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Dec 31

Protenix-Mini: Efficient Structure Predictor via Compact Architecture, Few-Step Diffusion and Switchable pLM

Lightweight inference is critical for biomolecular structure prediction and other downstream tasks, enabling efficient real-world deployment and inference-time scaling for large-scale applications. In this work, we address the challenge of balancing model efficiency and prediction accuracy by making several key modifications, 1) Multi-step AF3 sampler is replaced by a few-step ODE sampler, significantly reducing computational overhead for the diffusion module part during inference; 2) In the open-source Protenix framework, a subset of pairformer or diffusion transformer blocks doesn't make contributions to the final structure prediction, presenting opportunities for architectural pruning and lightweight redesign; 3) A model incorporating an ESM module is trained to substitute the conventional MSA module, reducing MSA preprocessing time. Building on these key insights, we present Protenix-Mini, a compact and optimized model designed for efficient protein structure prediction. This streamlined version incorporates a more efficient architectural design with a two-step Ordinary Differential Equation (ODE) sampling strategy. By eliminating redundant Transformer components and refining the sampling process, Protenix-Mini significantly reduces model complexity with slight accuracy drop. Evaluations on benchmark datasets demonstrate that it achieves high-fidelity predictions, with only a negligible 1 to 5 percent decrease in performance on benchmark datasets compared to its full-scale counterpart. This makes Protenix-Mini an ideal choice for applications where computational resources are limited but accurate structure prediction remains crucial.

  • 6 authors
·
Jul 15

Learning Yourself: Class-Incremental Semantic Segmentation with Language-Inspired Bootstrapped Disentanglement

Class-Incremental Semantic Segmentation (CISS) requires continuous learning of newly introduced classes while retaining knowledge of past classes. By abstracting mainstream methods into two stages (visual feature extraction and prototype-feature matching), we identify a more fundamental challenge termed catastrophic semantic entanglement. This phenomenon involves Prototype-Feature Entanglement caused by semantic misalignment during the incremental process, and Background-Increment Entanglement due to dynamic data evolution. Existing techniques, which rely on visual feature learning without sufficient cues to distinguish targets, introduce significant noise and errors. To address these issues, we introduce a Language-inspired Bootstrapped Disentanglement framework (LBD). We leverage the prior class semantics of pre-trained visual-language models (e.g., CLIP) to guide the model in autonomously disentangling features through Language-guided Prototypical Disentanglement and Manifold Mutual Background Disentanglement. The former guides the disentangling of new prototypes by treating hand-crafted text features as topological templates, while the latter employs multiple learnable prototypes and mask-pooling-based supervision for background-incremental class disentanglement. By incorporating soft prompt tuning and encoder adaptation modifications, we further bridge the capability gap of CLIP between dense and sparse tasks, achieving state-of-the-art performance on both Pascal VOC and ADE20k, particularly in multi-step scenarios.

  • 3 authors
·
Aug 30

Knowing You Don't Know: Learning When to Continue Search in Multi-round RAG through Self-Practicing

Retrieval Augmented Generation (RAG) has shown strong capability in enhancing language models' knowledge and reducing AI generative hallucinations, driving its widespread use. However, complex tasks requiring multi-round retrieval remain challenging, and early attempts tend to be overly optimistic without a good sense of self-skepticism. Current multi-round RAG systems may continue searching even when enough information has already been retrieved, or they may provide incorrect answers without having sufficient information or knowledge. Existing solutions either require large amounts of expensive human-labeled process supervision data or lead to subpar performance. This paper aims to address these limitations by introducing a new framework, SIM-RAG, to explicitly enhance RAG systems' self-awareness and multi-round retrieval capabilities. To train SIM-RAG, we first let a RAG system self-practice multi-round retrieval, augmenting existing question-answer pairs with intermediate inner monologue reasoning steps to generate synthetic training data. For each pair, the system may explore multiple retrieval paths, which are labeled as successful if they reach the correct answer and unsuccessful otherwise. Using this data, we train a lightweight information sufficiency Critic. At inference time, the Critic evaluates whether the RAG system has retrieved sufficient information at each round, guiding retrieval decisions and improving system-level self-awareness through in-context reinforcement learning. Experiments across multiple prominent RAG benchmarks show that SIM-RAG is an effective multi-round RAG solution. Furthermore, this framework is system-efficient, adding a lightweight component to RAG without requiring modifications to existing LLMs or search engines, and data-efficient, eliminating the need for costly human-annotated mid-step retrieval process supervision data.

  • 4 authors
·
May 5