StatQuest: Hierarchical Clustering

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Hierarchical clustering is often used with heatmaps and with machine learning type stuff. It's no big deal, though, and based on just a few simple concepts. If you want to draw a heatmap using R, I've put some sample code on my webiste: statquest.org/statquest-hiera...
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#statquest #ML #clustering

Опубликовано:

6 июл 2024

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Комментарии : 361

@statquest 2 года назад

Support StatQuest by buying my book The StatQuest Illustrated Guide to Machine Learning or a Study Guide or Merch!!! statquest.org/statquest-store/

@anamulmbdu 6 лет назад

The intro song removed my fear of clustering. Thanks for the awesome video.

@nemothekitten3994 Год назад

going on a statequest😌

@Aemilindore 3 года назад

You're a person who saved me lots of time and pain. Thank you. I wish you the best

@statquest 3 года назад

Thank you very much! :)

@kristinomalley4519 Год назад

You are, and I cannot stress this enough, a national treasure!! The ease in how you explain things that have eluded me for over a decade and make it click is truly a gift. Thank you so freaking much!!!

@statquest Год назад

Wow, thank you!

@julieboissiere4553 2 года назад

I used to watch your videos while I was a student. It’s been 3 years since my graduation and I’m still here (I’m changing jobs and need to review some stuff). Thank you a lot for your incredible work

@statquest 2 года назад

Congratulations on the new job! BAM! :)

@brunomartel4639 4 года назад

this video proved that "hard" stuff =badly explained stuff

@sindhujas7807 3 года назад

so fuckin true. Not sorry for swearing. Happy learning guys

@gummybear8883 3 года назад

if you can't explain something in simple terms, then you don't understand it that well.

@julius4858 3 года назад

@@gummybear8883 or you've been a professor for 20 years and are so deep into a topic that you completely forgot how people approach new problems. Your sentence really only applies to novices trying to be teachers.

@Joreselin 3 года назад

@@julius4858 We could just change it to: if you can't explain something in simple terms, then you can't teach it that well.

@julius4858 3 года назад

@@Joreselin Yeah, that is absolutely true. Many of my professors for theoretical computer science are experts on various fields but man do their explanations suck. That's why I have to watch youtube videos for stuff like this.

@davidescobar4449 5 лет назад

I have to congratulate you for this video, it gives the basic notions of the hierarchical cluster easy and fast. Bravo!

@rajshrestha9484 4 года назад

I can't thank you enough. Such clear and helpful explanations. Great.

@statquest 4 года назад

Thanks! :)

@EthosDemerzel 3 года назад

you can, with patreon

@chikken007 4 года назад

I already watched some of your videos. This one I watched because I want to apply hierarchical clustering in my thesis. It is about time I buy one of your sweaters. I hope this supports you. Thanks for all the truly great explanations.THANK YOU!

@statquest 4 года назад

Thank you very much!!! :)

@yamikag8363 2 года назад

your videos help me see the "big picture" of concepts. after your videos, I can actually understand what is going on and why we are doing something. Thank you!

@statquest 2 года назад

Happy to help!

@fadikhattar290 Год назад

I still don't believe how this content is free. Thank you sir!

@statquest Год назад

Thanks!

@stephenwood9252 Год назад

Love your videos. The fact that you make it so simple shows the depth of your understanding.

@statquest Год назад

Thank you!

@scraps7624 2 года назад

This channel is a treasure! Absolutely incredible job my man

@statquest 2 года назад

Thank you so much 😀!

@pragyamishra9083 2 года назад

The visualizations and simplicity of explanations as well as great examples motivate me to keep learning. Thank you so much for making it so interesting. I'll try to do my bit by buying a t-shirt. 😊

@statquest 2 года назад

Wow! Thank you very much! :)

@The_TusharMishra 6 месяцев назад

hi pragya

@liranzaidman1610 4 года назад

Very nice. I use this in Python and it's a really good way to cluster. Another thing - from coding aspect, it's only 1 line of code in Seaborn, very easy.

@statquest 4 года назад

Thanks for sharing!

@jingsilu5568 2 года назад

Thank you for clearly explaining the details at a moderate speed! You save me lots of time!

@statquest 2 года назад

Thank you!

@davidcartwright337 5 лет назад

great videos, I like the way you explain these topics

@congchen170 7 лет назад

Joshua's video is always helpful. Next time, probably k-means clustering.

