John M. Drake

In Praise of the AI-Drafted Email I’m going to risk sounding contrarian: I like receiving AI-written emails.

(Potentially) unpopular opinion. Too long for BlueSky so please read on Substack.

jdrakephd.substack.com/p/in-praise-...

Drake's Dispatches | John Drake | Substack Occasional essays and reflections on science, health, environment, and the policies that shape them. Click to read Drake's Dispatches, by John Drake, a Substack publication.

Hi folks - I've mostly migrated to substack. Would love to see my friends here follow me over there, too. It's the main place I'll be posting about ecology, environment, health, epidemiology, academia, and related topics.

jdrakephd.substack.com

S4DM: Small Sample Size Species Distribution Modeling Implements a set of distribution modeling methods that are suited to species with small sample sizes (e.g., poorly sampled species or rare species). While these methods can also be used on well-sample...

Software: we released S4DM (R package) on CRAN implementing plug-and-play + density-ratio workflows:
cran.r-project.org/web/packages...

We advocate ensembles that span assumptions (tight vs broad): they can improve predictions and explicitly map disagreement/uncertainty when data are scarce.

Also: for small samples, training AUC / CV AUC is a weak proxy for independent presence–absence performance; specificity & accuracy carry better.

For ≤20 occurrences, lots of methods are ~indistinguishable from Maxnet on AUC—but they spread across a big sensitivity–specificity gradient, producing very different binary maps.

Main result: no single algorithm wins everywhere.
Maxnet is best on average, but some alternative method beats it for 72% of species.

We compare 3 “data-deficient” families:
• plug-and-play (estimate presence & background densities, take the ratio)
• density-ratio (estimate ratio directly; includes MaxEnt/Maxnet)
• environmental-range (estimate niche limits; e.g., range-bagging)

Problem: SDMs often fail for rare / poorly sampled species—which is most species, and many of the ones we most care about for conservation.

Flexible methods for species distribution modeling with small samples Species distribution models (SDMs) predict where species live or could potentially live and are a key resource for ecological research and conservation decision-making. However, current SDM methods o....

New paper out today 🧵
Flexible methods for species distribution modeling with small samples (Ecography, OA). nsojournals.onlinelibrary.wiley.com/doi/10.1002/...

This #openaccess work was a collaborative effort with Robbie Richards, Ben Carlson, @jdrakephd.bsky.social, and Cory Merow. All code and data are freely available on Github (github.com/bmaitner/sma...) or Dryad (doi.org/10.5061/drya...).

After experimenting for a few months, I've decided mostly to migrate over to Substack. I hope those who follow me here and previously followed me on Twitter will forgive the disruption and click below to follow me there.

Leveraging Systems-of-Systems Analysis to Strengthen Epidemic Intelligence for Preparedness and Response | Health Security The COVID-19 pandemic exposed significant gaps in the coordination and integration of efforts required to effectively manage large-scale infectious disease outbreaks. A successful response to such cri...

Our new paper in #HealthSecurity argues that epidemic intelligence needs a #systems-of-systems framework—integrating #epidemiology, behavior, supply chains, policy, and ecology—rather than siloed models that talk past one another.

Includes an #H5N1 case study.

www.liebertpub.com/doi/10.1177/...

Applied to COVID-19 in California, the approach yields more accurate and more stable short-term forecasts than RNNs, LSTMs, GRUs, Transformers, and naïve baselines.

🔗 royalsocietypublishing.org/doi/10.1098/...

A challenge in epidemic forecasting is that ML models overfit while mechanistic models miss changing transmission conditions. Our new JR Soc Interface paper tests whether physics-informed neural networks—which embed an epidemiological ODE system inside a neural net—can address this.

Biological modeling is organized inquiry, but how should we think about the process?

My new paper in #EcologyLetters argues that we should model like experimentalists: define treatments, measure responses, validate, perturb, repeat.

👉 doi.org/10.1111/ele....

Do you agree?

Understanding avian influenza mortality Three theories could explain why the North American H5N1 epidemic has not been more deadly

New essay out in #Science: why is the human fatality rate from the current #H5N1 outbreak so much lower than in past outbreaks?

