q-bio.GNMar 6, 2026

How Private Are DNA Embeddings? Inverting Foundation Model Representations of Genomic Sequences

Authors: Sofiane Ouaari, Jules Kreuer, Nico Pfeifer

Organizations: Methods in Medical Informatics, Department of Computer Science, University of Tuebingen, Germany · Institute for Bioinformatics and Medical Informatics (IBMI), University of Tuebingen, Germany

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Abstract

DNA foundation models have become transformative tools in bioinformatics and healthcare applications. Trained on vast genomic datasets, these models can be used to generate sequence embeddings, dense vector representations that capture complex genomic information. These embeddings are increasingly being shared via Embeddings-as-a-Service (EaaS) frameworks to facilitate downstream tasks, while supposedly protecting the privacy of the underlying raw sequences. However, as this practice becomes more prevalent, the security of these representations is being called into question. This study evaluates the resilience of DNA foundation models to model inversion attacks, whereby adversaries attempt to reconstruct sensitive training data from model outputs. In our study, the model's output for reconstructing the DNA sequence is a zero-shot embedding, which is then fed to a decoder. We evaluated the privacy of three DNA foundation models: DNABERT-2, Evo 2, and Nucleotide Transformer v2 (NTv2). Our results show that per-token embeddings allow near-perfect sequence reconstruction across all models. For mean-pooled embeddings, reconstruction quality degrades as sequence length increases, though it remains substantially above random baselines. Evo 2 and NTv2 prove to be most vulnerable, especially for shorter sequences with reconstruction similarities > 90%, while DNABERT-2's BPE tokenization provides the greatest resilience. We found that the correlation between embedding similarity and sequence similarity was a key predictor of reconstruction success. Our findings emphasize the urgent need for privacy-aware design in genomic foundation models prior to their widespread deployment in EaaS settings. Training code, model weights and evaluation pipeline are released on: https://github.com/not-a-feature/DNA-Embedding-Inversion.

Figures & tables

Fig. 1: Overall Pipeline of the model inversion attack scenario on DNA Foundation Models shared embedding
Fig. 2: Left: Collision embedding analysis for mean embeddings of sequences of length l=100l=100 . The figure shows the normalised Euclidean distances of all pairwise combinations of a random subsample of 2,0002{,}000 unique sequences (see Appendix D for all sequence lengths). Right: Per-position reconstruction accuracy for per-token embeddings at sequence length l=100l=100 .
Fig. 3: Mean-pooled reconstruction performance across sequence lengths for the encoder-only architecture: (a) Levenshtein similarity and (b) nucleotide accuracy.
Appendix figures & tables17 assets

Supplementary material from the paper’s appendix.

