Diffusion Model with Representation Alignment for Protein Inverse Folding

Protein inverse folding is a fundamental problem in bioinformatics, aiming to recover the amino acid sequences from a given protein backbone structure. Despite the success of existing methods, they struggle to fully capture the intricate inter-residue relationships critical for accurate sequence prediction. We propose a novel method that leverages diffusion models with representation alignment (DMRA), which enhances diffusion-based inverse folding by (1) proposing a shared center that aggregates contextual information from the entire protein structure and selectively distributes it to each residue; and (2) aligning noisy hidden representations with clean semantic representations during the denoising process. This is achieved by predefined semantic representations for amino acid types and a representation alignment method that utilizes type embeddings as semantic feedback to normalize each residue. In experiments, we conduct extensive evaluations on the CATH4.2 dataset to demonstrate that DMRA outperforms leading methods, achieving state-of-the-art performance and exhibiting strong generalization capabilities on the TS50 and TS500 datasets.

Impromptu Cybercrime Euphemism Detection

Detecting euphemisms is essential for content security on various social media platforms, but existing methods designed for detecting euphemisms are ineffective in impromptu euphemisms. In this work, we make a first attempt to an exploration of impromptu euphemism detection and introduce the Impromptu Cybercrime Euphemisms Detection (ICED) dataset. Moreover, we propose a detection framework tailored to this problem, which employs context augmentation modeling and multi-round iterative training. Our detection framework mainly consists of a coarse-grained and a fine-grained classification model. The coarse-grained classification model removes most of the harmless content in the corpus to be detected. The fine-grained model, impromptu euphemisms detector, integrates context augmentation and multi-round iterations training to better predicts the actual meaning of a masked token. In addition, we leverage ChatGPT to evaluate the mode's capability. Experimental results demonstrate that our approach achieves a remarkable 76-fold improvement compared to the previous state-of-the-art euphemism detector.

Accelerating Vision Diffusion Transformers with Skip Branches

Diffusion Transformers (DiT), an emerging image and video generation model architecture, has demonstrated great potential because of its high generation quality and scalability properties. Despite the impressive performance, its practical deployment is constrained by computational complexity and redundancy in the sequential denoising process. While feature caching across timesteps has proven effective in accelerating diffusion models, its application to DiT is limited by fundamental architectural differences from U-Net-based approaches. Through empirical analysis of DiT feature dynamics, we identify that significant feature variation between DiT blocks presents a key challenge for feature reusability. To address this, we convert standard DiT into Skip-DiT with skip branches to enhance feature smoothness. Further, we introduce Skip-Cache which utilizes the skip branches to cache DiT features across timesteps at the inference time. We validated effectiveness of our proposal on different DiT backbones for video and image generation, showcasing skip branches to help preserve generation quality and achieve higher speedup. Experimental results indicate that Skip-DiT achieves a 1.5x speedup almost for free and a 2.2x speedup with only a minor reduction in quantitative metrics. Code is available at https://github.com/OpenSparseLLMs/Skip-DiT.git.

Rethinking Visual Dependency in Long-Context Reasoning for Large Vision-Language Models

Large Vision-Language Models (LVLMs) excel in cross-model tasks but experience performance declines in long-context reasoning due to overreliance on textual information and reduced visual dependency. In this study, we empirically analyze LVLMs in long-context reasoning, revealing that increased context length leads to a higher dependence on language at the expense of visual dependency. To address this issue, we propose a novel training-free context pruning method that selectively removes less critical textual information. Our approach enhances visual dependency and reduces textual noise, thereby improving LVLM performance in long-context reasoning. We validate our method by constructing a long-context dataset, demonstrating its effectiveness across various LVLMs. Moreover, further analysis confirms the robustness of different token pruning strategies and preliminary explores scaling laws between pruning rates and context length.

SURf: Teaching Large Vision-Language Models to Selectively Utilize Retrieved Information

Large Vision-Language Models (LVLMs) have become pivotal at the intersection of computer vision and natural language processing. However, the full potential of LVLMs Retrieval-Augmented Generation (RAG) capabilities remains underutilized. Existing works either focus solely on the text modality or are limited to specific tasks. Moreover, most LVLMs struggle to selectively utilize retrieved information and are sensitive to irrelevant or misleading references. To address these challenges, we propose a self-refinement framework designed to teach LVLMs to Selectively Utilize Retrieved Information (SURf). Specifically, when given questions that are incorrectly answered by the LVLM backbone, we obtain references that help correct the answers (positive references) and those that do not (negative references). We then fine-tune the LVLM backbone using a combination of these positive and negative references. Our experiments across three tasks and seven datasets demonstrate that our framework significantly enhances LVLMs ability to effectively utilize retrieved multimodal references and improves their robustness against irrelevant or misleading information. The source code is available at https://github.com/GasolSun36/SURf.

