arXiv subjects

Elay Dahan

Publications and source records attributed to Elay Dahan.

4 recordsLinked to original sources

arXiv2026

JEPA-DNA: Grounding Genomic Foundation Models through Joint-Embedding Predictive Architectures

Genomic Foundation Models (GFMs) typically rely on Masked Language Modeling (MLM) or Next-Token Prediction (NTP) to learn the "Laws of Nature". While effective at capturing local syntax, these generative paradigms prioritize token-level reconstruction over high-level functional context. We introduce JEPA-DNA, a model-agnostic continual training framework that integrates a Joint-Embedding Predictive Architecture (JEPA) with traditional generative objectives. By supervising global sequence embeddings in a latent space, JEPA-DNA forces models to predict the functional representations of masked genomic segments, shifting the learning signal from token recovery to semantic alignment. We evaluate JEPA-DNA on 17 diverse genomic benchmark tasks, demonstrating consistent gains in linear probing and zero-shot performance regardless of the underlying GFM architecture or generative objective, and establishing a new state-of-the-art for GFMs under the linear-probing protocol. Through extensive ablation studies, we further characterize the synergistic interplay between generative and latent objectives. Our code is provided in the supplementary material.

cs.AI↗

arXiv2026

VANDAM: Viewing a nucleotide sequence with DNA molecular priors

Contemporary Genomic Foundation Models (GFMs) rely on a DNA-as-a-string paradigm that employs masked token prediction objectives for pretraining. However, this abstraction does not explicitly model the biochemical, structural, and physical properties essential to biological function. Many molecular properties can be estimated from sequence using established biophysical models, so their utility lies not in providing an independent modality, but in introducing priors that training objectives can explicitly exploit. We introduce VANDAM, a framework that extends the training of GFMs with DNA molecular priors. In self-supervised training, VANDAM predicts regional molecular properties from pooled representations. When functional labels are available and can reward retaining molecular priors, local features are additionally injected at the input. VANDAM consistently improves downstream performance across four architecture families and nine held-out genomic tasks by complementing token-based objectives. Probing experiments further demonstrate that the use of molecular priors generalizes to other unseen molecular properties.

cs.LG↗

arXiv2024

CSG: A Context-Semantic Guided Diffusion Approach in De Novo Musculoskeletal Ultrasound Image Generation

The use of synthetic images in medical imaging Artificial Intelligence (AI) solutions has been shown to be beneficial in addressing the limited availability of diverse, unbiased, and representative data. Despite the extensive use of synthetic image generation methods, controlling the semantics variability and context details remains challenging, limiting their effectiveness in producing diverse and representative medical image datasets. In this work, we introduce a scalable semantic and context-conditioned generative model, coined CSG (Context-Semantic Guidance). This dual conditioning approach allows for comprehensive control over both structure and appearance, advancing the synthesis of realistic and diverse ultrasound images. We demonstrate the ability of CSG to generate findings (pathological anomalies) in musculoskeletal (MSK) ultrasound images. Moreover, we test the quality of the synthetic images using a three-fold validation protocol. The results show that the synthetic images generated by CSG improve the performance of semantic segmentation models, exhibit enhanced similarity to real images compared to the baseline methods, and are undistinguishable from real images according to a Turing test. Furthermore, we demonstrate an extension of the CSG that allows enhancing the variability space of images by synthetically generating augmentations of anatomical geometries and textures.

cs.CV↗

arXiv2024

Semantic Segmentation Refiner for Ultrasound Applications with Zero-Shot Foundation Models

Despite the remarkable success of deep learning in medical imaging analysis, medical image segmentation remains challenging due to the scarcity of high-quality labeled images for supervision. Further, the significant domain gap between natural and medical images in general and ultrasound images in particular hinders fine-tuning models trained on natural images to the task at hand. In this work, we address the performance degradation of segmentation models in low-data regimes and propose a prompt-less segmentation method harnessing the ability of segmentation foundation models to segment abstract shapes. We do that via our novel prompt point generation algorithm which uses coarse semantic segmentation masks as input and a zero-shot prompt-able foundation model as an optimization target. We demonstrate our method on a segmentation findings task (pathologic anomalies) in ultrasound images. Our method's advantages are brought to light in varying degrees of low-data regime experiments on a small-scale musculoskeletal ultrasound images dataset, yielding a larger performance gain as the training set size decreases.

cs.CV↗