Appendix

Fig. 4: Token count vs. sequence length for the three foundation models. Evo 2 (char-level) produces exactly ll tokens, NTv2 (single nt and 6-mer) follows a fixed compression ratio, and DNABERT-2 (BPE) exhibits variable, content-dependent tokenisation. Shaded regions indicate ±1\pm 1 standard deviation computed.
Fig. 5: Collision analysis: pairwise normalised Euclidean distance distributions for mean-pooled embeddings across all evaluated sequence lengths.
Fig. 6: UMAP projections of mean-pooled DNABERT-2 embeddings across all sequence lengths.
Fig. 7: UMAP projections of mean-pooled NTv2 embeddings across all sequence lengths.
Fig. 8: UMAP projections of mean-pooled Evo 2 embeddings across all sequence lengths.
Fig. 9: Euclidean distance vs. sequence similarity correlation for DNABERT-2 across all sequence lengths.
Fig. 10: Euclidean distance vs. sequence similarity correlation for NTv2 across all sequence lengths.
Fig. 11: Euclidean distance vs. sequence similarity correlation for Evo 2 across all sequence lengths.
ModelSimilarity10152025303540455060708090100
DNABERT-2Cosine0.01540.01540.02890.02890.03450.03450.04000.04000.04330.04330.04790.04790.06800.06800.06690.06690.06830.06830.07830.07830.08520.08520.09440.09440.12110.12110.11270.1127
Euclidean0.02240.02240.02830.02830.03840.03840.03990.03990.03810.03810.04540.04540.07170.07170.05710.05710.04600.04600.06700.06700.06710.06710.08800.08800.10630.10630.10050.1005
Evo 2Cosine0.1484\mathbf{0.1484}0.3775\mathbf{0.3775}0.4405\mathbf{0.4405}0.3260\mathbf{0.3260}0.2660\mathbf{0.2660}0.2307\mathbf{0.2307}0.2108\mathbf{0.2108}0.2096\mathbf{0.2096}0.1976\mathbf{0.1976}0.1847\mathbf{0.1847}0.17600.17600.16620.16620.17360.17360.16800.1680
Euclidean0.07030.07030.2986\mathbf{0.2986}0.4354\mathbf{0.4354}0.3176\mathbf{0.3176}0.2538\mathbf{0.2538}0.2164\mathbf{0.2164}0.19190.19190.1890\mathbf{0.1890}0.1730\mathbf{0.1730}0.15620.15620.14740.14740.13250.13250.14100.14100.13550.1355
NTv2Cosine0.09910.09910.09180.09180.08160.08160.09150.09150.06350.06350.13110.13110.18230.18230.14140.14140.13530.13530.14460.14460.1796\mathbf{0.1796}0.1747\mathbf{0.1747}0.1857\mathbf{0.1857}0.2226\mathbf{0.2226}
Euclidean0.1008\mathbf{0.1008}0.09500.09500.08690.08690.09840.09840.07170.07170.14870.14870.1992\mathbf{0.1992}0.15420.15420.14930.14930.1590\mathbf{0.1590}0.1896\mathbf{0.1896}0.1879\mathbf{0.1879}0.2012\mathbf{0.2012}0.2310\mathbf{0.2310}
Appendix
TABLE I: Spearman correlation between embedding similarity (cosine / Euclidean) and sequence similarity (Levenshtein) for different models and sequence lengths.
ModelKey HyperparametersApprox. Parameters
Encoderd=128d=128 , h=8h=8 , L=6L=6 , dff=1024d_{ff}=1024 , dropout =0.1=0.1≈12\approx 12 M
Decoderd=128d=128 , h=8h=8 , L=6L=6 , dff=1024d_{ff}=1024 , dropout =0.1=0.1≈12\approx 12 M
ResNetd=256d=256 , 4 blocks, k=5k=5≈22\approx 22 M
MLP (per-token)[256,256,128][256,256,128] , dropout =0.2=0.2≈0.3\approx 0.3 M
Nearest Neighbour non-parametric
Appendix
TABLE II: Inversion model architectures and approximate parameter counts (excluding input projection, which varies by foundation model embedding dimension).
Figure 14
