Ken Koon Wong
kenkoonwong.bsky.social
Ken Koon Wong
@kenkoonwong.bsky.social
data science enthusiast #rstats. infectious disease provider. lazy gardener. tai chi practitioner. life long learner. views are my own. RT or like != endorsement. https://www.kenkoonwong.com/
Pinned
I finally understood B-splines by working through the Cox-deBoor algorithm step-by-step, discovering they’re just weighted combo of basis functions that make non-linear regression linear. What surprised me is going through Bayesian statistics helped me understand the engine behind the model! #rstats
Understanding Basis Spline (B-spline) By Working Through Cox-deBoor Algorithm | Everyday Is A School Day
I finally understood B-splines by working through the Cox-deBoor algorithm step-by-step, discovering they're just weighted combinations of basis functions that make non-linear regression linear. What ...
www.kenkoonwong.com
Reposted by Ken Koon Wong
AI-assisted review for CLABSI detection showed 93.2% accuracy vs. 90% AI-alone and 88.2% expert review. It took 14 mins vs. 25 mins for experts. AI was preferred in 52% cases. 🏥💻✨##idsky
Using generative artificial intelligence to identify central line-associated bloodstream infections
Central line-associated blood stream infection (CLABSI) surveillance is mandated and publicly reported in United States hospitals but requires manual chart review. Generative artificial intelligence (AI) may facilitate CLABSI identification.MethodsWe performed a retrospective cohort study of CLABSI surveillance using standardized prompts, clinical data, and Centers for Disease Control and Prevention definitions. In 11 hospitals, 24 infection control (IC) nurses and physicians retrospectively reviewed 220 CLABSI/non CLABSI bacteremias. Three methods of review were compared to original facility expert review: 1) AI-assist review, 2) AI-alone review, and 3) repeat expert review. Disagreement between any method of review was adjudicated by a 2-expert physician referee panel.ResultsAI-assist review had a 93.2% (205/220, 95% CI: 89.0–96.1) overall accuracy (agreement with facility reporting or refereeing panel) vs. AI-alone review, 90.0% (198/220, 95% CI: 85.3–93.6) overall accuracy or repeat expert review, 88.2% (97/110, 95% CI: 80.1–93.6) overall accuracy. Inter-site variability was greater for repeat expert review than AI-assist. AI-assist review required a median of 14 minutes (interquartile range, IQR 6-25.5) vs. 25 minutes (IQR 11-43) for repeat expert (p = 0.0001). AI-assist review was reported as low effort in 52% of cases vs. 21% of repeat expert cases (p < 0.0001). AI-assist review was reported as somewhat or very objective in 72% of cases vs. 61% of repeat expert cases (p=0.092).ConclusionsCLABSI detection by AI methods was at least as accurate as traditional methods, better liked by experts, faster and less variable. AI-assisted review could improve healthcare-associated infection reporting.
academic.oup.com
November 23, 2025 at 2:30 PM
Reposted by Ken Koon Wong
Study of 196 households (623 participants) showed no difference in SSTI incidence after 3 months. Integrated-Approach reduced SSTIs at 6-9 months for those with prior SSTIs. 📉##idsky
Evaluating Personal and Environmental Decolonization Strategies for Children with Skin and Soft Tissue Infection and Their Households – A Randomized Clinical Trial
Staphylococcus aureus colonization predisposes to skin and soft tissue infection (SSTI). Given the waning effectiveness of decolonization, we evaluated periodic personal decolonization and household environmental decontamination to reduce SSTIs among households affected by S. aureus.MethodsHouseholds of children with community-associated S. aureus SSTI participated in an open-label randomized trial. After baseline decolonization, households were randomized 1:1:1 to a 3-month decolonization intervention: 1) Periodic-Personal (twice weekly chlorhexidine bathing and monthly intranasal mupirocin application); 2) Environmental-Hygiene (weekly household surface disinfection and enhanced laundry measures); or 3) Integrated-Approach of both Periodic-Personal and Environmental-Hygiene. Over 9 months, participants and household surfaces were sampled at 5 study visits to detect S. aureus; SSTI incidence was recorded. The primary outcome was household-level cumulative SSTI at 3 months, comparing the Integrated-Approach to the combined Personal-Periodic and Environmental-Hygiene groups.ResultsBetween 2015-2021, 196 index patients and their household contacts (n=623) were enrolled. Cumulative SSTI incidence did not differ between groups during the 3-month intervention. In index patients and household contacts with SSTI in the year prior to enrollment, SSTI incidence was lower among the Integrated-Approach at 6- and 9-months compared to the combined Periodic-Personal and Environmental-Hygiene groups. In multivariable analyses, prior year SSTI was associated with subsequent SSTI; intervention group was not significant. All interventions reduced MRSA, but not MSSA, personal colonization over 9 months.ConclusionsWhile an Integrated-Approach of prolonged personal and environmental decolonization reduced SSTIs among participants with prior year SSTI, prior SSTI strongly predicted SSTI incidence longitudinally. Novel prevention strategies are needed.
academic.oup.com
November 24, 2025 at 12:30 PM
Finally understood TMLE’s “doubly robust” property through simulation. Works well when either outcome OR treatment model is correct. XGBoost + TMLE captured complex relationships without manual specification. It worked on simulated complex data, would it work in real world? 🤔 #rstats #idsky #episky
Bias, Variance, and Doubly Robust Estimation: Testing The Promise of TMLE in Simulated Data | Everyday Is A School Day
Finally understood TMLE's "doubly robust" property through simulation. Works well when either outcome OR treatment model is correct. XGBoost + TMLE captured complex relationships without manual specif...
www.kenkoonwong.com
November 17, 2025 at 1:55 AM
#IDWeek2025 had the lowest post count since 2022 (1,272 posts). While top posters shifted to Bluesky, X remained on par—the key difference was engagement rates favoring Bluesky. Grateful to learn so much from our SoMe community! 📊💙🙏

