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Show HN: TabPFN v2 – A SOTA foundation model for small tabular data (nature.com)

152 points by onasta ↗ HN
I am excited to announce the release of TabPFN v2, a tabular foundation model that delivers state-of-the-art predictions on small datasets in just 2.8 seconds for classification and 4.8 seconds for regression compared to strong baselines tuned for 4 hours. Published in Nature, this model outperforms traditional methods on datasets with up to 10,000 samples and 500 features.

The model is available under an open license: a derivative of the Apache 2 license with a single modification, adding an enhanced attribution requirement inspired by the Llama 3 license: https://github.com/PriorLabs/tabpfn. You can also try it via API: https://github.com/PriorLabs/tabpfn-client

TabPFN v2 is trained on 130 million synthetic tabular prediction datasets to perform in-context learning and output a predictive distribution for the test data points. Each dataset acts as one meta-datapoint to train the TabPFN weights with SGD. As a foundation model, TabPFN allows for fine-tuning, density estimation and data generation.

Compared to TabPFN v1, v2 now natively supports categorical features and missing values. TabPFN v2 performs just as well on datasets with or without these. It also handles outliers and uninformative features naturally, problems that often throw off standard neural nets.

TabPFN v2 performs as well with half the data as the next best baseline (CatBoost) with all the data.

We also compared TabPFN to the SOTA AutoML system AutoGluon 1.0. Standard TabPFN already outperforms AutoGluon on classification and ties on regression, but ensembling multiple TabPFNs in TabPFN v2 (PHE) is even better.

There are some limitations: TabPFN v2 is very fast to train and does not require hyperparameter tuning, but inference is slow. The model is also only designed for datasets up to 10k data points and 500 features. While it may perform well on larger datasets, it hasn't been our focus.

We're actively working on removing these limitations and intend to release new versions of TabPFN that can handle larger datasets, have faster inference and perform in additional predictive settings such as time-series and recommender systems.

We would love for you to try out TabPFN v2 and give us your feedback!

50 comments

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instanceofme
Related: CARTE-AI, which can also deal with multiple tables.

https://soda-inria.github.io/carte/ https://arxiv.org/pdf/2402.16785

The paper includes a comparison to TabPFN v1 (among others), noting the lack of categorical & missing values handling which v2 now seems to have. Would be curious to see an updated comparison.

onasta
TabPFN is better on numerical data since v1 (see figure 6 in the CARTE paper). CARTE's main strength in on text features, which are now also supported for TabPFN v2 API version (https://github.com/PriorLabs/tabpfn-client). We compared this to CARTE and found our model to be generally quite better, and much faster. CARTE multi-table approach is also very interesting, and we want to tackle this setting in the future.
bbstats
looks amazing - finally, DL that beats a tuned catboost?
_giorgio_
It's probably the same model with the same limitations, released nearly two years ago?

https://arxiv.org/abs/2207.01848

ersiees
No, it is *much* stronger, a different architecture and scales to 10x the number of examples. It can also do regression now, and handle categorical features. Please, have a quick look at the abstract before making such claims.
onasta
There have been a ton of improvements! Much better performance overall, way larger data size limit (1K-->10K rows, 100-->500 features), regression support, native categorical data and missing values handling, much better support for uninformative or outlier features etc.
enigmaa99
I tried this on a few CARTE datasets and it works surprisingly better!! Woahhh
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peepeepoopoo99
How can you train a tabular foundation model when the tabular features themselves are inherently domain-specific? Is there some kind of preprocessing step beforehand to match the inference time features with their closest analogues in the training set?
ersiees
Yes, there are normalizations applied before the features are fed to the neural network. Additionally, the neural network is trained on a very diverse set of artificial datasets.
hooloovoo_zoo
Were your benchmark methods tuned per dataset or across datasets?
ersiees
Tuned per dataset
noahho
Up to 4 hrs of tuning per dataset / split (10-fold CV)
gcr
Thanks for such a cool project! It's immediately apparent how to use it and I appreciate the brief examples.