Fig. 14: Mean-pooled reconstruction evaluation across sequence lengths. Left column: Levenshtein similarity; right column: nucleotide accuracy. Top row: DNABERT-2, middle row: NTv2, bottom row: Evo 2.
Figure 16
MethodMetric10152025303540455060708090100
DecoderLevenshtein0.45±0.190.45\pm 0.190.44±0.150.44\pm 0.150.45±0.110.45\pm 0.110.46±0.100.46\pm 0.100.45±0.100.45\pm 0.100.46±0.090.46\pm 0.090.46±0.080.46\pm 0.080.46±0.080.46\pm 0.080.46±0.080.46\pm 0.080.47±0.070.47\pm 0.070.47±0.070.47\pm 0.070.46±0.070.46\pm 0.070.46±0.060.46\pm 0.060.46±0.060.46\pm 0.06
Accuracy0.37±0.210.37\pm 0.210.33±0.160.33\pm 0.160.33±0.130.33\pm 0.130.32±0.120.32\pm 0.120.31±0.110.31\pm 0.110.31±0.100.31\pm 0.100.31±0.090.31\pm 0.090.31±0.090.31\pm 0.090.30±0.090.30\pm 0.090.30±0.080.30\pm 0.080.30±0.080.30\pm 0.080.29±0.070.29\pm 0.070.29±0.070.29\pm 0.070.29±0.070.29\pm 0.07
ResNetLevenshtein0.44±0.170.44\pm 0.170.44±0.120.44\pm 0.120.45±0.100.45\pm 0.100.46±0.090.46\pm 0.090.45±0.080.45\pm 0.080.46±0.080.46\pm 0.080.46±0.080.46\pm 0.080.46±0.070.46\pm 0.070.46±0.070.46\pm 0.070.46±0.060.46\pm 0.060.47±0.060.47\pm 0.060.46±0.060.46\pm 0.060.46±0.050.46\pm 0.050.47±0.050.47\pm 0.05
Accuracy0.34±0.200.34\pm 0.200.32±0.150.32\pm 0.150.31±0.120.31\pm 0.120.31±0.110.31\pm 0.110.30±0.100.30\pm 0.100.30±0.090.30\pm 0.090.30±0.090.30\pm 0.090.30±0.080.30\pm 0.080.30±0.080.30\pm 0.080.29±0.070.29\pm 0.070.29±0.070.29\pm 0.070.29±0.070.29\pm 0.070.29±0.060.29\pm 0.060.28±0.060.28\pm 0.06
EncoderLevenshtein0.46±0.190.46\pm 0.190.45±0.140.45\pm 0.140.46±0.110.46\pm 0.110.47±0.100.47\pm 0.100.47±0.090.47\pm 0.090.47±0.080.47\pm 0.080.47±0.080.47\pm 0.080.47±0.080.47\pm 0.080.48±0.070.48\pm 0.070.47±0.070.47\pm 0.070.48±0.060.48\pm 0.060.47±0.060.47\pm 0.060.47±0.060.47\pm 0.060.47±0.050.47\pm 0.05
Accuracy0.37±0.220.37\pm 0.220.34±0.160.34\pm 0.160.33±0.130.33\pm 0.130.32±0.120.32\pm 0.120.32±0.110.32\pm 0.110.31±0.100.31\pm 0.100.31±0.090.31\pm 0.090.31±0.090.31\pm 0.090.31±0.080.31\pm 0.080.30±0.080.30\pm 0.080.30±0.070.30\pm 0.070.29±0.070.29\pm 0.070.29±0.060.29\pm 0.060.29±0.060.29\pm 0.06
Appendix
TABLE III: Reconstruction results for DNABERT-2 embeddings.
MethodMetric10152025303540455060708090100
DecoderLevenshtein0.53±0.130.53\pm 0.130.96±0.050.96\pm 0.050.89±0.080.89\pm 0.080.82±0.080.82\pm 0.080.73±0.080.73\pm 0.080.67±0.080.67\pm 0.080.63±0.070.63\pm 0.070.56±0.070.56\pm 0.070.53±0.070.53\pm 0.070.50±0.060.50\pm 0.060.47±0.060.47\pm 0.060.45±0.060.45\pm 0.060.44±0.060.44\pm 0.060.43±0.050.43\pm 0.05
Accuracy0.51±0.140.51\pm 0.140.96±0.050.96\pm 0.050.87±0.100.87\pm 0.100.80±0.100.80\pm 0.100.70±0.100.70\pm 0.100.62±0.090.62\pm 0.090.58±0.090.58\pm 0.090.53±0.080.53\pm 0.080.50±0.080.50\pm 0.080.47±0.070.47\pm 0.070.44±0.060.44\pm 0.060.43±0.060.43\pm 0.060.42±0.060.42\pm 0.060.41±0.060.41\pm 0.06
ResNetLevenshtein0.55±0.120.55\pm 0.120.91±0.080.91\pm 0.080.86±0.080.86\pm 0.080.97±0.060.97\pm 0.060.91±0.090.91\pm 0.090.82±0.090.82\pm 0.090.71±0.080.71\pm 0.080.65±0.070.65\pm 0.070.62±0.060.62\pm 0.060.56±0.060.56\pm 0.060.52±0.050.52\pm 0.050.49±0.050.49\pm 0.050.46±0.050.46\pm 0.050.47±0.050.47\pm 0.05
