Quantifying Error Tolerance in Synthetic Data: An Atomic-level Operand vs. Operator Perturbation Study
Authors: Jiaxiang Liu, Chenhao Yuan, Shuwen Xu, Boxuan Xing, Xiusheng Huang, Yinhao Xu, Hao Liu, Wenhao Teng, Xiangwen Liao, Pengfei Cao, Jun Zhao, Kang Liu
Organizations: C2DL, Institute of Automation, Chinese Academy of Sciences, Beijing, China · School of Artificial Intelligence, University of Chinese Academy of Sciences · Department of Gastrointestinal Surgery Fujian Provincial Cancer Hospital · College of Computer and Data Science, Fuzhou University
Synthetic data generation has become a cornerstone for advancing large language models. However, the lack of the quantitative analysis for error tolerance became a critical bottleneck. Consequently, current filtering strategies fluctuate between two extremes: they are either overly aggressive, risking the exclusion of potentially valuable samples, or overly permissive, failing to eliminate erroneous samples effectively. To bridge this gap, this paper introduces Atomic Tree Operation Modeling (ATOM), a framework that decomposes data into functional units (f(x)→y). ATOM distinguishes benign Operand x perturbations from fatal Operator f perturbations. The former are needlessly discarded by aggressive filtering, while the latter slip through permissive filtering. Our experiments reveal a double dissociation: models are robust to operand perturbations but collapse under operator perturbations. By prioritizing operator over aggressive operand precision, our ATOM-synthesized data outperforms rigorous baselines (e.g., +3.1% gain over LIMA), suggesting that operator diversity matters more than operand precision. Our code is available at https://github.com/Lut-hub/ATOM.
Figures & tables
Figure 1: The illustration of extract atomic functions and two types of perturbations: Operand Perturbations modify x while updating y to keep f valid, e.g., Contains(xk7q)→ m3p / n8s / t4v . And Operator Perturbations keep x fixed but modify y to violate f , e.g., Contains(\text{primary colors})\rightarrow\text{{\color[rgb]{0.75,0,0.25}purple}/{\color[rgb]{0.5,0.5,0.5}gray}/{\color[rgb]{0,1,0}green}} .
Figure 2: The pipeline of our A tomic T ree O peration M odeling ( ATOM ) framework. ATOM consists of two phases: 1) Atomic Tree Construction, which builds an operator hierarchy where leaf nodes define concrete atomic operators, and 2) Atomic Data Synthesis, which supports both Atomic-QA and Atomic-X.
Figure 3: Performance comparison of LLaMA3.1 across Atomic-QA, Operand-Perturbed Atomic-QA, and Operator-Perturbed Atomic-QA. Dashed lines denote the average performance for each setting.
Figure 4: MCQ accuracy vs. training data scale (main plot), with model agreement under replaced vs. original entity settings. Agreement Rate is the proportion of questions both models answer correctly.
Figure 5: CKA similarity of the output hidden states between different trained models. The lower part represents the CKA similarity of Qwen 2.5-7B, while the upper part represents LLaMA 3.1-8B.
Model Family
ARC- Challenge
ARC- Easy
BoolQ
Hotpot- QA
Open- BookQA
PIQA
RACE
SIQA
SQuADv2
Wino- Grande
Avg
LLaMA3.1-8B
Base
0.549
0.847
0.820
0.106
0.366
0.807
0.433
0.529
0.375
0.765
0.560
All Average
0.564
0.850
0.855
0.127
0.387
0.812
0.464
0.548
0.381
0.768
0.576
Instruct
0.558
0.854
0.870
0.209
0.362
0.811
0.464
0.548
0.420
0.764
0.586
LIMA
0.552
0.848
0.828
0.134
0.368
0.808
0.432
0.529
0.377
0.773
0.565
Condor
0.563
0.854
0.855
0.117
0.382
0.811
0.470
0.546
0.378
0.770
0.575
Magpie
0.575
0.845
0.859
0.122
0.380
0.808
0.464
0.563
0.374
0.761
0.575
Table 1: Overall performance across all training datasets on LLaMA3.1-8B and Qwen3-8B. Color-coded cells ( green / red ) are used to indicate performance above or below the mean across methods (All Average), with darker colors representing better or worse performance. The results for Qwen2.5-7B and Qwen2.5-14B are in Table 3 .
Figure 6: Radar plot of corpus diversity.
Figure 7: Average accuracy for LLaMA 3.1-8B and Qwen 2.5-7B on Atomic-Alpaca with operator perturbations at controlled rates (§ 7 ). Dashed lines: upper bound from training only on correct samples, truncated at 60% to approximate the solid lines’ data scale. See Figure 17 for Atomic-MetaMath.
Figure 8: Cohen’s Kappa between filtering methods (IFD, Length, Style) and ground-truth error labels as a function of sample error rate, evaluated on Atomic-Alpaca and Atomic-MetaMath .
Appendix figures & tables26 assets
Supplementary material from the paper’s appendix.