@abhayjoshi2121 2 года назад

You are simply amazing !! I love your style and simplicity and the word is BAM! .. your videos are very informative and worth going through... thanks for all your hard work in simplifying the complex topics

@statquest 2 года назад

Thank you so much!!

@99harshini 4 года назад

Absolutely brilliant..Thank you sooo much for your time and effort!

@statquest 4 года назад

Thanks! :)

@gurkanyesilyurt4461 3 года назад

you saved yet another day Josh. Thank you

@statquest 3 года назад

Bam! :)

@calebsawe8307 2 года назад

I am super grateful for this video. You are such an excellent teacher! Thank you for being such a "you"

@statquest 2 года назад

Wow, thank you!

@urjaswitayadav3188 7 лет назад

Great explanation. Thanks StatQuest!

@anastasiyakuznetsova8797 2 года назад

The best as always! Love this channel! It's super easy to understand

@statquest 2 года назад

Thanks!

@websciencenl7994 Год назад

StatQuest is the Best! Teaching is an art...and these are master pieces.

@statquest Год назад

WOW! Thank you very much! :)

@user-vg8dp5tb9w Год назад

This channels is truly a treasure trove! I was wondering if you could do a video on consensus clustering? I.e. how to evaluate clustering across multiple models and parameters. You are awesome!

@statquest Год назад

I'll keep that in mind.

@HiasHiasHias 14 дней назад

StatQuest never disappoints

@statquest 13 дней назад

BAM! :)

@LBsCuriosity 5 лет назад

really awesome video! This will help me with my test. Thank you!

@fellsantfernandoargentin2072 6 лет назад

Congratulations from Brazil!

@vishk123 6 месяцев назад

Thank you for allowing me to ascend the stats hierarchy!

@statquest 6 месяцев назад

bam! :)

@rodrigohaasbueno8290 5 лет назад

I love this channel so much

@statquest 5 лет назад

Thank you! :)

@LetWorkTogether 4 года назад

I love this. Your video is wonderful!

@statquest 4 года назад

Thank you! :)

@eamiller12 2 года назад

THANK YOU! This is has been SO HELPFUL!

@statquest 2 года назад

bam!

@farzanaferdousi9885 3 года назад

Your explanation is very clear to me and i see all your video, you are very friendly to me. I like you very much.

@statquest 3 года назад

Thank you! 😃

@loftyTHEOWNER 2 года назад

I would like to add that: - single-linkage (comparing the closest points of 2 clusters) tends to form more elliptic clusters; - complete-linkage tends to form more globular clusters. So, that means that not scaling your data, scaling with a StandardScaler, or with a MinMaxScaler will affect your clustering.

@statquest 2 года назад

Noted!

@Paulamiz 3 года назад

Watching this after watching your more recent videos. Missed your 'BAM's a lot!!! You should remake these old videos again! Thanks :)

@statquest 3 года назад

bam! :)

@Paulamiz 3 года назад

@@statquest 😍

@vakarthi4 2 года назад

Found this gem of a channel today. Agreed on the fun rhymes and puns.

@proggenius2024 2 месяца назад

awesome content and delivery

@statquest 2 месяца назад

Glad you think so!

@2327853 4 года назад

@StatQuest please explain probability and Naive Bayes. Thanks in advance! I am a huge fan of your way of teaching and your small songs creations. Keep up the good work!

@statquest 4 года назад

Thanks! Naive Bayes is on the to-do list.

@createyouridea8602 4 года назад

@@statquest waiting. plz .

@saikiranjajula2033 4 года назад

Thank You Sir, It was awesome to learn from you.

@statquest 4 года назад

BAM! :)

@shamanthrajreddy1230 2 года назад

Excellent explanation!

@statquest 2 года назад

Thanks!

@robertogff 3 года назад

Congratulations! your video is so great! you explain is a very clear and simple way.

@statquest 3 года назад

Thank you! 😃

@12bjab 5 лет назад

just beautiful!

@isha996 6 лет назад

Please add a video on Latin Square design, Joshua! I am going to pass my stats final tomorrow, only because of your videos :D your students are lucky.

@isha996 6 лет назад

The CPA and clustering question was worth 30% of total marks on my exam today, and I managed to write them so well only because of your videos. you're a savior. Thank you!!

