Dataset pruning has been widely studied for 2D images to remove redundancy and accelerate training, while particular pruning methods for 3D data remain largely unexplored. In this work, we study dataset pruning for 3D data, where its observed common long-tail class distribution nature make optimization under conventional evaluation metrics Overall Accuracy (OA) and Mean Accuracy (mAcc) inherently conflicting, and further make pruning particularly challenging. To address this, we formulate pruning as approximating the full-data expected risk with a weighted subset, which reveals two key errors: coverage error from insufficient representativeness and prior-mismatch bias from inconsistency between subset-induced class weights and target metrics. We propose representation-aware subset selection with per-class retention quotas for long-tail coverage, and prior-invariant teacher supervision using calibrated soft labels and embedding-geometry distillation. The retention quota also serves as a switch to control the OA-mAcc trade-off. Extensive experiments on 3D datasets show that our method can improve both metrics across multiple settings while adapting to different downstream preferences. Our code is available at https://github.com/XiaohanZhao123/3D-Dataset-Pruning.
Figures & tables
Figure 1
Figure 2: Illustration of our 3D-Pruner framework, which comprises: (1) base principles (utilizing embedding signals, minimum floor selection, and optimizing structural likelihood in post-pruning training) that remain robust and beneficial across different priors, derived from theoretical analysis of the shared region, and (2) a steering warper that balances between the two priors.
Figure 3: Selection composition across algorithms. Incomparable scalar scores (loss, EL2N) bias selection toward many-shot classes. Geometric embedding selection is more robust but still partially affected by class distribution, under-selecting certain classes. SGS mitigates this, also enabling a flexible balancing.
Hard
KD
Rebalancing
OA
mAcc
OA
mAcc
CB-Samp. (CB)
79.02
61.20
82.09
64.56
CB-Loss
77.45
62.16
81.94
63.57
IB-Samp. (IB)
79.92
58.41
82.04
64.02
Sqrt-Samp. (Sqrt)
80.00
60.10
81.21
64.81
Mean ± Std
79.10 ± 1.18
60.47 ± 1.61
81.82 ± 0.41
64.24 ± 0.56
Table 2: KD improves accuracy and reduces sensitivity to rebalancing. Rebalancing policies include instance-balanced sampling (IB), class-balanced sampling (CB), and square-root sampling (Sqrt) ( Kang et al., 2019 ) , plus class-balanced loss (CB-Loss) ( Cui et al., 2019 ) . Results are obtained on ShapeNet55 with PointNet++, with imbalanced set selected by FL-RBF ( Wei et al., 2015 ) .
Signal
ρ (Corr. w/ Size) ↓
R2 (Dep. on Size) ↓
Overlap ↑
Imbalance Ratio ↓
Embedding
-0.306
0.148
96%
1.88x
Loss
0.635
0.145
26%
40.94x
EL2N
0.594
0.164
30%
33.01x
Entropy
0.731
0.481
26%
7.84x
Table 3: Signal Audit. We measure correlation ( ρ ) and dependence ( R2 ) of class-aggregated signal magnitude on class size, and head/tail score overlap. For embeddings, magnitude is distance to the class center. Embedding signals show minimal class-frequency dependence and high cross-class overlap , whereas scalar signals (Loss, EL2N) are dominated by the training prior, causing extreme selection imbalance (up to 40 × ).
Figure 4: Comparison of pruning methods across various datasets, models, and budgets on point cloud modality.
Figure 5: Impact of robust distillation methods: Calibrated Soft Label (CSL) and Embedding Geometry Distillation (EGD) on OA and mAcc. Results are obtained on PointNet++.
Figure 6: Comparison of pruning methods on mesh modality, legend following Fig. 4
ModelNet40
ScanObjectNN
ShapeNet55
m=400
m=800
m=1600
m=150
m=300
m=600
m=550
m=1100
m=2200
Metric Type
Selection Policy
OA
mAcc
OA
mAcc
OA
mAcc
OA
mAcc
OA
mAcc
OA
mAcc
OA
mAcc
OA
mAcc
OA
mAcc
Scalar Scores
Global Selection
Loss
56.36
47.76
75.97
65.97
88.24
82.43
35.84
35.60
52.36
51.37
63.15
61.10
55.21
20.12
60.13
25.34
67.87
25.38
GradNorm
44.61
35.72
70.22
59.32
87.96
79.62
45.70
36.22
51.84
42.47
60.40
50.63
62.82
22.60
67.39
27.18
71.06
31.54
Entropy
58.71
49.24
77.84
68.37
88.37
82.74
34.46
34.80
50.97
49.68
63.21
62.30
66.47
24.06
75.59
33.00
79.57
41.27
Table 4: Fair comparison of selection strategies on ModelNet40 , ScanObjectNN , and ShapeNet55 with Calibrated Soft Label and Embedding Geometry Distillation from 3D-Pruner applied to all baselines.
Figure 7: Preferences steering with different K.
Figure 8: Transferability of 3D-Pruner across different architecture. Results are based on m=1100 on ShapeNet55.
Appendix figures & tables4 assets
Supplementary material from the paper’s appendix.
