Nirjhor Datta

Nirjhor Datta, Swakkhar Shatabda, M Sohel Rahman

Large pre-trained DNA language models such as DNABERT-2, Nucleotide Transformer, and HyenaDNA have demonstrated strong performance on various genomic benchmarks. However, most applications rely on expensive fine-tuning, which works best when the training and test data share a similar distribution. In this work, we investigate whether task-specific fine-tuning is always necessary. We show that simple embedding-based pipelines that extract fixed representations from these models and feed them into lightweight classifiers can achieve competitive performance. In evaluation settings with different data distributions, embedding-based methods often outperform fine-tuning while reducing inference time by 10x to 20x. Our results suggest that embedding extraction is not only a strong baseline but also a more generalizable and efficient alternative to fine-tuning, especially for deployment in diverse or unseen genomic contexts. For example, in enhancer classification, HyenaDNA embeddings combined with zCurve achieve 0.68 accuracy (vs. 0.58 for fine-tuning), with an 88% reduction in inference time and over 8x lower carbon emissions (0.02 kg vs. 0.17 kg CO2). In non-TATA promoter classification, DNABERT-2 embeddings with zCurve or GC content reach 0.85 accuracy (vs. 0.89 with fine-tuning) with a 22x lower carbon footprint (0.02 kg vs. 0.44 kg CO2). These results show that embedding-based pipelines offer over 10x better carbon efficiency while maintaining strong predictive performance. The code is available here: https://github.com/NIRJHOR-DATTA/EMBEDDING-IS-ALMOST-ALL-YOU-NEED.

Nirjhor Datta, Md. Golam Rabiul Alam

The ability to selectively remove knowledge from medical segmentation networks is increasingly important for privacy compliance, ethical deployment, and continual dataset revision. We introduce Erase to Retain, a controllable unlearning framework for medical image segmentation that achieves targeted forgetting without full retraining. Our method uses a teacher-student distillation paradigm with Low-Rank Adaptation (LoRA) constrained subspace updates, enabling the student network to erase lesion-specific or class-specific representations in low-rank decoder spaces while preserving global anatomical understanding. During the strong unlearning phase, LoRA modules are adversarially optimized to contradict the teacher's confident predictions on a designated forget subset, enforcing semantic removal. This is followed by a gentle restoration phase that recovers generalization on retained data through head-only supervised refinement. For ISIC segmentation, the student reduces forget-set IoU from 0.875 to 0.509 while maintaining competitive performance on the retain and validation splits (0.647 to 0.677 IoU). On the cross-domain CHASE dataset, Erase to Retain consistently lowers forget-set IoU while preserving utility on retain and validation sets. For ISIC classification, our method decreases accuracy on the forget subset from 87.0 percent to 64.1 percent while improving retain accuracy from 83.9 percent to 90.6 percent. These results demonstrate that LoRA-based subspace unlearning provides a practical pathway toward responsible, controllable, and reversible unlearning in medical image analysis, enabling models to forget sensitive samples or structures while preserving performance where it matters most.