MemoryMamba: Memory-Augmented State Space Model for Defect Recognition

As automation advances in manufacturing, the demand for precise and sophisticated defect detection technologies grows. Existing vision models for defect recognition methods are insufficient for handling the complexities and variations of defects in contemporary manufacturing settings. These models especially struggle in scenarios involving limited or imbalanced defect data. In this work, we introduce MemoryMamba, a novel memory-augmented state space model (SSM), designed to overcome the limitations of existing defect recognition models. MemoryMamba integrates the state space model with the memory augmentation mechanism, enabling the system to maintain and retrieve essential defect-specific information in training. Its architecture is designed to capture dependencies and intricate defect characteristics, which are crucial for effective defect detection. In the experiments, MemoryMamba was evaluated across four industrial datasets with diverse defect types and complexities. The model consistently outperformed other methods, demonstrating its capability to adapt to various defect recognition scenarios.

Streamlined Photoacoustic Image Processing with Foundation Models: A Training-Free Solution

Foundation models have rapidly evolved and have achieved significant accomplishments in computer vision tasks. Specifically, the prompt mechanism conveniently allows users to integrate image prior information into the model, making it possible to apply models without any training. Therefore, we propose a method based on foundation models and zero training to solve the tasks of photoacoustic (PA) image segmentation. We employed the segment anything model (SAM) by setting simple prompts and integrating the model's outputs with prior knowledge of the imaged objects to accomplish various tasks, including: (1) removing the skin signal in three-dimensional PA image rendering; (2) dual speed-of-sound reconstruction, and (3) segmentation of finger blood vessels. Through these demonstrations, we have concluded that deep learning can be directly applied in PA imaging without the requirement for network design and training. This potentially allows for a hands-on, convenient approach to achieving efficient and accurate segmentation of PA images. This letter serves as a comprehensive tutorial, facilitating the mastery of the technique through the provision of code and sample datasets.

InsectMamba: Insect Pest Classification with State Space Model

The classification of insect pests is a critical task in agricultural technology, vital for ensuring food security and environmental sustainability. However, the complexity of pest identification, due to factors like high camouflage and species diversity, poses significant obstacles. Existing methods struggle with the fine-grained feature extraction needed to distinguish between closely related pest species. Although recent advancements have utilized modified network structures and combined deep learning approaches to improve accuracy, challenges persist due to the similarity between pests and their surroundings. To address this problem, we introduce InsectMamba, a novel approach that integrates State Space Models (SSMs), Convolutional Neural Networks (CNNs), Multi-Head Self-Attention mechanism (MSA), and Multilayer Perceptrons (MLPs) within Mix-SSM blocks. This integration facilitates the extraction of comprehensive visual features by leveraging the strengths of each encoding strategy. A selective module is also proposed to adaptively aggregate these features, enhancing the model's ability to discern pest characteristics. InsectMamba was evaluated against strong competitors across five insect pest classification datasets. The results demonstrate its superior performance and verify the significance of each model component by an ablation study.

Residual-based Language Models are Free Boosters for Biomedical Imaging

In this study, we uncover the unexpected efficacy of residual-based large language models (LLMs) as part of encoders for biomedical imaging tasks, a domain traditionally devoid of language or textual data. The approach diverges from established methodologies by utilizing a frozen transformer block, extracted from pre-trained LLMs, as an innovative encoder layer for the direct processing of visual tokens. This strategy represents a significant departure from the standard multi-modal vision-language frameworks, which typically hinge on language-driven prompts and inputs. We found that these LLMs could boost performance across a spectrum of biomedical imaging applications, including both 2D and 3D visual classification tasks, serving as plug-and-play boosters. More interestingly, as a byproduct, we found that the proposed framework achieved superior performance, setting new state-of-the-art results on extensive, standardized datasets in MedMNIST-2D and 3D. Through this work, we aim to open new avenues for employing LLMs in biomedical imaging and enriching the understanding of their potential in this specialized domain.

MAGIS: LLM-Based Multi-Agent Framework for GitHub Issue Resolution

In software evolution, resolving the emergent issues within GitHub repositories is a complex challenge that involves not only the incorporation of new code but also the maintenance of existing functionalities. Large Language Models (LLMs) have shown promise in code generation and understanding but face difficulties in code change, particularly at the repository level. To overcome these challenges, we empirically study the reason why LLMs mostly fail to resolve GitHub issues and analyze some impact factors. Motivated by the empirical findings, we propose a novel LLM-based Multi-Agent framework for GitHub Issue reSolution, MAGIS, consisting of four kinds of agents customized for the software evolution: Manager, Repository Custodian, Developer, and Quality Assurance Engineer agents. This framework leverages the collaboration of various agents in the planning and coding process to unlock the potential of LLMs to resolve GitHub issues. In experiments, we employ the SWE-bench benchmark to compare MAGIS with popular LLMs, including GPT-3.5, GPT-4, and Claude-2. MAGIS can resolve 13.94% GitHub issues, which significantly outperforms the baselines. Specifically, MAGIS achieves an eight-fold increase in resolved ratio over the direct application of GPT-4, the based LLM of our method. We also analyze the factors for improving GitHub issue resolution rates, such as line location, task allocation, etc.