Appendix
ShapeNet55
ModelNet40
ScanObjectNN
Model
OA
mAcc
OA
mAcc
OA
mAcc
PointNeXt-S
91.11
83.47
93.15
90.60
87.20
85.80
PointNet++
91.08
82.83
92.95
90.34
86.12
84.37
PointVector-S
91.00
82.96
90.15
85.31
87.37
85.64
Appendix
Table 5: Cross-dataset evaluation across 3D backbones. Overall accuracy (OA) and mean accuracy (mAcc) on ShapeNet55, ModelNet40, and ScanObjectNN.
Figure 9: Additional results on relaxed budgets on ShapeNet55. The gap on OA becomes smaller given larger budget, yet our 3D-Pruner remains the best on the mAcc.
ModelNet40
m=400
m=800
m=1200
Metric Type
Selection Policy
OA
mAcc
OA
mAcc
OA
mAcc
Scalar Scores
Stratified Sampling
Balance-EL2N
60.60
56.71
76.83
74.72
82.85
80.68
NUCS-EL2N
57.06
52.99
72.89
70.68
81.27
78.40
CCS-CP-EL2N
68.25
57.17
78.83
70.07
83.12
75.21
Appendix
Table 6: Comparison of different pruning methods on ModelNet40, MeshMAE. The pruning methods are selected from the most competitive ones based on the performance on the MeshNet.
PointNeXt-S
PointVector-S
m=550
m=1100
m=2200
m=550
m=1100
m=2200
Method
OA
mAcc
OA
mAcc
OA
mAcc
OA
mAcc
OA
mAcc
OA
mAcc
Loss
71.32
31.82
75.90
41.46
78.38
40.01
71.75
28.02
74.71
34.17
76.35
35.37
GradNorm
76.75
37.96
79.36
43.69
82.25
53.49
80.25
49.30
82.76
56.60
84.31
60.24
Entropy
72.01
30.96
74.98
34.71
78.91
41.62
71.99
31.82
75.93
38.64
78.05
42.24
EL2N
71.71
31.69
76.57
36.99
78.04
41.45
70.47
26.15
74.42
30.29
78.29
37.66
Appendix
Table 7: Additional results on PointNeXt and PointVector.
Dataset pruning reduces a large training set to a representative subset while preserving model performance. Existing geometry-based methods typically assume that nearby points in embedding space share similar properties. Rather than imposing this assumption, we derive geometric selection criteria by reformulating unbiased subset selection as a variance minimization problem. Unbiasedness ensures that unweighted subset averages recover full-dataset averages in expectation, including losses and gradients at fixed model parameters. Specifically, we characterize a family of unbiased subset selection algorithms as a high-dimensional polytope. In this context, minimizing the expected sampling variance is a linear objective. Differences in sampling variance, averaged over rigid motions, admit closed-form pairwise expressions. Because the polytope has high dimension, directly applying standard linear programming is impractical. We instead use these expressions to construct an efficient vertex walk that optimizes an approximation of the variance objective while preserving unbiasedness, yielding a method that requires neither labels nor model training during selection. Across CIFAR-10, MNIST, and CelebA benchmarks, our method matches or exceeds uniform sampling in mean test accuracy at every evaluated budget and outperforms competing geometric methods in several settings, particularly at small selection budgets. Beyond dataset pruning, the same framework reduces stochastic-gradient variance by increasing diversity within mini-batches while keeping the batch size unchanged.
Rodrigo Schuller, Francisco Ganacim
Instituto de Matem´atica Pura e Aplicada (IMPA) Rio de Janeiro, Brazil
The performance of deep learning models is affected by not only data quantity but also data quality. Data pruning is a process by which practitioners can reduce the size of a dataset by only keeping the most important training data points, thereby achieving similar test set performance. We empirically investigate two popular data pruning methods under noisy and noiseless conditions and show that these methods fail in the presence of significant label noise. We highlight that the success of data pruning is distinctly affected by three factors: redundancy in the dataset, the presence of problematic samples, and interdependence between samples. We perform a detailed investigation on commonly used benchmark classification datasets and neural network architectures. We find that our observations are consistent across data distributions and training protocols.
Leon Freese, Marthinus W. Theunissen
Faculty of Engineering, North-West University, South Africa · Centre for Artificial Intelligence Research (CAIR), South Africa · National Institute for Theoretical and Computational Sciences (NITheCS), South Africa
Dataset pruning reduces the storage and training costs of deep learning by selecting an informative subset from a large dataset. However, most existing pruning methods require fully labeled data, which limits their applicability in realistic settings where unlabeled data are abundant and annotation is costly. Recent label-free pruning methods address this issue, but they rely on features from pretrained models to estimate example difficulty. This dependence can be unreliable when the target dataset differs substantially from the pretraining distribution. We propose SemiPrune, a label-efficient dataset pruning framework, using only a small randomly labeled subset, that uses semi-supervised learning to generate pseudo-labels for unlabeled data, allowing existing supervised pruning methods that require label information to be seamlessly applied to the resulting pseudo-labeled training pool. We then estimate example difficulty from pseudo-label-induced training dynamics and select a coreset. By learning directly from the target dataset, our method better captures the target distribution and provides more reliable signals for difficulty estimation and coreset selection. We validate our approach on domain-specific, image-corrupted, and long-tailed datasets, where it achieves state-of-the-art performance among label-free and label-efficient baselines, while also demonstrating competitive performance on standard benchmarks.