#idsky
#IDWeek2025 Posts/Tweets Analysis | Everyday Is A School Day
IDWeek2025 had the lowest post count since 2022 (1,272 posts). While top posters shifted to Bluesky, X remained on par—the key difference was engagement rates favoring Bluesky. Grateful to learn so mu...
www.kenkoonwong.com
October 27, 2025 at 1:32 AM
Ever wondered what M184V, K65R actually mean? I learnt it from rebuilding Stanford’s HIV resistance algorithm from scratch to find out. Spoiler: it took tons of code to match their 3-line tool. But the lesson was worth it

#idsky #hivsky #bioconductor #rstats #sierrapy #bioinformatics
My Attempt To Reproduce Stanford HIVdb Sequence and Mutation Analysis From Scratch | Everyday Is A School Day
Ever wondered what M184V, K65R actually mean? I learnt it from rebuilding Stanford's HIV resistance algorithm from scratch to find out. Spoiler: it took tons of code to match their 3-line tool. But th...
www.kenkoonwong.com
October 11, 2025 at 3:51 AM
Learned RNA-seq workflow using C. diff data from a study 🧬. Processed raw reads thru fastp → kallisto → DESeq2 pipeline. Results matched the original paper’s findings, with clear differential expression between mucus and control conditions 📊.

#idsky #microsky #rstats #deseq2 #bioconductor
Learning And Exploring The Workflow of RNA-Seq Analysis - A Note To Myself | Everyday Is A School Day
Learned RNA-seq workflow using C. difficile data from a published study 🧬. Processed raw reads through fastp → kallisto → DESeq2 pipeline. Results matched the original paper's findings, with clear dif...
www.kenkoonwong.com
September 27, 2025 at 9:00 PM
Hands-on with @nanoporetech.com workflow: pod5 → BAM → assembly -> polish! Processed M. tuberculosis from raw signals to complete genome using #dorado + #samtools + #flye. Fascinating how thousands of contigs became one 4M+ bp sequence.

#idsky #tbsky #microsky #bioinformatics
Exploring The Workflow of The Oxford Nanopore Technologies (ONT) from pod5 to Polished Asembly - A Note To Myself | Everyday Is A School Day
Hands-on with Oxford Nanopore workflow: pod5 → BAM → assembly! Processed M. tuberculosis from raw signals to complete genome using dorado + flye. Fascinating how thousands of contigs became one 4M+ bp...
www.kenkoonwong.com
September 21, 2025 at 4:50 PM
Reposted by Ken Koon Wong
Come join #IDSky at the unofficial @idweek.bsky.social Social Media Meet-Up!

All are welcome.
September 16, 2025 at 1:55 AM
Reposted by Ken Koon Wong
Join us this #IDWeek2025 for a SoMe meet-up! One of the highlights every year of the conference is meeting all of you! #IDSky
Come join #IDSky at the unofficial @idweek.bsky.social Social Media Meet-Up!

