional depiction of a collapse in leadership I’ve ever read. Bonus: there’s the fanatic movie adaptation, and it turns out that my grandfather was a US Navy seaman on the same kind of ship (destroyer) in the same South Pacific typhoon in WW II that the played a heavy role in the book’s later half, which is a cool personal connection.

I read The Orenda by Joesph Boyden on the shores of Georgian Bay not far from where the action in the novel would have been set (this was before controversy over Boyden’s identity had reached mainstream). Last year I read Winter World by the incredible Bernd Heinrich. He is one of the very best science writers working today and I’ve read a few of his books, this was my favourite of the bunch.

There have been some forgettable books as well, nothing bad, but things that felt like just passing the time (some sea faring adventure books by Clive Cussler, a biography of John Adams, Pinker’s How the Mind Works).

On the Shelf This Month

So what I am reading now?

  1. I’m 1/2 way through the epic fantasy The Name of the Wind by Patrick Rothfuss and it’s just fantastic. I expect to finish this soon and have lined up the following books next.
  2. Astrophysics for People in a Hurry by Neil deGrasse Tyson. I’m not in a hurry, but my daughter got this for me last year and I looked at the first chapter, quite amazed at what an incredibly good writer Tyson is. It’s a quick read, but one that I think I’ll really enjoy.
  3. Other Minds by Peter Godfrey Smith, is a book about the nature of consciousness and an emphasis on cognition and intelligence in cephalopods. Nonhuman intelligence (primates, social insects, birds, cephalopods, machines) is a topic that I expect to occupy more of my time and thinking in the next few years. There have been mixed reviews of this, though, so I’m approaching it with caution. I have no problem quitting a book that starts to fall apart.
  4. Strange Affair by Peter Robinson. This will be the 8th novel I’ve read by Robinson. I’m reading this series in no particular order, I just found this in a used book store last week for 99¢ so could not pass it up.

I’m not sure I’ll get through these this month, but we’ll see. As I said, this is my month for reading for pleasure, not out of compulsion. There’s no better way to read, and I’m looking forward to enjoying the ideas, the words, the characters, and the concepts. If you’re also planning on some reading for the summer or have done some summer reading already, here’s hoping you found a new favourite book or author.

A Curated Reading List

Fact: I do not read enough of the literature any more. I don’t really read anything. I read manuscripts that I am reviewing, but that’s not really sufficient to stay abreast of the field. I assign readings for classes, to grad students, and trainees and we may discuss current trends. This is great for lab, but for me the effect is something like me saying to my lab “read this and tell me what happened”. And I read twitter.

But I always have a list of things I want to read. What better way to work through these papers than to blog about them, right?

So this the first instalment of “Paul’s Curated Reading List”. I’m going to focus on cognitive science approaches to categorization and classification behaviour. That is my primary field, and the one I most want to stay abreast of. In each instalment, I’ll pick a paper that was published in the last few months, a preprint, or a classic. I’ll read it, summarize it, and critique. I’m not looking to go after anyone or promote anyone. I just want to stay up to date. I’ll have a new instalment on a regular basis (once every other week, once a month, etc.). I’m doing this for me.

So without further introduction, here is Reading List Item #1…

Smith, J. D., Jamani, S., Boomer, J., & Church, B. A. (2018). One-back reinforcement dissociates implicit-procedural and explicit-declarative category learning. Memory & Cognition,46(2), 261–273.

Background

This paper was published on line last fall but was just published officially in Feb of 2018. I came across it this morning and I was looking at the “Table of Contents” email from Memory & Cognition. Full disclosure, the first author was my grad advisor from 1995-2000, though we have’t collaborated since then (save for a chapter). He’s now at Georgia State and has done a lot of fascinating work on metacognition in non-human primates.

The article describes a single study on classification/category learning. The authors are working within a multiple systems approach of category learning. According to this framework, a verbally-mediated, explicit system learns categories by trying to abstract use a rule, and a procedurally-mediated, implicit system learns categories by Stimulus Response (S-R) association. Both systems have well-specified neural underpinnings. These two systems work together but sometimes they are in competition. I know this theory well and have published quite of few papers on the topic. So of course, I wanted to read this one.

