arXiv subjects

Nirjhor Datta

Publications and source records attributed to Nirjhor Datta.

5 recordsLinked to original sources

arXiv2026

Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models

Genomic foundation models are increasingly reused as frozen feature extractors for downstream sequence prediction, offering a compute-efficient alternative to full fine-tuning. However, it remains unclear when biological information encoded by these models is accessible without task-specific adaptation. We present a representation-accessibility analysis of frozen genomic language models across regulatory, epigenetic, promoter, splice-site, and variant-effect prediction tasks. We evaluate DNABERT-2, Nucleotide Transformer, HyenaDNA, GENERATOR-v2, and Omni-DNA under unified frozen-probing protocols, while separating diagnostic readout analyses from validation-selected checks. Our results reveal a consistent task-dependent pattern: frozen probes recover 95-100 % of fine-tuned performance on promoter tasks, but average splice-site recovery drops to 60-88 %. Frozen embeddings are also competitive on broad Genomic Benchmark tasks such as coding-region and species-discrimination classification, but show larger gaps on some regulatory and OCR tasks. Layer-wise probing, in-silico mutagenesis, variant-effect prediction, and embedding geometry show that local biological signal is partially present in frozen representations, but is not always accessible through final pooled embeddings.

q-bio.GN↗

arXiv2026

Enlight: Fast Low-Light Image Enhancement via Multi-Objective Optimization and Shadow-Aware Refinement

We present ENLIGHT, a fast and training free framework for low-light image enhancement based on direct optimization of a perceptual objective. Unlike deep learning approaches that require large scale training data and supervision, ENLIGHT operates in a zero-shot manner by optimizing image quality at inference time. The method employs a two stage global to local optimization strategy. In the first stage, ENLIGHT performs global illumination adjustment to improve visibility while maintaining structural consistency and avoiding excessive noise enhancement. In the second stage, a shadow aware refinement selectively improves low-intensity regions through masked local optimization, enhancing visibility without overexposure. To balance quality and efficiency, we introduce two modes: Fast, which uses a multi-objective formulation combining entropy, gradient preservation, and noise regularization, and Ultrafast, which reduces computational cost via a lightweight approximation of the same objective. The framework is optimizer agnostic and supports both evolutionary and lightweight local search methods. Experiments on BAID, Backlit300, LIME, MEF, NPE, and DICM demonstrate that ENLIGHT achieves competitive perceptual quality (MUSIQ, NIQE, BRISQUE) with significantly lower inference time. Qualitative results further show improved contrast, preserved structural details, and controlled noise amplification, making ENLIGHT a practical and interpretable alternative to learning based methods.

cs.CV↗

arXiv2025

Erase to Retain: Low Rank Adaptation Guided Selective Unlearning in Medical Segmentation Networks

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.

cs.CV↗

arXiv2025

Embedding Is (Almost) All You Need: Retrieval-Augmented Inference for Generalizable Genomic Prediction Tasks

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.

q-bio.GN↗

arXiv2025

Entropy-Driven Genetic Optimization for Deep-Feature-Guided Low-Light Image Enhancement

Image enhancement methods often prioritize pixel level information, overlooking the semantic features. We propose a novel, unsupervised, fuzzy-inspired image enhancement framework guided by NSGA-II algorithm that optimizes image brightness, contrast, and gamma parameters to achieve a balance between visual quality and semantic fidelity. Central to our proposed method is the use of a pre trained deep neural network as a feature extractor. To find the best enhancement settings, we use a GPU-accelerated NSGA-II algorithm that balances multiple objectives, namely, increasing image entropy, improving perceptual similarity, and maintaining appropriate brightness. We further improve the results by applying a local search phase to fine-tune the top candidates from the genetic algorithm. Our approach operates entirely without paired training data making it broadly applicable across domains with limited or noisy labels. Quantitatively, our model achieves excellent performance with average BRISQUE and NIQE scores of 19.82 and 3.652, respectively, in all unpaired datasets. Qualitatively, enhanced images by our model exhibit significantly improved visibility in shadowed regions, natural balance of contrast and also preserve the richer fine detail without introducing noticable artifacts. This work opens new directions for unsupervised image enhancement where semantic consistency is critical.

cs.CV↗