@saipanchajanya5980 4 года назад

This is Awesome...... Please Make a session on K Modes, KNN and K Prototypes

@statquest 4 года назад

Here's a complete list of my videos so far: statquest.org/video-index/

@nnnyin6967 Год назад

I am preparing my actuarial exam and you saved me a lot❤

@statquest Год назад

Good luck! :)

@fabiomaia3433 3 года назад

Hey Josh! Your videos are great! Thank you for the effort you've put on it! If you allow me... have you considered making videos explaining DBSCAN and HDBSCAN?

@statquest 3 года назад

Yes, I've thought about those topics and may make a video about them.

@preranadas4037 4 года назад

Hello Josh! The videos are soooooooo goooood! These are BAMMMMM Good!! 1 request - Could you please create a video on LCA - Latent Class Analysis? Maybe by comparing it to k-means clustering? I cannot be more thankful!

@LoriSchomp 3 года назад

would like this too

@jonathanlam7204 7 месяцев назад

Thank you. Better than university teaching

@statquest 7 месяцев назад

Thanks!

@alyssawang144 3 года назад

fantastic explanation, thank you so much for this video.

@statquest 3 года назад

Thanks!

@tymothylim6550 3 года назад

Thank you very much for this video! It was really well done :)

@statquest 3 года назад

Glad you liked it!

@jovanmampusti4025 2 года назад

Thank you so much sir! This is very helpful and very informative.

@statquest 2 года назад

Glad it was helpful!

@balajicanchi5538 6 лет назад

Explained in a simple manner.

@CapoeiraPiper 3 года назад

Man your videos are soo super helpful! THANK YOU (ps consider the color library viridis to make it easier for the colorblind)

@statquest 3 года назад

Thanks!

@sonakshigarg4273 4 года назад

You can explain the same concept with may be some other datasets and better visualisation other than heatmap

@cfonsecaparis812 2 года назад

Hi Josh, I am really enjoying your videos specially the wha whas and bam !! , you make stats sound easy but also fun! Thank you! I wonder if you could please do a video to explain the different uses of PCA and HCA, when do you use one or the other? In the mean time I will watch your videos on PCA and HCA :) hooray!

@statquest 2 года назад

BAM! Thank you very much! I'll keep that topic in mind.

@mojtabasardarmehni453 3 года назад

Great as always! Thanks.

@statquest 3 года назад

Thank you! :)

@ardaugurlu8673 5 лет назад

Good job mr josh.

@statquest 5 лет назад

Thank you!

@yyma8037 4 года назад

Great video! Do you have any plans to talk about co-clustering, look forward to it.

@oliviagallupova9199 4 года назад

You saved me a week

@statquest 4 года назад

Awesome! :)

@muhammadiqbalmarzuki 4 года назад

This video is super duper bam bam double double bam! Will you cover more advanced clustering techniques such as model-based clustering (MCLUST) and weighted gene co-expression network analysis (WGCNA)? I'm learning about these things now for my research, and will be very grateful if you can cover these topics for me. Thanks! :)

@statquest 4 года назад

Thanks! :)

@lukehebert6207 4 года назад

Very helpful, thank you!

@statquest 4 года назад

Thanks! :)

@setareht7546 2 года назад

Thank you for all your videos clearly explaining complex concepts. Can you also make video(s) on different bi-clustering methods?

@statquest 2 года назад

I'll keep that in mind.

@MrKingoverall 4 года назад

I LOVE YOU JOSH !

@statquest 4 года назад

@python_information601 2 года назад

Nice explanation 👍👍

@statquest 2 года назад

Thanks!

@maikfranke2303 Год назад

Amazing! Your Videos are so much comrehensible. I really enjoy watching!!!*_*

@statquest Год назад

Thank you!

@subhabrataghosh9831 3 года назад

Excellent Sir

@statquest 3 года назад

Thanks!

@veloisamascarenhas7531 5 лет назад

how can clustering be applied on spectral data?

@zzzluke8906 8 месяцев назад

Hi Josh, amazing video as always. Think you can come up with video on how to determine the best number of clusters to have? I get the Elbow method, but I really struggle with the inconsistent method. I was looking at the inconsistency coefficients, and I am confused to do they include singleton clusters, or are singleton clusters excluded. I am also confused about what exactly is the "jump" in the inconsistent coefficient that we are supposed to look out for.

@statquest 8 месяцев назад

I'll keep that topic in mind.

@italosayan4747 6 лет назад

beautiful BRO!

