Continuous Diffusion Transformers for Designing Synthetic Regulatory Elements

We present a parameter-efficient Diffusion Transformer (DiT) for generating 200bp cell-type-specific regulatory DNA sequences. By replacing the U-Net backbone of DNA-Diffusion with a transformer denoiser equipped with a 2D CNN input encoder, our model matches the U-Net's best validation loss in 13 epochs (60$\times$ fewer) and converges 39% lower, while reducing memorization from 5.3% to 1.7% of generated sequences aligning to training data via BLAT. Ablations show the CNN encoder is essential: without it, validation loss increases 70% regardless of positional embedding choice. We further apply DDPO finetuning using Enformer as a reward model, achieving a 38$\times$ improvement in predicted regulatory activity. Cross-validation against DRAKES on an independent prediction task confirms that improvements reflect genuine regulatory signal rather than reward model overfitting.

Understanding the Limits of Vision Language Models Through the Lens of the Binding Problem

Recent work has documented striking heterogeneity in the performance of state-of-the-art vision language models (VLMs), including both multimodal language models and text-to-image models. These models are able to describe and generate a diverse array of complex, naturalistic images, yet they exhibit surprising failures on basic multi-object reasoning tasks -- such as counting, localization, and simple forms of visual analogy -- that humans perform with near perfect accuracy. To better understand this puzzling pattern of successes and failures, we turn to theoretical accounts of the binding problem in cognitive science and neuroscience, a fundamental problem that arises when a shared set of representational resources must be used to represent distinct entities (e.g., to represent multiple objects in an image), necessitating the use of serial processing to avoid interference. We find that many of the puzzling failures of state-of-the-art VLMs can be explained as arising due to the binding problem, and that these failure modes are strikingly similar to the limitations exhibited by rapid, feedforward processing in the human brain.