I explore three possible explanations—and what they mean for pandemic risk.

www.science.org/doi/10.1126/...

Newly expanded version of my guide to scientific writing -- known as the “15 steps” -- published in PLOS Computational Biology. Special thanks to Éric Marty for creating a fantastic visualization.

Check it out: journals.plos.org/ploscompbiol...

#ScientificWriting #PLOSComputationalBiology

Excited to share that I’m joining @bigbiology.bsky.social this season as a recurring guest host. Marty Martin and I teamed up on my first episode with @jaapderoode.bsky.social, and it's just dropped. Hope you enjoy it.

#diseaseecology

“Globalisation, global change and emerging infectious diseases” with @jdrakephd.bsky.social

How do globalisation and climate change influence the rise of new pandemics? Join in person or online – open to all.

Register: www.oxfordmartin.ox.ac.uk/events/globa...

Stream: youtube.com/live/80kXZlQ...

Biological modeling is organized inquiry, but how should we think about the process?

My new paper in #EcologyLetters argues that we should model like experimentalists: define treatments, measure responses, validate, perturb, repeat.

👉 doi.org/10.1111/ele....

Do you agree?

Why are flu vaccination rates stuck?

We studied how “medical mindsets” (naturalist/technologist, minimalist/maximalist, doubter/believer) affect vaccine hesitancy.

These attitudes matter and could help tailor communication to boost uptake.

Read about it in #Vaccine 👉 doi.org/10.1016/j.va...

What if we take a systems approach to thinking about transboundary animal diseases? Our framework, just out in #TrendsInParasitology, suggests common vulnerabilities and opportunities for intervention.

#TADs

authors.elsevier.com/a/1lshW5Eb1x...

Understanding avian influenza mortality Three theories could explain why the North American H5N1 epidemic has not been more deadly

New essay out in #Science: why is the human fatality rate from the current #H5N1 outbreak so much lower than in past outbreaks?

I explore three possible explanations—and what they mean for pandemic risk.

www.science.org/doi/10.1126/...

Newly expanded version of my guide to scientific writing -- known as the “15 steps” -- published in PLOS Computational Biology. Special thanks to Éric Marty for creating a fantastic visualization.

Check it out: journals.plos.org/ploscompbiol...

#ScientificWriting #PLOSComputationalBiology

How do human-wildlife interfaces and seasonality interact during disease emergence? Our team has created a model, inspired by the #spillover of #Ebola, to better understand the interplay.

Read more about our research: royalsocietypublishing.org/doi/10.1098/...

Saad Bhamla Is A Polymath Philanthropy backs bold science as federal funds shrink. Schmidt Polymaths support Saad Bhamla’s work on biomechanics of everyday organisms from ripple bugs to flamingos.

Science philanthropy is alive and well. Schmidt Sciences has just announced eight new awards through its Schmidt Polymaths program.

www.forbes.com/sites/johndr...

Flyer advertising upcoming MIDAS Trainee Network event on How to Write a Strong Manuscript. The event will take place on Thurs 9/25 at 12pm ET with a presentation from Dr. John Drake from the University of Georgia, followed by Q&A and discussion. Register at: https://georgetown.zoom.us/meeting/register/rTEZP0pSQIqlLv_EyquGgQ

Ever read a paper & think, "wow 🤩 that was well written"?

Learn how to write your own *wow* paper with @midas-network.bsky.social trainees on Thurs 9/25 @ noon ET.

We'll hear from @jdrakephd.bsky.social on strategies for crafting & communicating a good story.

🔗 georgetown.zoom.us/meeting/regi...

An Algorithm For Controlling Epidemics Researchers adapt model predictive control from engineering to epidemic response, balancing health and economic costs under noisy, delayed data.

Interesting work by Kris Parag and Sandor Beregi using model predictive control for timing NPIs.

👉 Read my Forbes piece: www.forbes.com/sites/johndr...

Also: are there essays or papers you’ve found especially insightful on the ethics of AI in scholarly writing?