@AdnanGora 5 лет назад

Awesome video

@statquest 5 лет назад

Thank you! :)

@marahakermi-nt7lc 11 месяцев назад

ohh my god thanks josh u are so brilliant i think marvel should add another new superhero "josh starmer the life saver"

@statquest 11 месяцев назад

@locdaikathegreat3689 4 года назад

So cool the video!

@statquest 4 года назад

Thanks! :)

@MihirSriramVadali 7 дней назад

Great channel. Clearly explained all most all the topics i watched on ML. Here one question what does gene stands for is it features of the data ?

@statquest 7 дней назад

Yes, it's a feature.

@Sean-lz2dh Год назад

great video. thank you very much

@statquest Год назад

Thanks!

@raghavmoar3211 5 лет назад

Thanks for the video

@user-ib9lp8zx6x 6 лет назад

Hi, Joshua. Do you know the basics of pseudotime analysis in single-cell RNA-seq. Can you make a short video talking about the basics? Thanks!

@statquest 6 лет назад

I'll put that on the to-do list!

@surbhardwaj1721 3 года назад

Amazing explanation. Please make a video on Cluster evaluation. :)

@statquest 3 года назад

I'll keep that in mind.

@ankitabhavsar886 23 дня назад

the intro.......nice one bro🖐

@statquest 22 дня назад

bam! :)

@the_data_panda 5 лет назад

@StatQuest with Josh Starmer, in this video you are clustering and combining genes (the attributes of data), aren't you supposed to cluster and combine the samples? that's the inverse of the approach shown

@statquest 5 лет назад

You can cluster the samples or the genes, or both! It all depends on the question you are asking. For example, if I have some healthy people and some sick people, I might be interested in clustering the people (to see if healthy people form one cluster and unhealthy people form another) or I might be interested in clustering the genes. In this case I would find out which genes are correlated and up-regulated in healthy people compared to unhealthy people. Or I could do both. Does that make sense?

@user-gd2zf9ym4h 5 месяцев назад

You saved my life😇 Thank you very much. And I think the link for the sample code in R isn't available right now...

@statquest 5 месяцев назад

Yep, that's a really old link. Here's a new one: statquest.org/statquest-hierarchical-clustering/

@iranziemiler8135 4 года назад

Thank you

@mikecy5507 Год назад

Great channel! Clear explanations. In HCA, could you not follow up the clustering of rows (genes) by clustering the columns (samples)? Is this automatically done? Does not seem like the best heatmap would be produced if you just cluster/shuffle rows. Would have to cluster/shuffle columns, too, right? Also, must/should the data be standardized first?

@statquest Год назад

You can cluster both columns and rows. And sometimes standardizing helps, sometimes it doesn't. It's worth trying both options.

@mikecy5507 Год назад

@@statquest Thanks!

@naturelove9396 3 года назад

Hey you explain this very well and in very simple form thanks for this, I request you could you please make one video on DEGseq2, means finding DEG gene between the time points and then drawing the heatmap, volcano plot and cluster lines. Thanks

@statquest 3 года назад

I'll keep that in mind. I already have a few videos on DESeq2 here: statquest.org/video-index/

@samhobbs4996 4 года назад

Great video

@statquest 4 года назад

Thanks! :)

@khawlaou5385 Год назад

You're THE BEST

@statquest Год назад

Thanks!

@soffapute 3 года назад

Love the song!

@statquest 3 года назад

@manuelsokolov Год назад

Dear StatQuest! Thank you for the explanation. 1. What is the best would you would evaluate the algorithm (silluete score,...) to decide which clustering method and distance to use ( i undestand that silluete score is good to choose the number of k but not to decide between algorithms)? To decide the best algorithm i have been ploting PCA and color label by clusters created this way understanding if the clusters make sense or not? (however it is known by literature that PCA does not work well to evaluate binary data) 2. In the case that the data is binary, (e.g instead of expression data, genomic alteration data) what kind of distance would you use? Best Regards, Manuel

@statquest Год назад

1) I guess it depends. If I had "training" data, with known categories, I would compare how many times the data were correctly and incorrectly grouped. Otherwise, it really just boils down to subjective preference. 2) If you measure a lot of things, the euclidian distance will still work in this situation.

@yvonnemadegwa967 5 лет назад

Thank you very much! Can you teach software's? Like R-basic introduction, basics of how to arrange date with various commands?

