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Dec 30

CPKD: Clinical Prior Knowledge-Constrained Diffusion Models for Surgical Phase Recognition in Endoscopic Submucosal Dissection

Gastrointestinal malignancies constitute a leading cause of cancer-related mortality worldwide, with advanced-stage prognosis remaining particularly dismal. Originating as a groundbreaking technique for early gastric cancer treatment, Endoscopic Submucosal Dissection has evolved into a versatile intervention for diverse gastrointestinal lesions. While computer-assisted systems significantly enhance procedural precision and safety in ESD, their clinical adoption faces a critical bottleneck: reliable surgical phase recognition within complex endoscopic workflows. Current state-of-the-art approaches predominantly rely on multi-stage refinement architectures that iteratively optimize temporal predictions. In this paper, we present Clinical Prior Knowledge-Constrained Diffusion (CPKD), a novel generative framework that reimagines phase recognition through denoising diffusion principles while preserving the core iterative refinement philosophy. This architecture progressively reconstructs phase sequences starting from random noise and conditioned on visual-temporal features. To better capture three domain-specific characteristics, including positional priors, boundary ambiguity, and relation dependency, we design a conditional masking strategy. Furthermore, we incorporate clinical prior knowledge into the model training to improve its ability to correct phase logical errors. Comprehensive evaluations on ESD820, Cholec80, and external multi-center demonstrate that our proposed CPKD achieves superior or comparable performance to state-of-the-art approaches, validating the effectiveness of diffusion-based generative paradigms for surgical phase recognition.

  • 7 authors
·
Jul 4

Video Virtual Try-on with Conditional Diffusion Transformer Inpainter

Video virtual try-on aims to naturally fit a garment to a target person in consecutive video frames. It is a challenging task, on the one hand, the output video should be in good spatial-temporal consistency, on the other hand, the details of the given garment need to be preserved well in all the frames. Naively using image-based try-on methods frame by frame can get poor results due to severe inconsistency. Recent diffusion-based video try-on methods, though very few, happen to coincide with a similar solution: inserting temporal attention into image-based try-on model to adapt it for video try-on task, which have shown improvements but there still exist inconsistency problems. In this paper, we propose ViTI (Video Try-on Inpainter), formulate and implement video virtual try-on as a conditional video inpainting task, which is different from previous methods. In this way, we start with a video generation problem instead of an image-based try-on problem, which from the beginning has a better spatial-temporal consistency. Specifically, at first we build a video inpainting framework based on Diffusion Transformer with full 3D spatial-temporal attention, and then we progressively adapt it for video garment inpainting, with a collection of masking strategies and multi-stage training. After these steps, the model can inpaint the masked garment area with appropriate garment pixels according to the prompt with good spatial-temporal consistency. Finally, as other try-on methods, garment condition is added to the model to make sure the inpainted garment appearance and details are as expected. Both quantitative and qualitative experimental results show that ViTI is superior to previous works.

  • 7 authors
·
Jun 26

PepMLM: Target Sequence-Conditioned Generation of Peptide Binders via Masked Language Modeling

Target proteins that lack accessible binding pockets and conformational stability have posed increasing challenges for drug development. Induced proximity strategies, such as PROTACs and molecular glues, have thus gained attention as pharmacological alternatives, but still require small molecule docking at binding pockets for targeted protein degradation (TPD). The computational design of protein-based binders presents unique opportunities to access undruggable targets, but have often relied on stable 3D structures or predictions for effective binder generation. Recently, we have leveraged the expressive latent spaces of protein language models (pLMs) for the prioritization of peptide binders from sequence alone, which we have then fused to E3 ubiquitin ligase domains, creating a CRISPR-analogous TPD system for target proteins. However, our methods rely on training discriminator models for ranking heuristically or unconditionally-derived guide peptides for their target binding capability. In this work, we introduce PepMLM, a purely target sequence-conditioned de novo generator of linear peptide binders. By employing a novel masking strategy that uniquely positions cognate peptide sequences at the terminus of target protein sequences, PepMLM tasks the state-of-the-art ESM-2 pLM to fully reconstruct the binder region, achieving low perplexities matching or improving upon previously-validated peptide-protein sequence pairs. After successful in silico benchmarking with AlphaFold-Multimer, we experimentally verify PepMLM's efficacy via fusion of model-derived peptides to E3 ubiquitin ligase domains, demonstrating endogenous degradation of target substrates in cellular models. In total, PepMLM enables the generative design of candidate binders to any target protein, without the requirement of target structure, empowering downstream programmable proteome editing applications.

  • 13 authors
·
Oct 5, 2023