All are welcome.
September 16, 2025 at 2:40 AM
We learnt how to assemble DNA fragments from a recently published N. meningitidis outbreak study www.cdc.gov/mmwr/volumes... using SKESA 🧬, practiced using BLAST for species identification and MLST for strain typing, and explored how serogroups are determined!

#idsky #microsky #rstats
Learning About Assemblying DNA, BLAST, and Multiple Loci Sequence Testing (MLST) - A Note To Myself | Everyday Is A School Day
We learnt how to assemble DNA fragments from a recently published *N. meningitidis* outbreak study using SKESA 🧬, practiced using BLAST for species identification and MLST for strain typing, and explo...
www.kenkoonwong.com
September 15, 2025 at 11:06 PM
Ever wondered how DNA alignment actually works under the hood? 🧬 We coded the Needleman-Wunsch algorithm from scratch, working thru scoring matrices w simple examples like "CAT" vs "CT" before testing on E. coli sequences. Pretty neat to see the magic! ✨

#microsky #idsky #bioconductor #rstats
Building DNA Sequence Alignment With Needleman-Wunsch Algorithm From Scratch - A Note To My Self | Everyday Is A School Day
Ever wondered how DNA alignment actually works under the hood? 🧬 We coded the Needleman-Wunsch algorithm from scratch, working through scoring matrices by hand with simple examples like "CAT" vs "CT" ...
www.kenkoonwong.com
September 7, 2025 at 8:00 PM
Reposted by Ken Koon Wong
There have been many documented meningococcal meningitis outbreaks.

Here we describe our investigation and response to the first documented meningococcal conjunctivitis outbreak. 🧫

Contributions by 🌟🌟🌟 fellows @sucroselauren.bsky.social @ogallardo.bsky.social
#IDSky

www.cdc.gov/mmwr/volumes...
Outbreak of Neisseria meningitidis Conjunctivitis ...
This report describes 41 cases of Neisseria meningitidis conjunctivitis among military trainees living in a communal setting in Texas.
www.cdc.gov
September 4, 2025 at 10:05 PM
🧬🔬 Explore phylogenetic analysis from genome to tree! Basic workflow with #rstats #bioconductor. Learnt to work with large genomic data. Extract 16S rRNA from 10K+ E.coli strains using dataset dehydrate, barrnap for extraction, rapidNJ for tree building & FigTree for visualization.

#microsky #idsky
Learning The Basics of Phylogenetic Analysis | Everyday Is A School Day
🧬🔬 Explore phylogenetic analysis from genome to tree! Basic workflow with R/Bioconductor. Learnt to work with large genomic dataset. Extract 16S rRNA from 10K+ E.coli strains using dataset dehydrate, ...
www.kenkoonwong.com
August 31, 2025 at 3:07 PM
Instead of flashcards, we Rube Goldberg’d this with #Bioconductor ! Analyzed 3,280 E. coli genomes from NCBI, detecting ESBL genes in 84.4% of samples. CTX-M-15 was most common. Helped us understand gene nomenclature and sequence analysis! 📊🔬

#idsky #microsky #amr #rstats
Learning Antimicrobial Resistance (AMR) genes with Bioconductor | Everyday Is A School Day
Instead of flashcards, we Rube Goldberg'd this with Bioconductor! Analyzed 3,280 E. coli genomes from NCBI, detecting ESBL genes in 84.4% of samples. CTX-M-15 was most common. Helped us understand gen...
www.kenkoonwong.com
August 15, 2025 at 10:12 PM
Learn how to build a flash-card style question bank using Google Sheets as storage, #rstats Plumber API, and host it on a Digital Ocean droplet—step-by-step setup, deployment, and tips.

#idsky #medsky #meded
Creating A Question Bank Using Google Sheet, Plumber, and Digital Ocean Droplet | Everyday Is A School Day
Learn how to build a flash-card style question bank using Google Sheets as storage, R’s Plumber API, and host it on a Digital Ocean droplet—step-by-step setup, deployment, and tips.
www.kenkoonwong.com
June 18, 2025 at 6:24 PM
Reposted by Ken Koon Wong
Our review on hierarchical composite endpoints (HCEs) has just been published in @cidjournal.bsky.social:
doi.org/10.1093/cid/...

We provide a conceptual overview of HCEs, explain the different associated target parameters and analytic methods.