Appendix
Figure 9: The initial operator tree of Atomic-QA. Internal nodes represent abstract operator categories, and leaf nodes define concrete atomic operators.
Figure 10: The initial operator tree of Alpaca.
Figure 11: The initial operator tree of MetaMath.
Category
Benchmark
Shots
Metric
Text Comprehension and Information Integration
BoolQ
3
Accuracy
LongBench-HotpotQA
0
F1
RACE
3
Accuracy
SQuADv2
3
F1
Knowledge-Driven Reasoning
ARC-Challenge
3
Accuracy
ARC-Easy
3
Accuracy
Appendix
Table 2: Evaluation benchmarks and configurations.
Model Family
ARC- Challenge
ARC- Easy
BoolQ
Hotpot- QA
Open- BookQA
PIQA
RACE
SIQA
SQuADv2
Wino- Grande
Avg
Qwen2.5-7B
Base
0.590
0.860
0.872
0.216
0.390
0.803
0.459
0.576
0.421
0.754
0.594
All Average
0.586
0.859
0.875
0.190
0.399
0.800
0.474
0.572
0.364
0.747
0.587
Instruct
0.616
0.873
0.865
0.143
0.404
0.786
0.512
0.566
0.324
0.735
0.582
LIMA
0.586
0.861
0.871
0.207
0.396
0.801
0.459
0.574
0.424
0.757
0.594
Condor
0.597
0.864
0.874
0.185
0.392
0.801
0.471
0.580
0.396
0.755
0.591
Magpie
0.582
0.857
0.876
0.241
0.364
0.795
0.455
0.572
0.412
0.740
0.589
Appendix
Table 3: Overall performance across all training datasets on Qwen2.5-7B and Qwen2.5-14B. Color-coded cells ( green / red ) are used to indicate performance above or below the mean across methods (All Average), with darker colors representing better or worse performance.
Figure 12: Perplexity trends of LLaMA and Qwen models as a function of training data volume. The curve displays average PPL for both the original and entity-replaced variants, with an inset showing a zoomed region for the 30K–500K data range.
Figure 13: CKA variance across layers versus training data volume for LLaMA3.1-8B and Qwen2.5-7B, showing mean values (lines) and min–max ranges (shaded areas).
Dataset
Training Tokens
LIMA
627,993
Condor
21,131,550
Magpie
203,256,865
WizardLM
27,673,025
Alpaca
3,766,455
Self-Instruct
4,536,225
Appendix
Table 4: The number of training tokens in different datasets.
Figure 14: Performance comparison of Qwen2.5-7B across the Atomic-QA, Operand-Perturbed Atomic-QA, and Operator-Perturbed Atomic-QA settings. Each bar shows the model’s accuracy on individual tasks, while the dashed lines denote the average performance for each setting.
Figure 15: Performance comparison of Qwen2.5-14B across the Atomic-QA, Operand-Perturbed Atomic-QA, and Operator-Perturbed Atomic-QA settings. Each bar shows the model’s accuracy on individual tasks, while the dashed lines denote the average performance for each setting.
Figure 16: Performance comparison of Qwen3-8B across the Atomic-QA, Operand-Perturbed Atomic-QA, and Operator-Perturbed Atomic-QA settings. Each bar shows the model’s accuracy on individual tasks, while the dashed lines denote the average performance for each setting.
Model
Perturbation
Early
Middle
Late
Last layer
LLaMA3.1-8B
Operand
0.988
0.964
0.961
0.935
Operator
0.932
0.865
0.888
0.832
Base Model
0.942
0.743
0.668
0.745
Qwen2.5-7B
Operand
0.998
0.999
0.994
0.950
Operator
0.998
0.999
0.988
0.899
Base Model
0.997
0.999
0.973
0.773
Appendix
Table 5: Layer-wise CKA similarity against the model trained on clean Atomic-QA, averaged over the early, middle, and late thirds of the layers.
Model
Atomic-QA
Operator-Pert.
Operand-Pert.
w/ r.s.
w/ s.e.
LLaMA3.1-8B
35.80
36.53
99.76
35.82
Qwen3-8B
36.00
33.04
90.78
32.98
Qwen2.5-7B
43.33
42.17
136.24
42.32
Qwen2.5-14B
52.25
39.48
131.47
39.91
Appendix
Table 6: Average perplexity of training corpora evaluated by pretrained checkpoints. Operand-Pert. is reported for both the random-string construction (w/ r.s., used in \lx@sectionsign 5 ) and the LLM-rewritten synthetic-entity construction (w/ s.e., Appendix D.6 ).
Model
Perturbation
ARC- Challenge
ARC- Easy
BoolQ
Hotpot- QA
Open- BookQA
PIQA
RACE
SIQA
SQuADv2
Wino- Grande
LLaMA3.1-8B
w/ r.s.
0.587
0.856
0.858
0.159
0.413
0.814
0.478
0.549
0.394
0.770
w/ s.e.