Quick question: In the breast cancer example from the README, simple support vector machines from sklearn (the first thing i tried to compare baseline performance, incidentally) seem to outperform TabPFN. Is this expected? I know it's a baseline to demonstrate ease of use rather than SOTA performance, but I am curious.

    # (TabPFN)
    In [13]: print("ROC AUC:", roc_auc_score(y_test, prediction_probabilities[:, 1]))
    ROC AUC: 0.996299494264216

    # (LinearSVC)
    In [27]: from sklearn.svm import LinearSVC
    
    In [28]: clf=LinearSVC(C=0.01).fit(X_train, y_train)
    
    In [29]: roc_auc_score(y_test, clf.decision_function(X_test))
    Out[29]: 0.997532996176144
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noahho
Author here! The breast cancer dataset is simple and heavily saturated, so small differences between methods are expected. As you say, single-use examples can be noisy due to randomness in how the data is randomly split into training and testing sets especially for a saturated dataset like this one. Cross-validation reduces this variance by averaging over multiple splits. I just ran this below:

  TabPFN mean ROC AUC: 0.9973

  SVM mean ROC AUC: 0.9903

  TabPFN per split: [0.99737963 0.99639699 0.99966931 0.99338624 0.99966465]

  SVM per split: [0.99312152 0.98788077 0.99603175 0.98313492 0.99128102]

  from sklearn.model_selection import cross_val_score
  from tabpfn import TabPFNClassifier
  from sklearn.datasets import load_breast_cancer
  from sklearn.svm import LinearSVC
  import numpy as np

  data = load_breast_cancer()
  X, y = data.data, data.target

  # TabPFN
  tabpfn_clf = TabPFNClassifier()
  tabpfn_scores = cross_val_score(tabpfn_clf, X, y, cv=5, 
  scoring='roc_auc')
  print("TabPFN per split:", tabpfn_scores)
  print("TabPFN mean ROC AUC:", np.mean(tabpfn_scores))
  
  # SVM
  svm_clf = LinearSVC(C=0.01)
  svm_scores = cross_val_score(svm_clf, X, y, cv=5, 
  scoring='roc_auc')
  print("SVM per split:", svm_scores)
  print("SVM mean ROC AUC:", np.mean(svm_scores))
It's hard to communicate this properly, we should probably make sure to have a favourable example ready, but just included the simplest one!
gcr
thanks, this is helpful!

I certainly appreciate how the example in the README makes it instantly apparent how to use the code.

nickpsecurity
A while back, I was looking for a project amateurs could do for experimenting with Transformer alternatives and optimization algorithms. My concept was grabbing objective, test functions from the literature, making custom ones based on realistic data, and layering them together based on real-world depth. Then, training various approaches on them using consumer GPU’s or spot instances of high-end GPU’s.

What I read in this paper blew that idea out the water! I mean, it’s still doable but you’ve far exceeded it.

I love that you covered many types of structures, used 8x consumer GPU’s more like OSS folks do (widely-accessible pretraining), claim no copyright infringement for pretraining, and use enough techniques in ML that people can enjoy Googling stuff for days.

I do have some questions about what I might have overlooked in the paper.

1. Is the training data and code available to reproduce the model? And iteratively improve its architectural decisions?

2. Most authors claiming their data was legal or open were actually committing copyright infringement. Your method might dodge that if users generate their own synthetic data using methods they can verify aren’t themselves encumbered. Is that code available under open licensing? If not, would you offer it for a fee for companies or free for researchers?

3. What specific, common uses could amateurs try that would display the model’s ability in a business setting? (Both to drive more research or build products on the model.)

I thank you for your time.

ersiees
Author here!