@steventong.bsky.social @gurujosh.bsky.social
Making sense of hierarchical composite endpoints in randomized clinical trials – a primer for infectious disease clinicians and researchers
Hierarchical composite endpoints (HCEs) are increasingly being used in infectious diseases research. In this review aimed at educating the clinical reader,
doi.org
June 16, 2025 at 1:55 AM
Enjoyed learning penalized GAM math. Built penalty matrices, optimized λ using GCV, and implement our own GAM function.

Confusing? Yes! Rewarding? Oh yes!

#rstats
From Math to Code: Building GAM with Penalty Functions From Scratch | Everyday Is A School Day
Enjoyed learning penalized GAM math. Built penalty matrices, optimized λ using GCV, and implement our own GAM function. Confusing? Yes! Rewarding? Oh yes!
www.kenkoonwong.com
June 12, 2025 at 1:52 AM
Wow!!! You can do combo abx too!?!? Amazing!
Congratulations to Matthijs Berends and team for the release of the AMR for R package version 3!

I've been using this package to produce the AGAR Kids reports and can highly recommend.

amr-for-r.org

#Rstats #AMR #IDEpi #MedSky
June 8, 2025 at 12:53 PM
Just listened to this. Awesome insights!
June 4, 2025 at 11:47 AM
I finally understood B-splines by working through the Cox-deBoor algorithm step-by-step, discovering they’re just weighted combo of basis functions that make non-linear regression linear. What surprised me is going through Bayesian statistics helped me understand the engine behind the model! #rstats
Understanding Basis Spline (B-spline) By Working Through Cox-deBoor Algorithm | Everyday Is A School Day
I finally understood B-splines by working through the Cox-deBoor algorithm step-by-step, discovering they're just weighted combinations of basis functions that make non-linear regression linear. What ...
www.kenkoonwong.com
June 4, 2025 at 12:44 AM
We learnt to derive the Newton-Raphson algorithm from Taylor series approx. We’ll show how the 2nd-order Taylor expansion leads to the Newton-Raphson update formula, then compare individual parameter updates vs using the full Fisher Information matrix for faster convergence. Fascinating!

#rstats
Taylor Series Approximation To Newton Raphson Algorithm - A note for myself of the proof | Everyday Is A School Day
We learnt to derive the Newton-Raphson algorithm from Taylor series approximation and implements it for logistic regression in R. We'll show how the second-order Taylor expansion leads to the Newton-R...
www.kenkoonwong.com
May 25, 2025 at 6:08 PM
Refreshed my rusty calculus skills lately! 🤓 Finally understand what happens during complete separation and why those coefficient SE get so extreme. The math behind maximum likelihood estimation makes more sense now! Chain rule, quotient rule, matrix inversion are crucial!

#rstats
From Complete Separation To Maximum Likelihood Estimation in Logistic Regresion: A Note To Myself | Everyday Is A School Day
Refreshed my rusty calculus skills lately! 🤓 Finally understand what happens during complete separation and why those coefficient SE get so extreme. The math behind maximum likelihood estimation makes...
www.kenkoonwong.com
May 17, 2025 at 6:55 PM
In my simulations of Response Adaptive Randomization, I discovered it performs comparably to fixed 50-50 allocation in identifying treatment effects. The adaptive approach does appear to work! However, with only 10 trials, I’ve merely scratched the surface. Important limitations exist

#rstats
Simulating A Simple Response Adaptive Randomization - I Have To See It To Believe It | Everyday Is A School Day
In my simulations of Response Adaptive Randomization, I discovered it performs comparably to fixed 50-50 allocation in identifying treatment effects. The adaptive approach does appear to work! However...
www.kenkoonwong.com
May 4, 2025 at 9:49 PM
Reposted by Ken Koon Wong
Caring for patients with bronchiectasis poses a challenge for both pulmonologists and #AMSky teams.

Standard 14d treatments for exacerbations lack good evidence support.

This small RCT favors shorter durations such as 8d 👉🏻 publications.ersnet.org/content/erj/... #IDsky @bradspellberg.bsky.social
May 4, 2025 at 12:43 AM
Reposted by Ken Koon Wong
#IDsky

I did a post on the IDSA community board on the G0545 code. Check it out! I think you will find it interesting! 😊💰

my.idsociety.org/discussion/g...
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my.idsociety.org
May 2, 2025 at 1:28 AM