@statquest 5 лет назад

I have a handful of videos that teach you how to do certain things in R. They don't start at the very beginning, but I still go one step at a time. You can find these videos on the index page: statquest.org/video-index/

@yvonnemadegwa967 5 лет назад

@@statquest Thank you very much.

@daminithandele7237 4 года назад

Hi Josh! Can you please make a video on DBSCAN, if possible? Especially the parameter tuning part of it, I'm sure that would be of great help to lots of people.

@statquest 4 года назад

I'll keep that in mind.

@Argho555 2 месяца назад

Thank You

@statquest 2 месяца назад

@hamidkiangaikani 2 года назад

4.4 K likes, zero dislikes! You're awesome. Thanks very much

@statquest 2 года назад

bam!

@snay6869 Год назад

thank you so much!

@statquest Год назад

@mountainsunset816 Год назад

The opening is always funny

@statquest Год назад

@chuxbouch2793 3 года назад

You're amaaaaaazing

@statquest 3 года назад

Thanks!

@emamulmursalin9181 3 года назад

Great explanation Josh! Just one question, are we clustering samples(data points) or the Genes(features)? If we are clustering Genese, does not it mean that we are just clustering the correlated features?

@statquest 3 года назад

In this video we are clustering the genes, and yes, the idea is that correlated features are brought together. We could even just calculate the correlation coefficient for each pair and cluster based on those values.

@emamulmursalin9181 3 года назад

@@statquest Thanks for your reply. But I have seen some other blogs where authors are plotting 2D data points and using hierarchical clustering. So in real life we use hierarchical clustering for data clustering or feature clustering?

@statquest 3 года назад

@@emamulmursalin9181 I'm not sure what you mean by "data" clustering, however, we can cluster the rows or the columns with similar ease. It doesn't matter if one is features and the other is samples.

@emamulmursalin9181 3 года назад

@@statquest Sorry for using an unclear term. Actually I meant "samples" by using the term "data". So, can hierarchical clustering be used for "feature clustering" (for example, finding correlated features and remove the redundant features) and also as "sample clustering" (e.g. just like K means clustering ) ?

@statquest 3 года назад

@@emamulmursalin9181 Yes. We can cluster the rows just as easily as we cluster the columns.

@kanacaredes 3 года назад

Hi Josh!! We need a DBSCAN tutorial please!!!!

@statquest 3 года назад

I'll keep that in mind! :)

@monishaathikesavanpremalat7587 4 года назад

How to validate these clustering techniques? I mean for a given dataset, let’s assume I have tried various hierarchical clustering techniques like single linkage, complete linkage, etc using various distance matrix for each method. How to pick the right one from all these different clusters which has been formed for that particular dataset

@statquest 4 года назад

This is going to sound very disappointing, but since these methods are generally used to explore data and extract new insights from it, then you pick the method that gives you the most insight. So try them and see if one makes more sense than the others.

@anthonychan4478 5 лет назад

Hi Joshua, can you do a video on Gaussian Mixture Models? Also, your videos are awesome! Keep it up.

@statquest 5 лет назад

The good news is that is already on the To-Do list. I'll bump it up a notch since you requested it as well.

@jordanmakesmaps 5 лет назад

@@statquest, make that two requests! Thanks!

@statquest 5 лет назад

@@jordanmakesmaps Cool! It's in the top 10 things for me to do, so hopefully I'll get to it soon.

@jacobmoore8734 5 лет назад

@@statquestYes! Anytime people start talking about gaussian mixture models, EM, "sampling the posterior", and MCMCs - I get cold sweats.

@huikianong1695 3 года назад

Hi may I know how about the clustering of the column? Is it possible to cluster the column and row at the same time? Correct me if I am wrong, clustering the row meaning to group genes that have similar expression together from different sample ? Clustering column meaning to group the samples with similar gene expression?

@statquest 3 года назад

Sure! You can cluster both the rows and columns at the same time.

@tudorpricop5434 10 месяцев назад

At 7:28, we calculated the number 3.2 being the difference between gene 1 and gene 2. But the whole purpose of calculating is to figure out which gene is the most similar with gene 1 (for example). Now my question: After we compute the values between [gene 1 and gene 2], [gene 1 and gene 3] and [gene 1 and gene 4], we select the gene with the SMALLEST VALUE as the most similar gene to gene 1 ? Or the BIGGEST VALUE ? I think the smallest, but just to be sure..

@statquest 10 месяцев назад

In this case we want the smallest distance, which means the most similar.