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Transformer Architectures in Genomic Sequence Analysis Training | Long-Context Attention, DNABERT/Enformer, PEFT

NTHRYS >> Services >> Academic Services >> Training Programs >> Bioinformatics Training >> AI/ML, Data Science, Pipelines & Cloud >> Transformer Architectures in Genomic Sequence Analysis Training | Long-Context Attention, DNABERT/Enformer, PEFT

Transformer Architectures in Genomic Sequence Analysis — Hands-on

Go deep on Transformers purpose-built for genomics. Learn sequence tokenization strategies, positional encodings, long-context mechanisms, and parameter-efficient fine-tuning. You will implement and evaluate models for promoter/enhancer prediction, splice sites, variant effect scoring, and regulatory element discovery with best-practice reporting.

Transformer Architectures in Genomic Sequence Analysis
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Session 1
Fee: Rs 11,200
Tokenization, Embeddings & Positional Encodings
  • Sequence representations for DNA/RNA
  • k-mers / BPE byte/char tokens masking regimes
  • Embeddings & positional information
  • learned/sinusoidal ALiBi/Rotary (RoPE) relative positions
  • Toolchain & datasets
  • PyTorch/Transformers HuggingFace Datasets Genomics benchmarks
Session 2
Fee: Rs 15,400
Long-Sequence Attention & Genomics LMs
  • Efficient attention for long genomes
  • Longformer/BigBird Performer/Linformer Hyena/State Space
  • Pretrained genomics models
  • DNABERT Enformer Nucleotide Transformers
  • Applications & tasks
  • promoter/enhancer splice sites/TSS variant effect prediction
Session 3
Fee: Rs 19,800
PEFT, Training Efficiency & Evaluation
  • Parameter-Efficient Fine-Tuning (PEFT)
  • LoRA/IA3/Adapters prompt tuning frozen backbones
  • Training efficiency & robustness
  • mixed precision grad checkpointing distributed data parallel
  • Metrics & interpretability
  • ROC/PR, AUPRC attention rollout in-silico mutagenesis
Session 4
Fee: Rs 24,800
Mini Capstone: Variant/Regulatory Prediction
  • Build a genomics Transformer for a real task
  • Theory + Practical
  • Explain & validate biological relevance
  • motif discovery saliency/attributions replication on held-out chromosomes
  • Deliverables: code, metrics, report & model card
  • notebook/script ROC/PR plots PDF/HTML


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