Thanks :)

1. Only for the first version, not for this version. I am sorry! 2. Yeah ours is guaranteed ok, as we wrote code to generate it basically just from plain torch ops. The code to run inference is available, just not the training code and data generation. 3. We have put it to work on time series data, which is very business relevant for example https://github.com/liam-sbhoo/tabpfn-time-series, and we have a table in the Appendix with all datasets we evaluate on in our main analysis to give you some ideas for possible datasets.

nickpsecurity
“Yeah ours is guaranteed ok, as we wrote code to generate it basically just from plain torch ops.”

This is where there might be claims. It already sounds safer than training on copyrighted works. The only thing that could remain is if it was a derivative work by reusing parts of copyrighted works in your process.

So, I’m curious about how you produced the specifications that the data was generated from. In my case, I was going to just use open versions of all kinds of equations that I’d hand-convert to internal representations. Others might be fair use if my description were high level enough that it wasn’t close to theirs. Some I couldn’t use at all because they were patented and independent versions are prohibited by law.

Did you all also derive your causal models from real-world formulas and data sets? If so, did you have a rule about putting distance between your representation and theirs? Or was it an entirely-random, search process across endless configurations? (I have a hard time imagining the latter would work.)

tmostak
This looks amazing!

Just looking through the code a bit, it seems that the model both supports a (custom) attention mechanism between features and between rows (code uses the term items)? If so, does the attention between rows help improve accuracy significantly?

Generally, for standard regression and classification use cases, rows (observations) are seen to be independent, but I'm guessing cross-row attention might help the model see the gestalt of the data in some way that improves accuracy even when the independence assumption holds?

dist-epoch
Speculating, cross-row might give you information where you are in that row distribution.
ersiees
Author here: The new introduction of attention between features did make a big impact compared to the first variant of TabPFN. The old model handled every feature like it was completely different to be feature 5 vs 15, but actually features are typically more-or-less permutation invariant. So the logic is similar to why a CNN is better for images than an MLP.
patcon
Neat! Might this even be useful to impute missing data for a sparse network of votes, for a system like this (pol.is) whose goal is to do dimensional reduction and visualise the opinion space of divisive social topics: https://gwern.net/doc/sociology/2021-small.pdf

200 voters on 50 statements would fall within the 10,000 sample threshold. This is well within the bounds of some existing conversations with open data, so it could be tested... Potential values on each statement are agree/disagree/pass (+1/-1/0)

https://github.com/compdemocracy/openData/blob/master/brexit...

https://github.com/compdemocracy/openData/blob/master/brexit...

burglarhobbit
> 200 voters on 50 statements would fall within the 10,000 sample threshold.

I think you misinterpreted. 1 voter on 50 statements with (+1/-1/0) would be 1 datapoint with 50 features. 200 voters would be 200 rows with 50 features so you would not need to be concerned about the 10,000 sample threshold. Hope that helps your study.

storyweaver2
Did you compare the performance with o1 or Claude 3.5 Sonnet？
noahho
Author here! The fundamental challenge is that LLMs like O1 and Claude 3.5 simply aren't built for the unique structures of tabular data. When processing tables through LLMs, the inefficiencies quickly become apparent - tokenizing a 10,000 x 100 table as a sequence and numerical values as tokens creates massive inefficiencies.

There's some interesting work on using LLMs for tabular data (TabLLM: https://proceedings.mlr.press/v206/hegselmann23a.html), but this only works for datasets with tens of samples rather than the thousands of rows needed in real-world applications.

What o1 and other LLMs typically do is wrap around existing tabular tools like XGBoost or scikit-learn. While this works, they're ultimately constrained by these tools' limitations. We're taking a fundamentally different approach - building foundation models that natively understand tabular relationships and patterns. Our approach combines the benefits of foundation models with architectures specifically designed for tabular data structures.

pplonski86
Amazing results! Beating AutoML with single model is not easy :)

Could you please explain like I'm five what is doing a trick? You have model pre-trained on large set of small datasets and you leverage it to boost performance?

Training is fast, few seconds, but what is time needed to compute predictions?

