Daily Papers

The core challenge of de novo protein design lies in creating proteins with specific functions or properties, guided by certain conditions. Current models explore to generate protein using structural and evolutionary guidance, which only provide indirect conditions concerning functions and properties. However, textual annotations of proteins, especially the annotations for protein domains, which directly describe the protein's high-level functionalities, properties, and their correlation with target amino acid sequences, remain unexplored in the context of protein design tasks. In this paper, we propose Protein-Annotation Alignment Generation, PAAG, a multi-modality protein design framework that integrates the textual annotations extracted from protein database for controllable generation in sequence space. Specifically, within a multi-level alignment module, PAAG can explicitly generate proteins containing specific domains conditioned on the corresponding domain annotations, and can even design novel proteins with flexible combinations of different kinds of annotations. Our experimental results underscore the superiority of the aligned protein representations from PAAG over 7 prediction tasks. Furthermore, PAAG demonstrates a significant increase in generation success rate (24.7% vs 4.7% in zinc finger, and 54.3% vs 22.0% in the immunoglobulin domain) in comparison to the existing model. We anticipate that PAAG will broaden the horizons of protein design by leveraging the knowledge from between textual annotation and proteins.

Large Vision and Language Models (LVLMs) have shown strong performance across various vision-language tasks in natural image domains. However, their application to remote sensing (RS) remains underexplored due to significant domain differences in visual appearances, object scales, and semantics. These discrepancies hider the effective understanding of RS scenes, which contain rich, multi-level semantic information spanning from coarse-to-fine levels. Hence, it limits the direct adaptation of existing LVLMs to RS imagery. To address this gap, we propose a novel LVLM framework tailored for RS understanding, incorporating two core components: Semantic-augmented Multi-level Alignment and Semantic-aware Expert Modeling. First, to align multi-level visual features, we introduce the retrieval-based Semantic Augmentation Module which enriches the visual features with relevant semantics across fine-to-coarse levels (e.g., object- and scene-level information). It is designed to retrieve relevant semantic cues from a RS semantic knowledge database, followed by aggregation of semantic cues with user query and multi-level visual features, resulting in semantically enriched representation across multiple levels. Second, for Semantic-aware Expert Modeling, we design semantic experts, where each expert is responsible for processing semantic representation at different levels separately. This enables hierarchical semantic understanding from coarse to fine levels. Evaluations across multiple RS tasks-including scene classification and VQA, etc.-demonstrate that the proposed framework achieves consistent improvements across multiple semantic levels. This highlights its capability and effectiveness in bridging the gap between general LVLMs and unique demands of RS-specific vision-language understanding.

Vision-language pre-training like CLIP has shown promising performance on various downstream tasks such as zero-shot image classification and image-text retrieval. Most of the existing CLIP-alike works usually adopt relatively large image encoders like ResNet50 and ViT, while the lightweight counterparts are rarely discussed. In this paper, we propose a multi-level interaction paradigm for training lightweight CLIP models. Firstly, to mitigate the problem that some image-text pairs are not strictly one-to-one correspondence, we improve the conventional global instance-level alignment objective by softening the label of negative samples progressively. Secondly, a relaxed bipartite matching based token-level alignment objective is introduced for finer-grained alignment between image patches and textual words. Moreover, based on the observation that the accuracy of CLIP model does not increase correspondingly as the parameters of text encoder increase, an extra objective of masked language modeling (MLM) is leveraged for maximizing the potential of the shortened text encoder. In practice, an auxiliary fusion module injecting unmasked image embedding into masked text embedding at different network stages is proposed for enhancing the MLM. Extensive experiments show that without introducing additional computational cost during inference, the proposed method achieves a higher performance on multiple downstream tasks.

On a shutter press, modern handheld cameras capture multiple images in rapid succession and merge them to generate a single image. However, individual frames in a burst are misaligned due to inevitable motions and contain multiple degradations. The challenge is to properly align the successive image shots and merge their complimentary information to achieve high-quality outputs. Towards this direction, we propose Burstormer: a novel transformer-based architecture for burst image restoration and enhancement. In comparison to existing works, our approach exploits multi-scale local and non-local features to achieve improved alignment and feature fusion. Our key idea is to enable inter-frame communication in the burst neighborhoods for information aggregation and progressive fusion while modeling the burst-wide context. However, the input burst frames need to be properly aligned before fusing their information. Therefore, we propose an enhanced deformable alignment module for aligning burst features with regards to the reference frame. Unlike existing methods, the proposed alignment module not only aligns burst features but also exchanges feature information and maintains focused communication with the reference frame through the proposed reference-based feature enrichment mechanism, which facilitates handling complex motions. After multi-level alignment and enrichment, we re-emphasize on inter-frame communication within burst using a cyclic burst sampling module. Finally, the inter-frame information is aggregated using the proposed burst feature fusion module followed by progressive upsampling. Our Burstormer outperforms state-of-the-art methods on burst super-resolution, burst denoising and burst low-light enhancement. Our codes and pretrained models are available at https:// github.com/akshaydudhane16/Burstormer

