Tabular Data: Deep Learning is Not All You Need

Ravid Shwartz-ZivAmitai Armon

article2021Information Fusion2,296 citations

Demonstrates that XGBoost consistently outperforms specialized deep learning architectures across tabular benchmarks while requiring far less tuning, establishing that deep models are most valuable when ensembled with tree-based methods rather than used as standalone replacements.

arXiv: 2106.03253
  • Paper: TabNet: Attentive Interpretable Tabular Learning, Sercan Ö. Arik et al. (2019). Introduces TabNet, one of the primary deep learning architectures for tabular data whose empirical claims of outperforming gradient-boosted trees are directly evaluated and challenged by the source paper.
  • Paper: XGBoost: A Scalable Tree Boosting System, Tianqi Chen et al. (2016). Presents XGBoost, the foundational scalable gradient tree boosting framework that serves as the central baseline against which deep tabular architectures are benchmarked.
  • Paper: A comparative analysis of gradient boosting algorithms, Candice Bentéjac et al. (2019). Provides a comprehensive comparative analysis of modern gradient boosting algorithms, establishing standard benchmark methodologies and hyperparameter tuning dynamics for tree ensembles on tabular datasets.
  • Paper: CatBoost: unbiased boosting with categorical features, Liudmila Prokhorenkova et al. (2018). Introduces CatBoost and key techniques for handling categorical features in tree boosting, offering vital context for why tree ensembles excel on tabular data.
  • Paper: Greedy function approximation: A gradient boosting machine, Jerome H. Friedman (2001). Establishes the fundamental theoretical framework of gradient boosting machines that underpins tree ensemble baselines evaluated in the source study.
  • Paper: Accurate predictions on small data with a tabular foundation model, Noah Hollmann et al. (2025). Advances beyond the limitations of earlier deep tabular models discussed in the source by introducing TabPFN, a transformer-based tabular foundation model that achieves competitive predictive performance with in-context learning without extensive tuning.
Cover for Tabular Data: Deep Learning is Not All You Need

Abstract

A key element in solving real-life data science problems is selecting the types of models to use. Tree ensemble models (such as XGBoost) are usually recommended for classification and regression problems with tabular data. However, several deep learning models for tabular data have recently been proposed, claiming to outperform XGBoost for some use cases. This paper explores whether these deep models should be a recommended option for tabular data by rigorously comparing the new deep models to XGBoost on various datasets. In addition to systematically comparing their performance, we consider the tuning and computation they require. Our study shows that XGBoost outperforms these deep models across the datasets, including the datasets used in the papers that proposed the deep models. We also demonstrate that XGBoost requires much less tuning. On the positive side, we show that an ensemble of deep models and XGBoost performs better on these datasets than XGBoost alone.

Table of Contents

  • 1 Introduction
  • 2 Background
  • 2.1 Deep Neural Models for Tabular Data
  • 2.2 Model Ensemble
  • 3 Comparing the Models
  • 3.1 Experimental Setup
  • 3.1.1 Data-sets Description
  • 3.1.2 Implementation Details
  • 3.2 Results
  • 4 Discussion and Conclusions
  • References
  • A Tabular Data-sets Description
  • B Optimization of hyperparameters
  • B.1 CATBOOST
  • B.2 XGBoost
  • B.3 NODE
  • B.4 TabNet
  • B.5 DNF-Net
  • B.6 1D-CNN

Knowls

  1. Knowl 1 — Performance of Deep Tabular Architectures vs. XGBoost on Tabular Benchmarks

    data/table

    Across eleven tabular benchmarks spanning classification and regression tasks, deep learning models (TabNet, NODE, DNF-Net, and 1D-CNN) were evaluated alongside XGBoost, simple uniform ensembles, deep-only ensembles, and combined deep-plus-tree ensembles. Performance is measured using Mean Squared Error (MSE) for regression tasks (Rossmann and YearPrediction) and Cross-Entropy loss multiplied by a factor of 100 for classification tasks. Values represent the mean and standard error of the mean (SEM) over four training runs.