How large is the model?

ersiees
To put it very simply, the trick is that while the others train a new model for each problem, TabPFN is pre-trained to handle any kind of problem on the fly.

To draw a parallel to NLP: previously people trained a neural network for each kind of text classification they wanted to do, but then LLMs came around that pre-trained to learn to perform new tasks on the fly. Similarly, TabPFN learns to do new tasks on the fly just from the context (dataset) given.

Training and prediction in these models is by default one and the same, similar to how the prediction of the next token in an LLM is not split into learning from context and then doing the actual prediction. There is a way to split this even up, though, then the predictions, I believe, take something like 1/10s for medium-sized datasets.

Dowwie
Congrats on your release. What is the best way to share feedback? I would like to share with you what I believe to be a challenging problem that this may help with.
mlepath
Great work!

Do you see any artifacts from having trained on synthetic data? Is there a natural benchmark dataset (real tables in the wild)?

In my experience synthetic data can only take you so far, it has all the quirk the dataset creator can think of but the real value is usually in patterns they cannot. Vision took a huge leap forward with ImageNet dataset release

noahho
Thanks a lot! We don't see clear artifacts for the synth data. Part of the "trick" is to keep the capacity of our model low, it has only about 11M parameters. That forces the model to "learn an in-context learning algorithm" or in other words "do in-context learning rather than in-weigthts learning". Adding real data on top will help, agreed! The synthetic data is very broad, we started by a synth data prior that was just BNNs samples with differing sizes and thus super broad. Our new data samples functions more densely that are simpler to explain but could still sample almost any function (with the constraints that our networks aren't infinitely complex).
lcrmorin
Thanks for sharing this. Of course I will closely watch it because claiming to beat gbdts might be a bit early.

- It is not entirely clear how the datasets split is done. Do you make sure that the model is evaluated on unseen data ? More generally how does one knows whether a dataset was part of the training or not ?

- You mention some serious limitations (10k rows, 500 cols.). It seems a bit weird to have fixed numbers. Can these numbers be roughly balanced ? (eg. 1M rows, 5 columns ... ). Does these numbers scale with memory ? (what memory was used for the 10k rows / 500 cols figure ?)

jacob019
Found the web interface: https://ux.priorlabs.ai/ Really cool!

Just playing around with regression mode...

    A very simple dataset, powers of two: 
    1:2, 2:4, 3:8, 5:32, 6:64, 7:128 (missing the #4 value)
    Predictions (1-10): 
    1.582 5.236 13.150 22.943 37.584 67.475 109.945 155.322 218.001 10,300.425
    Error (1-10): 
    -26.4% 23.6% 39.2% 30.3% 14.9% 5.2% -16.4% -64.8% -134.9% -240.9%
... well, it has a positive slope

Let's see what happens if we copy the exact same values in the dataset 10 times first.

    Predictions (1-10): 
    1.993 3.967 7.986 18.138 31.965 64.140 128.125 126.607 130.667 161.756 
    Error (1-10): 
    -0.3% -0.8% -0.2% 11.8% -0.1% 0.2% 0.1% -102.2% -291.8% -533.1%
Interesting, repeated values give the model a lot more confidence of the known values. The interpolated #4 value is still off by 12%. It does not extrapolate well at all.

Looking forward to trying it on real world data with more features.

noahho
Yes! This makes sense from a learning perspective: More samples add additional evidence the datapoint is actually what you observed - based on one sample the model is closer to a mean regression (which would translate to more balanced class probabilities in classification). Transformers have trouble counting repeated entries (there was a famous failure case of ChatGPT, asking it to count the number of 1s and 0s in a string). This model has some tricks to solve this.
fuenal
Great work you guys! I have been following discussions on DL vs ML for tabular data for some time now and am very excited to see TabPFN perform so well. I would like to play around with it a bit and am wondering if there is a way to use TabPFN with larger sample sizes, say, 1000000 rows? Can I disable the 10000 sample limitation? I would appreciate a code example if so. Great work again!