Rogue Scholar Digest May 16, 2024


This is a summary of the Rogue Scholar blog posts published May 8 - May 15, 2024.


Martin Fenner

Front Matter


May 16, 2024

import requests
import locale
import re
from typing import Optional
import datetime
from IPython.display import Markdown

locale.setlocale(locale.LC_ALL, "en_US")
baseUrl = ""
published_since = "2024-05-08"
published_until = "2024-05-16"
feature_image = 1
include_fields = "title,authors,published_at,summary,blog_name,blog_slug,doi,url,image"
url = (
    + f"posts?&published_since={published_since}&published_until={published_until}&language=en&sort=published_at&order=asc&per_page=50&include_fields={include_fields}"
response = requests.get(url)
result = response.json()

def get_post(post):
    return post["document"]

def format_post(post):
    doi = post.get("doi", None)
    url = f"[{doi}]({doi})\n<br />" if doi else ""
    title = f"[{post['title']}]({doi})" if doi else f"[{post['title']}]({post['url']})"
    published_at = datetime.datetime.utcfromtimestamp(post["published_at"]).strftime(
        "%B %-d, %Y"
    blog = f"[{post['blog_name']}]({post['blog_slug']})"
    author = ", ".join([f"{x['name']}" for x in post.get("authors", None) or []])
    summary = post["summary"]
    return f"### {title}\n{url}Published {published_at} in {blog}<br />{author}<br />{summary}\n"

posts = [get_post(x) for i, x in enumerate(result["hits"])]
posts_as_string = "\n\n".join([format_post(x) for x in posts])

def doi_from_url(url: str) -> Optional[str]:
    """Return a DOI from a URL"""
    match =
    if match is None:
        return None

images = [x["image"] for x in posts if x.get("image", None) is not None]
image = images[feature_image]
markdown = f"![]({image})\n\n"
markdown += posts_as_string

Calculating the proportion of US state borders that are coastlines
Published May 8, 2024 in Andrew Heiss’s blog
Andrew Heiss
A few days ago, my wife, a bunch of my kids, and I were huddled around a big wall map of the United States, joking about the relative unimportance of Rhode Island, the smallest state in the US. It’s one of the states I never ever think about: …and it’s just so small . Amid the joking, my wife came to Rhode Island’s defense by declaring that even though it’s so small, it has one of the highest proportions of coastline to land borders.

Voter Turnout Among General Surgery Residents in the 2022 U.S. Midterm Election
Published May 8, 2024 in I.D.E.A.S.
Tejas S. Sathe
As residents within the healthcare profession, our first duty is to care for our patients. While working upwards of 80 hours per week pursuing that mission, it is hard to think of ourselves as anything beyond our job title. But we are also citizens. And while patient care remains a worthy North Star, decisions made by faraway policymakers can impact our patients as much as the assessments and plans we ourselves craft.

Generative Linker Design
Published May 10, 2024 in Corin Wagen
Corin Wagen
Much molecular design today can be boiled down to “put the right functional groups in exactly the right places.” In catalysis, proper positioning of functional groups to complement developing charge or engage in other stabilizing non-covalent interactions with the transition state can lead to vast rate accelerations.

Why EXACTLY is Google Scholar bad for evidence synthesis, systematic reviews?
Published May 12, 2024 in Aaron Tay’s Musings about librarianship
Aaron Tay
Let’s be clear here, Google Scholar is ill designed for use for systematic reviews . I am not trying to argue otherwise. (Obligatory warning, I am not a real systematic review librarian) But why exactly?

How to use Large Language Models to tag your data: A complete tutorial
Published May 13, 2024 in Stories by Research Graph on Medium
Xuzeng He
Using Mistral for Data tagging Author · Xuzeng He ( ORCID: 0009–0005–7317–7426) Introduction Data tagging, in simple terms, is the process of assigning labels or tags to your data so that they are easier to retrieve or analyse.

Automated Knowledge Graph Construction with Large Language Models — Part 2
Published May 13, 2024 in Stories by Research Graph on Medium
Amanda Kau
Automated Knowledge Graph Construction with Large Language Models — Part 2 Harvesting the Power and Knowledge of Large Language Models Author Amanda Kau ( ORCID : 0009–0004–4949–9284 ) Introduction Knowledge graphs (KGs) are a structured representation of data in a graphical format, in which entities are represented by nodes and are connected by edges representing relationships

Do bifurcated ribs imply single-segment neck muscles? Sometimes
Published May 13, 2024 in Sauropod Vertebra Picture of the Week
Mike Taylor
Here at SV-POW!, we love bifurcated cervical ribs. Those of Turiasaurus are one of the autapomorphies proposed by Royo-Torres et al. (2006:figure 1K). Their diagnosis of the new genus included “accessory process projecting caudodorsally from the dorsal margin of the shafts of proximal cervical ribs”. Here is the best example of such a rib in Turiasaurus , attached to its vertebra.