    Model Rossmann CoverType Higgs Gas Eye Gesture
    XGBoost 490.18±1.19490.18 \pm 1.19 3.13±0.093.13 \pm 0.09 21.62±0.3321.62 \pm 0.33 2.18±0.202.18 \pm 0.20 56.07±0.6556.07 \pm 0.65 80.64±0.8080.64 \pm 0.80
    NODE 488.59±1.24488.59 \pm 1.24 4.15±0.134.15 \pm 0.13 21.19±0.6921.19 \pm 0.69 2.17±0.182.17 \pm 0.18 68.35±0.6668.35 \pm 0.66 92.12±0.8292.12 \pm 0.82
    DNF-Net 503.83±1.41503.83 \pm 1.41 3.96±0.113.96 \pm 0.11 23.68±0.8323.68 \pm 0.83 1.44±0.091.44 \pm 0.09 68.38±0.6568.38 \pm 0.65 86.98±0.7486.98 \pm 0.74
    TabNet 485.12±1.93485.12 \pm 1.93 3.01±0.083.01 \pm 0.08 21.14±0.2021.14 \pm 0.20 1.92±0.141.92 \pm 0.14 67.13±0.6967.13 \pm 0.69 96.42±0.8796.42 \pm 0.87
    1D-CNN 493.81±2.23493.81 \pm 2.23 3.51±0.133.51 \pm 0.13 22.33±0.7322.33 \pm 0.73 1.79±0.191.79 \pm 0.19 67.90±0.6467.90 \pm 0.64 97.89±0.8297.89 \pm 0.82
    Simple Ensemble 488.57±2.14488.57 \pm 2.14 3.19±0.183.19 \pm 0.18 22.46±0.3822.46 \pm 0.38 2.36±0.132.36 \pm 0.13 58.72±0.6758.72 \pm 0.67 89.45±0.8989.45 \pm 0.89
    Deep Ensemble w/o XGBoost 489.94±2.09489.94 \pm 2.09 3.52±0.103.52 \pm 0.10 22.41±0.5422.41 \pm 0.54 1.98±0.131.98 \pm 0.13 69.28±0.6269.28 \pm 0.62 93.50±0.7593.50 \pm 0.75
    Deep Ensemble w XGBoost 485.33±1.29485.33 \pm 1.29 2.99±0.082.99 \pm 0.08 22.34±0.8122.34 \pm 0.81 1.69±0.101.69 \pm 0.10 59.43±0.6059.43 \pm 0.60 78.93±0.7378.93 \pm 0.73
    Model YearPrediction MSLR Epsilon Shrutime Blastchar
    XGBoost 77.98±0.1177.98 \pm 0.11 55.43±0.0255.43 \pm 0.02 11.12±0.0311.12 \pm 0.03 13.82±0.1913.82 \pm 0.19 20.39±0.2120.39 \pm 0.21
    NODE 76.39±0.1376.39 \pm 0.13 55.72±0.0355.72 \pm 0.03 10.39±0.0110.39 \pm 0.01 14.61±0.1014.61 \pm 0.10 21.40±0.2521.40 \pm 0.25
    DNF-Net 81.21±0.1881.21 \pm 0.18 56.83±0.0356.83 \pm 0.03 12.23±0.0412.23 \pm 0.04 16.80±0.0916.80 \pm 0.09 27.91±0.1727.91 \pm 0.17
    TabNet 83.19±0.1983.19 \pm 0.19 56.04±0.0156.04 \pm 0.01 11.92±0.0311.92 \pm 0.03 14.94±0.1314.94 \pm 0.13 23.72±0.1923.72 \pm 0.19
    1D-CNN 78.94±0.1478.94 \pm 0.14 55.97±0.0455.97 \pm 0.04 11.08±0.0611.08 \pm 0.06 15.31±0.1615.31 \pm 0.16 24.68±0.2224.68 \pm 0.22
    Simple Ensemble 78.01±0.1778.01 \pm 0.17 55.46±0.0455.46 \pm 0.04 11.07±0.0411.07 \pm 0.04 13.61±0.1413.61 \pm 0.14 21.18±0.1721.18 \pm 0.17
    Deep Ensemble w/o XGBoost 78.99±0.1178.99 \pm 0.11 55.59±0.0355.59 \pm 0.03 10.95±0.0110.95 \pm 0.01 14.69±0.1114.69 \pm 0.11 24.25±0.2224.25 \pm 0.22
    Deep Ensemble w XGBoost 76.19±0.2176.19 \pm 0.21 55.38±0.0155.38 \pm 0.01 11.18±0.0111.18 \pm 0.01 13.10±0.1513.10 \pm 0.15 20.18±0.1620.18 \pm 0.16