Accuracy0.52±0.130.52\pm 0.130.90±0.080.90\pm 0.080.84±0.100.84\pm 0.100.96±0.080.96\pm 0.080.88±0.120.88\pm 0.120.77±0.130.77\pm 0.130.64±0.110.64\pm 0.110.57±0.100.57\pm 0.100.54±0.090.54\pm 0.090.49±0.080.49\pm 0.080.46±0.070.46\pm 0.070.44±0.070.44\pm 0.070.42±0.060.42\pm 0.060.41±0.060.41\pm 0.06
EncoderLevenshtein0.58±0.120.58\pm 0.120.98±0.040.98\pm 0.040.99±0.030.99\pm 0.030.97±0.070.97\pm 0.070.92±0.090.92\pm 0.090.85±0.100.85\pm 0.100.76±0.090.76\pm 0.090.71±0.080.71\pm 0.080.66±0.070.66\pm 0.070.59±0.060.59\pm 0.060.53±0.050.53\pm 0.050.50±0.050.50\pm 0.050.48±0.050.48\pm 0.050.46±0.050.46\pm 0.05
Accuracy0.56±0.130.56\pm 0.130.98±0.040.98\pm 0.040.99±0.040.99\pm 0.040.96±0.090.96\pm 0.090.89±0.120.89\pm 0.120.80±0.140.80\pm 0.140.70±0.120.70\pm 0.120.63±0.110.63\pm 0.110.58±0.100.58\pm 0.100.52±0.090.52\pm 0.090.47±0.070.47\pm 0.070.45±0.070.45\pm 0.070.43±0.060.43\pm 0.060.42±0.060.42\pm 0.06
Appendix
TABLE IV: Reconstruction results for Evo 2 embeddings.
MethodMetric10152025303540455060708090100
DecoderLevenshtein0.88±0.120.88\pm 0.120.87±0.100.87\pm 0.100.82±0.110.82\pm 0.110.81±0.100.81\pm 0.100.77±0.100.77\pm 0.100.65±0.080.65\pm 0.080.64±0.080.64\pm 0.080.64±0.080.64\pm 0.080.62±0.070.62\pm 0.070.60±0.070.60\pm 0.070.57±0.060.57\pm 0.060.56±0.060.56\pm 0.060.53±0.060.53\pm 0.060.53±0.060.53\pm 0.06
Accuracy0.88±0.130.88\pm 0.130.86±0.120.86\pm 0.120.81±0.130.81\pm 0.130.79±0.120.79\pm 0.120.75±0.120.75\pm 0.120.59±0.100.59\pm 0.100.57±0.100.57\pm 0.100.57±0.100.57\pm 0.100.54±0.100.54\pm 0.100.52±0.100.52\pm 0.100.46±0.080.46\pm 0.080.45±0.080.45\pm 0.080.41±0.080.41\pm 0.080.41±0.070.41\pm 0.07
ResNetLevenshtein0.87±0.120.87\pm 0.120.86±0.100.86\pm 0.100.80±0.110.80\pm 0.110.78±0.100.78\pm 0.100.73±0.090.73\pm 0.090.64±0.080.64\pm 0.080.63±0.080.63\pm 0.080.63±0.080.63\pm 0.080.62±0.070.62\pm 0.070.59±0.080.59\pm 0.080.59±0.070.59\pm 0.070.58±0.070.58\pm 0.070.55±0.070.55\pm 0.070.56±0.070.56\pm 0.07
Accuracy0.86±0.140.86\pm 0.140.85±0.120.85\pm 0.120.78±0.120.78\pm 0.120.75±0.120.75\pm 0.120.70±0.110.70\pm 0.110.58±0.100.58\pm 0.100.57±0.100.57\pm 0.100.56±0.100.56\pm 0.100.54±0.100.54\pm 0.100.49±0.100.49\pm 0.100.48±0.100.48\pm 0.100.46±0.100.46\pm 0.100.42±0.090.42\pm 0.090.43±0.100.43\pm 0.10
EncoderLevenshtein0.90±0.110.90\pm 0.110.88±0.100.88\pm 0.100.86±0.110.86\pm 0.110.85±0.100.85\pm 0.100.80±0.100.80\pm 0.100.69±0.090.69\pm 0.090.66±0.080.66\pm 0.080.66±0.080.66\pm 0.080.65±0.080.65\pm 0.080.60±0.070.60\pm 0.070.60±0.070.60\pm 0.070.59±0.060.59\pm 0.060.55±0.060.55\pm 0.060.57±0.060.57\pm 0.06
Accuracy0.89±0.120.89\pm 0.120.87±0.110.87\pm 0.110.85±0.120.85\pm 0.120.83±0.120.83\pm 0.120.78±0.110.78\pm 0.110.64±0.110.64\pm 0.110.60±0.110.60\pm 0.110.60±0.110.60\pm 0.110.58±0.100.58\pm 0.100.52±0.100.52\pm 0.100.50±0.090.50\pm 0.090.48±0.090.48\pm 0.090.43±0.080.43\pm 0.080.44±0.080.44\pm 0.08
Appendix
TABLE V: Reconstruction results for NTv2 embeddings.
Fig. 17: Reconstruction performance of mean embeddings for sequences of length l=10 to 100l=10\text{ to }100 for (a) DNABERT-2, (b) Evo 2, (c) NTv2 and the random baseline (gray).

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