Finding Equilibrium in a Hyperconnected World: The Struggle Against Burnout
Published May 13, 2024 in Everything is Connected
Ernesto Priego
I ’ve lost count of how often I start my blog posts by admitting I haven’t blogged in a while. Long-form blogging seems to be on its way out, but it still holds a unique place in social media—it’s a constant source of guilt, never feeling frequent, good, seen, or shared enough. Now that’s out of the way, I want to briefly share some thoughts I’ve been mulling over recently.

Regime shift still cometh?
Published May 13, 2024 in Jabberwocky Ecology
Morgan Ernest
Back when I had optimistic views of my time, I vowed to do more blogging this year. Sadly, life had other plans. But I return with an update to an earlier post on the Portal rodent community. To recap, in April 2023, my student Pat Dumandan and I were afraid. Afraid that Chaetodipus penicillatus (the Desert pocket mouse) was about to undergo a population explosion.

Going for DOI registration
Published May 13, 2024 in Front Matter
Martin Fenner
Starting this week, all DOIs for the Rogue Scholar blog posts are registered and updated using the new commonmeta Go library, replacing the commonmeta Python library. Authors and readers of blogs archived by Rogue Scholar shouldn’t notice a difference, but going forward this change will make it easier to manage the DOIs (close to 16K DOIs for currently 93 blogs) registered for Rogue Scholar blog posts.

There’s no such thing as sustainable research software
Published May 13, 2024 in Daniel S. Katz’s blog
Daniel S. Katz
(with contributions from Michelle Barker, Neil Chue Hong, Matthew Turk, Jeffrey Carver, Hannah Cohoon, and James Howison) Ok, this title is a bit of a teaser, but what I really mean is that while we can say that research software has been sustained, we can’t predict with certainty that it will be sustained in the future, or even fully know what factors we should use to make an uncertain prediction.

Ride That Ridm: A New Session on Mixcloud, or, A Note On Vinyl-only Sets as Erfahrung
Published May 14, 2024 in Everything is Connected
Ernesto Priego
I ’ve written here before about what it means to me to spend some time playing records and recording them the sessions to share later (also here). Taking the time to select, play, listen to and later rearrange and make recordings of my playing/listening sessions is for me akin to meditating, attentively watching a good film, reading a good book for pleasure or doing research.

Prompt engineering: A Way to Smartly Use AI
Published May 14, 2024 in Stories by Research Graph on Medium
Dhruv Gupta
Author Dhruv Gupta ( ORCID : 0009–0004–7109–5403) Introduction Large Language Models (LLMs) have become the new face of Natural language processing (NLP). With their generative power and ability to comprehend human language, the human reliance on these models is increasing every day. However, the LLMs have been known to hallucinate and thus produce wrong outputs.

The Good, The Bad, and Hamiltonian Monte Carlo
Published May 15, 2024 in Bayesically Speaking
Matías Castillo-Aguilar
Introduction Hey there, fellow science enthusiasts and stats geeks! Welcome back to the wild world of Markov Chain Monte Carlo (MCMC) algorithms. This is part two of my series on the powerhouse behind Bayesian Inference . If you missed the first post, no worries! Just hop on over here and catch up before we dive deeper into the MCMC madness.

New Postgraduate Taught Degree: Data, Policy and Society MSc
Published May 15, 2024 in Everything is Connected
Ernesto Priego
I am very pleased to announce the launch of our new master’s degree on Data, Policy and Society at City, University of London! I am honoured to be a co-director of this programme along the marvelous Elinor Carmi in this exciting collaboration between the Department of Sociology &

Imagined Future: Data democracy at Pint of Science 2074
Published May 15, 2024 in Bastian Greshake Tzovaras
Bastian Greshake Tzovaras
Enoch’s Hammer of Luddite fame, at the Tolson Memorial Museum. I gave a talk at the Pint of Science Festival – an international science festival that takes places at local pubs and cafes across the world – this evening.

Aurora Over Ohio
Published May 15, 2024 in Triton Station
Stacy McGaugh
And pretty much everywhere else First, a pretty picture: The sun is nearing the peak of its eleven year sunspot cycle. That means lots of sunspots and associated activity. Solar prominences, visible to the naked eye during the eclipse, are bands of plasma entrained in the magnetic field connecting pairs of sunspots. Once in a while, these break out in solar flares.

JOSSCast #10: Defect Structure Searching – Irea Mosquera-Lois and Seán Kavanagh on ShakeNBreak
Published May 16, 2024 in Journal of Open Source Software Blog |
Arfon M. Smith
Subscribe Now: Apple, Spotify, YouTube, RSS Irea Mosquera-Lois and Seán Kavanagh join Arfon and Abby to discuss releasing software based on important research observations, earning a PhD, and building ShakeNBreak, a defect structure searching method that better identifies low-energy structures. Irea is a PhD Student at Imperial College London. Seán is an Environmental Fellow at Harvard University.

The integration of large language models (LLMs) with Neo4j-based knowledge graphs
Published May 16, 2024 in Stories by Research Graph on Medium
Wenyi Pi
Enhancing Data Interactivity with LLMs and Neo4j Knowledge Graphs Author Wenyi Pi ( ORCID : 0009–0002–2884–2771) Introduction Since OpenAI launched ChatGPT, a large language model (LLM) based chatbot, in 2023, it has set off a technological wave.

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