    The benchmark shows two core patterns: first, each deep model demonstrates competitive performance primarily on the datasets introduced in its originating paper, but underperforms on datasets outside its original study. Second, XGBoost outperforms deep models on 8 of the 11 datasets when evaluated on datasets new to those models (p<0.005p < 0.005 under the non-parametric Friedman test). The combined ensemble of XGBoost and deep neural networks achieves the overall best results across 7 of 11 tasks.

  2. Knowl 2 — Generalization Deterioration of Deep Tabular Models on Unseen Datasets

    empirical result

    When evaluated on datasets not included in their original introducing papers (unseen datasets), deep neural models exhibit substantial performance degradation compared to the dataset-best model. The geometric mean of the relative performance increase/deterioration across unseen datasets is:

    Model Average Relative Deterioration (%)
    Deep Ensemble w XGBoost 2.32
    Simple Ensemble 3.15
    XGBoost 3.34
    Deep Ensemble w/o XGBoost 6.91
    1D-CNN 7.56
    TabNet 10.51
    DNF-Net 11.96
    NODE 14.21

    Individual deep tabular networks degrade by 7.56%7.56\% to 14.21%14.21\% relative to the top performer on unseen datasets, whereas standalone XGBoost experiences only a 3.34%3.34\% deterioration. The hybrid ensemble combining all deep architectures with XGBoost attains the lowest deterioration (2.32%2.32\%, with all pairwise differences yielding p<0.005p < 0.005 except one).

  3. Knowl 3 — Ensembling Deep Learning Models with XGBoost for Tabular Data

    model/method

    To combine deep models (TabNet, NODE, DNF-Net, 1D-CNN) and gradient boosted decision trees (XGBoost), two ensembling schemes are used over KK base models with parameter sets θ1,,θK\theta_1, \dots, \theta_K:

    1. Uniform Mixture Ensemble: p(yx)=1Kk=1Kp(yx,θk)p(y \mid x) = \frac{1}{K} \sum_{k=1}^K p(y \mid x, \theta_k)

    2. Validation-Loss-Weighted Ensemble: p(yx)=k=1Klkvalp(yx,θk)p(y \mid x) = \sum_{k=1}^K l_k^{\text{val}} p(y \mid x, \theta_k) where lkvall_k^{\text{val}} represents the normalized validation loss weight assigned to the kk-th model such that k=1Klkval=1\sum_{k=1}^K l_k^{\text{val}} = 1. Each base learner is trained independently on the entire training set to minimize bias, and predictions are aggregated to reduce prediction variance.

  4. Knowl 4 — Comparative Superiority of Hybrid Deep-Tree Ensembles over Homogeneous Ensembles

    empirical result

    Ensembling both XGBoost and deep tabular networks yields statistically significant improvements over homogeneous ensembles:

    1. A combined ensemble of XGBoost and deep models outperforms an ensemble consisting solely of deep networks (Deep Ensemble w/o XGBoost) across all tested datasets (p<0.005p < 0.005).
    2. A combined ensemble of XGBoost and deep models outperforms an ensemble composed exclusively of classical machine learning models (XGBoost, SVM, and CatBoost) with p<0.005p < 0.005.

    This confirms that deep architectures and tree-based gradient boosting models learn complementary representations on tabular datasets, making heterogeneous ensembling strictly superior to ensembling either model family alone.

  5. Knowl 5 — Validation-Loss-Based Model Selection for Ensemble Pruning

    empirical result

    When computational or latency constraints restrict the number of base models in an ensemble, greedy selection based on validation loss provides the most effective subset selection strategy.