0.572 ( − 0.015)
0.862 ( + 0.006)
0.860 ( + 0.002)
0.158 ( − 0.001)
0.408 ( − 0.005)
0.825 ( + 0.011)
0.476 ( − 0.002)
0.552 ( + 0.003)
0.401 ( + 0.007)
0.770 ( + 0.000)
Qwen2.5-7B
w/ r.s.
0.588
0.854
0.877
0.306
0.412
0.799
0.483
0.570
0.386
0.746
w/ s.e.
0.609 ( + 0.021)
0.842 ( − 0.012)
0.884 ( + 0.007)
0.313 ( + 0.007)
0.408 ( − 0.004)
0.801 ( + 0.002)
0.476 ( − 0.007)
0.570 ( + 0.000)
0.381 ( − 0.005)
0.746 ( + 0.000)
Qwen2.5-14B
w/ r.s.
0.659
0.884
0.876
0.364
0.452
0.817
0.512
0.576
0.406
0.795
w/ s.e.
0.659 ( + 0.000)
0.877 ( − 0.007)
0.880 ( + 0.004)
0.362 ( − 0.002)
0.455 ( + 0.003)
0.809 ( − 0.008)
0.527 ( + 0.015)
0.576 ( + 0.000)
0.408 ( + 0.002)
0.793 ( − 0.002)
Appendix
Table 7: Downstream performance of the two operand-perturbation constructions. w/ r.s. : random strings ( \lx@sectionsign 5 ); w/ s.e. : plausible but synthetic entities generated with the same LLM-rewriting protocol as the operator perturbation. Parenthesised values are deltas relative to w/ r.s.
Model
Training Data
Atomic-QA
w/ r.s.
w/ s.e.
LLaMA3.1-8B
Atomic-QA
1.0
–
–
w/ r.s.
0.935
1.0
–
w/ s.e.
0.942
0.956
1.0
Qwen2.5-7B
Atomic-QA
1.0
–
–
w/ r.s.
0.950
1.0
–
w/ s.e.
0.945
0.967
1.0
Appendix
Table 8: Last-layer CKA similarity among models trained on clean Atomic-QA and the two operand-perturbation constructions.
Training Data
LLaMA3.1-8B
Qwen3-8B
Naive
0.457
0.534
Operand-Perturbed
0.439
0.558
Operator-Perturbed
0.298
0.392
Appendix
Table 9: Performance on the closed-world evaluation set for models trained on 20k closed-world data over synthetic entities with artificial relations.
Training Data
Tokens
Model
Avg. Perf.
Atomic-LIFD-20K
535,706
LLaMA3.1-8B
0.583 ( ↑ 0.018 )
Qwen3-8B
0.627 ( ↑ 0.025 )
Qwen2.5-7B
0.623 ( ↑ 0.029 )
Qwen2.5-14B
0.638 ( ↑ 0.036 )
LIMA
627,993
LLaMA3.1-8B
0.565
Qwen3-8B
0.602
Appendix
Table 10: Performance comparison between Atomic-LIFD-20K and LIMA at matched data scale.
Dataset
TTR
MTLD
MSTTR
MATTR
Vendi
LogDet
Atomic-QA
0.2688
226.97
0.8689
0.8695
4.2840
− 1187.36
Atomic-LIFD-20K
0.2671
263.11
0.8817
0.8817
4.2963
− 1169.71
Atomic-LIFD-100K
0.2616
253.22
0.8820
0.8806
4.2854
− 1182.44
Appendix
Table 11: Diversity metrics of Atomic-QA and its LIFD-filtered subsets.
Model
Epoch 2
Epoch 3
Epoch 4
Epoch 5
LLaMA-3.1-8B
0.9995
0.9984
0.9961
0.9922
Qwen2.5-7B
0.9996
0.9986
0.9970
0.9944
Appendix
Table 12: CKA similarity between LIMA-finetuned and base models across training epochs.
Model
Epoch 2
Epoch 3
Epoch 4
Epoch 5
LLaMA-3.1-8B
0.565
0.563
0.566
0.564
Qwen2.5-7B
0.594
0.592
0.601
0.594
Appendix
Table 13: Average performance of LIMA-finetuned models across training epochs.
Figure 17: Accuracy on GSM8K, MATH-500, and MathQA for LLaMA 3.1-8B and Qwen 2.5-7B fine-tuned on Atomic-MetaMath with operator-level perturbations at controlled rates. Corresponds to Figure 7 , which reports Atomic-Alpaca on general benchmarks.
Figure 18: Accuracy degradation under increasing atomic function error rates for (a) LLaMA and (b) Qwen. The x-axis denotes the proportion of erroneous atomic functions in the training set, while the y-axis represents the performance of the trained model.
Figure 19: Relationship between the atomic function error rate and the resulting percentage of wrong samples.
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Yang Ba, Michelle V. Mancenido, Rong Pan
School of Computing and Augmented Intelligence, Arizona State University · School of Mathematical and Natural Sciences, Arizona State University
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Anjir Ahmed Chowdhury, Syed Zawad, Feng Yan
Department of Computer Science University of Houston · IBM Research