Automatic radiology report generation has attracted enormous research interest due to its practical value in reducing the workload of radiologists. However, simultaneously establishing global correspondences between the image (e.g., Chest X-ray) and its related report and local alignments between image patches and keywords remains challenging. To this end, we propose an Unify, Align and then Refine (UAR) approach to learn multi-level cross-modal alignments and introduce three novel modules: Latent Space Unifier (LSU), Cross-modal Representation Aligner (CRA) and Text-to-Image Refiner (TIR). Specifically, LSU unifies multimodal data into discrete tokens, making it flexible to learn common knowledge among modalities with a shared network. The modality-agnostic CRA learns discriminative features via a set of orthonormal basis and a dual-gate mechanism first and then globally aligns visual and textual representations under a triplet contrastive loss. TIR boosts token-level local alignment via calibrating text-to-image attention with a learnable mask. Additionally, we design a two-stage training procedure to make UAR gradually grasp cross-modal alignments at different levels, which imitates radiologists' workflow: writing sentence by sentence first and then checking word by word. Extensive experiments and analyses on IU-Xray and MIMIC-CXR benchmark datasets demonstrate the superiority of our UAR against varied state-of-the-art methods.

Medical image segmentation plays a crucial role in assisting healthcare professionals with accurate diagnoses and enabling automated diagnostic processes. Traditional convolutional neural networks (CNNs) often struggle with capturing long-range dependencies, while transformer-based architectures, despite their effectiveness, come with increased computational complexity. Recent efforts have focused on combining CNNs and transformers to balance performance and efficiency, but existing approaches still face challenges in achieving high segmentation accuracy while maintaining low computational costs. Furthermore, many methods underutilize the CNN encoder's capability to capture local spatial information, concentrating primarily on mitigating long-range dependency issues. To address these limitations, we propose QTSeg, a novel architecture for medical image segmentation that effectively integrates local and global information. QTSeg features a dual-mix attention decoder designed to enhance segmentation performance through: (1) a cross-attention mechanism for improved feature alignment, (2) a spatial attention module to capture long-range dependencies, and (3) a channel attention block to learn inter-channel relationships. Additionally, we introduce a multi-level feature distribution module, which adaptively balances feature propagation between the encoder and decoder, further boosting performance. Extensive experiments on five publicly available datasets covering diverse segmentation tasks, including lesion, polyp, breast cancer, cell, and retinal vessel segmentation, demonstrate that QTSeg outperforms state-of-the-art methods across multiple evaluation metrics while maintaining lower computational costs. Our implementation can be found at: https://github.com/tpnam0901/QTSeg (v1.0.0)

Activation steering offers a promising approach to controlling the behavior of Large Language Models by directly manipulating their internal activations. However, most existing methods struggle to jointly steer multiple attributes, often resulting in interference and undesirable trade-offs. To address this challenge, we propose Multi-Subspace Representation Steering (MSRS), a novel framework for effective multi-attribute steering via subspace representation fine-tuning. MSRS reduces inter-attribute interference by allocating orthogonal subspaces to each attribute, isolating their influence within the model's representation space. MSRS also incorporates a hybrid subspace composition strategy: it combines attribute-specific subspaces for unique steering directions with a shared subspace for common steering directions. A dynamic weighting function learns to efficiently integrate these components for precise control. During inference, MSRS introduces a token-level steering mechanism that dynamically identifies and intervenes on the most semantically relevant tokens, enabling fine-grained behavioral modulation. Experimental results show that MSRS significantly reduces attribute conflicts, surpasses existing methods across a range of attributes, and generalizes effectively to diverse downstream tasks.

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

This paper investigates approaches to enhance the reasoning capabilities of Large Language Model (LLM) agents using Reinforcement Learning (RL). Specifically, we focus on multi-turn tool-use scenarios, which can be naturally modeled as Markov Decision Processes (MDPs). While existing approaches often train multi-turn LLM agents with trajectory-level advantage estimation in bandit settings, they struggle with turn-level credit assignment across multiple decision steps, limiting their performance on multi-turn reasoning tasks. To address this, we introduce a fine-grained turn-level advantage estimation strategy to enable more precise credit assignment in multi-turn agent interactions. The strategy is general and can be incorporated into various RL algorithms such as Group Relative Preference Optimization (GRPO). Our experimental evaluation on multi-turn reasoning and search-based tool-use tasks with GRPO implementations highlights the effectiveness of the MDP framework and the turn-level credit assignment in advancing the multi-turn reasoning capabilities of LLM agents in complex decision-making settings. Our method achieves 100% success in tool execution and 50% accuracy in exact answer matching, significantly outperforming baselines, which fail to invoke tools and achieve only 20-30% exact match accuracy.