    Evaluating three model selection policies—(1) ranking models by validation loss, (2) selecting models based on sample-level predictive confidence/uncertainty, and (3) random ordering—demonstrates that validation-loss-based selection achieves near-optimal ensemble loss with only the top 3 models. In contrast, confidence-based and random selection strategies exhibit slower convergence and significantly inferior predictive performance for early subset sizes (p<0.005p < 0.005).

  6. Knowl 6 — Hyperparameter Optimization Efficiency and Convergence Dynamics

    empirical result

    Under Bayesian hyperparameter optimization using HyperOpt across 1,000 iterations:

    1. Iteration Convergence: XGBoost reaches a performance plateau in significantly fewer optimization steps than deep tabular architectures (NODE, DNF-Net, TabNet, 1D-CNN), which require hundreds of additional trials to discover competitive configurations.
    2. Computational Runtime: Standalone XGBoost training and tuning is more than an order of magnitude faster in wall-clock time compared to the deep tabular neural networks.
    3. Default Robustness: The rapid plateau of XGBoost indicates greater robustness to initial hyperparameter settings compared to tabular deep networks, whose performance is highly sensitive to architecture-specific hyperparameter search spaces.
  7. Knowl 7 — Tabular Evaluation Benchmark Suite and Standardization Protocol

    experimental setup

    The benchmark protocol encompasses 11 diverse tabular datasets spanning binary classification, multi-class classification, and regression tasks:

    Dataset Features Classes Samples Source / Paper
    Gesture Phase 32 5 9.8k9.8\text{k} OpenML (DNF-Net)
    Gas Concentrations 129 6 13.9k13.9\text{k} OpenML (DNF-Net)
    Eye Movements 26 3 10.9k10.9\text{k} OpenML (DNF-Net)
    Epsilon 2000 2 500k500\text{k} PASCAL Challenge 2008 (NODE)
    YearPrediction 90 1 515k515\text{k} Million Song Dataset (NODE)
    Microsoft (MSLR) 136 5 964k964\text{k} MSLR-WEB10K (NODE)
    Rossmann Store Sales 10 1 1018k1018\text{k} Kaggle (TabNet)
    Forest Cover Type 54 7 580k580\text{k} Kaggle (TabNet)
    Higgs Boson 30 2 800k800\text{k} Kaggle (TabNet)
    Shrutime 11 2 10k10\text{k} Kaggle (New dataset)
    Blastchar 20 2 7k7\text{k} Kaggle (New dataset)

    Standardization and Training Protocol:

    • Features are standardized to zero mean and unit variance using statistics derived strictly from training partitions.
    • Stratified splits follow the source papers (e.g., 80%/20%80\%/20\% train/validation for Epsilon, YearPrediction, MSLR, Shrutime, Blastchar; 70%/10%/20%70\%/10\%/20\% train/val/test for Eye, Gesture, Year).
    • Deep models are trained with the Adam optimizer without learning rate schedules, utilizing batch size optimization and early stopping after 100 consecutive epochs without validation loss improvement.
    • Hyperparameter optimization is executed for 1,000 steps per dataset per model using HyperOpt.
  8. Knowl 8 — Hyperparameter Search Spaces for Tree-Based and Deep Tabular Models

    experimental setup

    Hyperparameter search spaces optimized via Bayesian optimization (HyperOpt) for 1,000 steps across models are defined as follows:

    XGBoost:

    • Number of estimators: Uniform [100,4000][100, 4000]
    • Eta (learning rate): Log-Uniform [e7,1][e^{-7}, 1]
    • Max depth: Discrete uniform [1,10][1, 10]
    • Subsample: Uniform [0.2,1][0.2, 1]
    • Colsample bytree: Uniform [0.2,1][0.2, 1]
    • Colsample bylevel: Uniform [0.2,1][0.2, 1]
    • Min child weight: Log-Uniform [e16,e5][e^{-16}, e^5]
    • Alpha, Lambda, Gamma: Choice {0,Log-Uniform[e16,e2]}\{0, \text{Log-Uniform}[e^{-16}, e^2]\}

