Latent Diffusion Models for Controllable RNA Sequence Generation

This paper presents RNAdiffusion, a latent diffusion model for generating and optimizing discrete RNA sequences. RNA is a particularly dynamic and versatile molecule in biological processes. RNA sequences exhibit high variability and diversity, characterized by their variable lengths, flexible three-dimensional structures, and diverse functions. We utilize pretrained BERT-type models to encode raw RNAs into token-level biologically meaningful representations. A Q-Former is employed to compress these representations into a fixed-length set of latent vectors, with an autoregressive decoder trained to reconstruct RNA sequences from these latent variables. We then develop a continuous diffusion model within this latent space. To enable optimization, we train reward networks to estimate functional properties of RNA from the latent variables. We employ gradient-based guidance during the backward diffusion process, aiming to generate RNA sequences that are optimized for higher rewards. Empirical experiments confirm that RNAdiffusion generates non-coding RNAs that align with natural distributions across various biological indicators. We fine-tuned the diffusion model on untranslated regions (UTRs) of mRNA and optimize sample sequences for protein translation efficiencies. Our guided diffusion model effectively generates diverse UTR sequences with high Mean Ribosome Loading (MRL) and Translation Efficiency (TE), surpassing baselines. These results hold promise for studies on RNA sequence-function relationships, protein synthesis, and enhancing therapeutic RNA design.

Gradient Guidance for Diffusion Models: An Optimization Perspective

Diffusion models have demonstrated empirical successes in various applications and can be adapted to task-specific needs via guidance. This paper introduces a form of gradient guidance for adapting or fine-tuning diffusion models towards user-specified optimization objectives. We study the theoretic aspects of a guided score-based sampling process, linking the gradient-guided diffusion model to first-order optimization. We show that adding gradient guidance to the sampling process of a pre-trained diffusion model is essentially equivalent to solving a regularized optimization problem, where the regularization term acts as a prior determined by the pre-training data. Diffusion models are able to learn data's latent subspace, however, explicitly adding the gradient of an external objective function to the sample process would jeopardize the structure in generated samples. To remedy this issue, we consider a modified form of gradient guidance based on a forward prediction loss, which leverages the pre-trained score function to preserve the latent structure in generated samples. We further consider an iteratively fine-tuned version of gradient-guided diffusion where one can query gradients at newly generated data points and update the score network using new samples. This process mimics a first-order optimization iteration in expectation, for which we proved O(1/K) convergence rate to the global optimum when the objective function is concave.

Rank-DETR for High Quality Object Detection

Modern detection transformers (DETRs) use a set of object queries to predict a list of bounding boxes, sort them by their classification confidence scores, and select the top-ranked predictions as the final detection results for the given input image. A highly performant object detector requires accurate ranking for the bounding box predictions. For DETR-based detectors, the top-ranked bounding boxes suffer from less accurate localization quality due to the misalignment between classification scores and localization accuracy, thus impeding the construction of high-quality detectors. In this work, we introduce a simple and highly performant DETR-based object detector by proposing a series of rank-oriented designs, combinedly called Rank-DETR. Our key contributions include: (i) a rank-oriented architecture design that can prompt positive predictions and suppress the negative ones to ensure lower false positive rates, as well as (ii) a rank-oriented loss function and matching cost design that prioritizes predictions of more accurate localization accuracy during ranking to boost the AP under high IoU thresholds. We apply our method to improve the recent SOTA methods (e.g., H-DETR and DINO-DETR) and report strong COCO object detection results when using different backbones such as ResNet-$50$, Swin-T, and Swin-L, demonstrating the effectiveness of our approach. Code is available at \url{https://github.com/LeapLabTHU/Rank-DETR}.

GlyphControl: Glyph Conditional Control for Visual Text Generation

Recently, there has been a growing interest in developing diffusion-based text-to-image generative models capable of generating coherent and well-formed visual text. In this paper, we propose a novel and efficient approach called GlyphControl to address this task. Unlike existing methods that rely on character-aware text encoders like ByT5 and require retraining of text-to-image models, our approach leverages additional glyph conditional information to enhance the performance of the off-the-shelf Stable-Diffusion model in generating accurate visual text. By incorporating glyph instructions, users can customize the content, location, and size of the generated text according to their specific requirements. To facilitate further research in visual text generation, we construct a training benchmark dataset called LAION-Glyph. We evaluate the effectiveness of our approach by measuring OCR-based metrics and CLIP scores of the generated visual text. Our empirical evaluations demonstrate that GlyphControl outperforms the recent DeepFloyd IF approach in terms of OCR accuracy and CLIP scores, highlighting the efficacy of our method.