VANDAM: Viewing a nucleotide sequence with DNA molecular priors

arXiv:2610.00411 · cs.LG, stat.ML · Submitted 2026-09-30 · Read on arXiv

cs.LG, stat.ML

Submitted: 2026-09-30

Updated: 2026-09-30

Terminology

• Alignment — 12× in this paper · explained in 1 episode
• Tokenization — 9× in this paper · explained in 2 episodes
• Foundation Model — 8× in this paper · explained in 3 episodes
• Foundation Models — 8× in this paper · explained in 7 episodes
• Grounding — 8× in this paper · explained in 3 episodes
• Transformer — 8× in this paper · explained in 2 episodes
• Ablation — 7× in this paper · explained in 1 episode
• Embeddings — 6× in this paper · explained in 2 episodes
• Linear probe — 6× in this paper · explained in 2 episodes
• Local Feature Injection — 5× in this paper
• Accuracy — 4× in this paper · explained in 1 episode
• Benchmark — 4× in this paper · explained in 2 episodes
• Adaptation — 3× in this paper · explained in 1 episode
• Residualization — 3× in this paper · explained in 2 episodes
• Benchmarking — 2× in this paper · explained in 3 episodes
• Calibration — 2× in this paper · explained in 7 episodes
• Linear Probing — 2× in this paper · explained in 2 episodes
• Region Property Prediction — 2× in this paper
• Regularization — 2× in this paper · explained in 3 episodes
• Representation Learning — 2× in this paper · explained in 2 episodes
• Abstraction — 1× in this paper · explained in 1 episode
• Aggregation — 1× in this paper · explained in 1 episode
• Alternation — 1× in this paper · explained in 1 episode
• Core — 1× in this paper · explained in 2 episodes
• Downstream Tasks — 1× in this paper · explained in 2 episodes
• Inverse Participation Ratio (IPR) — 1× in this paper · explained in 2 episodes
• Perplexity — 1× in this paper · explained in 3 episodes

Sources

• JEPA-DNA: Grounding Genomic Foundation Models through Joint-Embedding Predictive Architectures
• D3LM: A Discrete DNA Diffusion Language Model for Bidirectional DNA Understanding and Generation

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