    CatBoost:

    • Learning rate: Log-Uniform [e5,1][e^{-5}, 1]
    • Random strength: Discrete uniform [1,20][1, 20]
    • Max size: Discrete uniform [0,25][0, 25]
    • L2 leaf regularization: Log-Uniform [1,10][1, 10]
    • Bagging temperature: Uniform [0,1][0, 1]
    • Leaf estimation iterations: Discrete uniform [1,20][1, 20]

    NODE:

    • Learning rate: Log-Uniform [e5,1][e^{-5}, 1] and Log-Uniform [e4,0.5][e^{-4}, 0.5]
    • Number of layers: Discrete uniform [1,10][1, 10]
    • Total tree count: Choice {256,512,1024,2048}\{256, 512, 1024, 2048\}
    • Tree depth: Discrete uniform [4,9][4, 9]
    • Tree output dimension: Discrete uniform [1,5][1, 5]
    • Batch size: Choice {512,1024,2048,4096,8192}\{512, 1024, 2048, 4096, 8192\}

    TabNet:

    • Learning rate: Log-Uniform [e5,1][e^{-5}, 1]
    • Feature dimension, Output dimension: Discrete uniform [20,60][20, 60]
    • Number of steps: Discrete uniform [1,8][1, 8]
    • Batch normalization epsilon: Uniform [e5,e1][e^{-5}, e^{-1}]
    • Relaxation factor: Uniform [0.3,2][0.3, 2]
    • Batch size: Choice {512,1024,2048,4096,8192}\{512, 1024, 2048, 4096, 8192\}

    DNF-Net:

    • Number of formulas: Discrete uniform [256,2048][256, 2048]
    • Feature selection beta: Discrete uniform [102,2][10^{-2}, 2]
    • Learning rate: Log-Uniform [e4,0.5][e^{-4}, 0.5]
    • Batch size: Choice {512,1024,2048,4096,8192}\{512, 1024, 2048, 4096, 8192\}

    1D-CNN:

    • Hidden layer sizes: Discrete uniform [100,4000][100, 4000]
    • Number of layers: Discrete uniform [1,6][1, 6]
    • Learning rate: Log-Uniform [e4,0.5][e^{-4}, 0.5]
    • Batch size: Choice {512,1024,2048,4096,8192}\{512, 1024, 2048, 4096, 8192\}

Coverage note — All primary empirical findings, benchmark datasets, ensembling methods, subset selection dynamics, and hyperparameter search spaces have been fully captured. Summary overviews of prior published model architectures (TabNet, NODE, DNF-Net) were omitted as they represent existing work reviewed by the paper rather than original contributions.

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Citation

MLA
Shwartz-Ziv, R., and A. Armon. “Tabular Data: Deep Learning Is Not All You Need”. arXiv, 2021, http://arxiv.org/abs/2106.03253v2.
APA
Shwartz-Ziv, R., & Armon, A. (2021). Tabular Data: Deep Learning is Not All You Need. arXiv. http://arxiv.org/abs/2106.03253v2
Chicago
Shwartz-Ziv, R., and A. Armon. 2021. “Tabular Data: Deep Learning Is Not All You Need”. arXiv. http://arxiv.org/abs/2106.03253v2.
Harvard
Shwartz-Ziv, R. and Armon, A. (2021) “Tabular Data: Deep Learning is Not All You Need”, arXiv [Preprint]. Available at: http://arxiv.org/abs/2106.03253v2.
Vancouver
1. Shwartz-Ziv R, Armon A (2021) Tabular Data: Deep Learning is Not All You Need. arXiv

BibTeX

@article{shwartzziv2021tabular,
  title = {Tabular Data: Deep Learning is Not All You Need},
  author = {Shwartz-Ziv, Ravid and Armon, Amitai},
  year = {2021},
  journal = {arXiv},
  url = {http://arxiv.org/abs/2106.03253v2},
  eprint = {2106.03253}
}
Metadata:arXiv

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