A common paradigm in this field is to introduce a manipulation that is predicted to impair or enhance one of the systems and leave the other unharmed in order to create a behavioural dissociation. The interference in this paper was a 1-back feedback manipulation. In one condition, participants received feedback right after their decision and in another, they received feedback about their decision on the previous trial. Smith et al. reasoned that the feedback delay would disrupt the S-R learning mechanism of the procedural/implicit system, because it would interfere with the temporal congruity stimulus and response. It should have less of an effect on the explicit system, since learners can use working memory to verbalize the rule they used and the response they made.

Methods

In the experiment, Smith et al. taught people to classify a large set (480) of visual stimuli that varied along two perceptual dimensions into two categories. You get 480 trials, and on each trial you see shape, make a decision, get feedback, and see another shape, and so on. The stimuli themselves are rectangles that vary in terms of size (dimension 1) and pixel density (dimension two). The figure below shows examples of range. There was no fixed set of exemplars, but “each participant received his or her own sample of randomly selected category exemplars appropriate to the assigned task”.

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They used a 2 by 2 design with two between-subject factors. The first factor was category set. Participants learned either a rule based category (RB) in which a single dimension (size or density) creates an easily-verbalized rule, or an information integration category (II) in which both dimensions need to be integrated at a pre decisional stage. This II category can’t be learned very easily by a verbal rule and many studies have suggested it’s being learned by the procedural system. The figure below shows how many hundreds of individual exemplars would be divided into two categories for each of the each of the category sets (RB and II).

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The second factor was feedback. After each decision, you either received feedback right after you made a decisions (0Back) or you received feedback one trial later (1Back). This creates a heavier task demand, so it should make it harder to learn the RB categories at first because the task creates a heavier working memory load. But it should interfere with II learning by the procedural system because the 1-Back disturbs the S-R association.

Results

So what did they find? The learning data are plotted below and suggest that the 1Back feedback made it harder to learn the RB categories at first, and seemed to hurt the II categories at the end. The 3-way ANOVA (Category X Feedback X Block) provided evidence to that effect, but it’s not an overwhelming effect. Smith et al.’s decision to focus a follow up analysis on the final block was not very convincing. Essentially, they compared means and 95% CIs for the final block for each of the four cells and found that performance in the two RB conditions did not differ, but performance in the two II conditions did. Does that mean that the feedback was disrupting the feedback? I’m not sure. Maybe participants in that condition (II-1Back) were just getting weary of a very demanding task. A visual inspection of the data seems to support that alternative conclusion as well.  Exploring the linear trends might have been a stronger approach.

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The second analysis was a bit more convincing. They fit each subject’s data with a rule model and an II model. Each model tried to account for each subject’s final 100 trials. This is pretty easy to do and you are just looking to see which model provides the most likely account of the data. You can then plot the best fitting model. For subjects who learned the RB category, the optimal rule should be the vertical partition and for the II category, the optimal model is the diagonal partition.

As seen the figure below, the feedback did not change the strategy very much for subjects who learned the RB categories. Panel (a) and (b) show that the best-fitting model was usually a rule based one (the vertical partition). The story is different for subjects learning II categories. First, there is way more variation in best fitting model. Second, very few subjects in the 1-back condition (d) show evidence of the using the optimal rule (the diagonal partition).

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Conclusions

Smith et al concluded: “We predicted that 1-Back reinforcement would disable associative, reinforcement-driven learning and the II category-learning processes that depend on it. This disabling seems to have been complete” But that’s a strong conclusion. Too strong. Based on the modelling, the more measured conclusion seems to be that about 7-8 of the 30 subjects in the II-0Back condition learned the optimal rule (the diagonal) compared to about 1 subject in the II-1Back. Maybe a just handful of keener’s ended up in the II-0Back and learned the complex structure? It’s not easy to say. There is some evidence in favour of Smith et al’s conclusion but its not at all clear.

I still enjoyed reading the paper. The task design is clever, and the predictions flow logically from the theory (which is very important).It’s incremental work. It adds to the literature on the multiple systems theory but does not (in my opinion) rule out a single-system approach. But I wish they had done a second study as an internal replication to explore the stability of the result. Or maybe a second study with the same category structure but different stimuli. It’s incremental work. It adds to the literature on the multiple systems theory but does not (in my opinion) rule out a single-system approach.

Tune in a few weeks for the next instalment. Follow my blog if you like and check the tag to see the full list. As the list grows, I may create a better structure for these, too.