N. Xu

Fang Wu, Shuting Jin, Xiangru Tang et al.

Among these, D-peptides are resistant to proteolysis, exhibit greater in vivo stability, and are easier to synthesize. Despite advances in deep learning for peptide discovery, the scarcity of natural D-protein data limits the transfer of existing generative models to the D-peptide chemical space. We propose D-Flow, a full-atom flow-based framework for de novo D-peptide design. Conditioned on receptor binding, D-Flow uses structural representations incorporating backbone frames, side-chain angles, and discrete amino acid types. A mirror-image algorithm is implemented to address the lack of training data for D-proteins by converting the chirality of L-receptors. Furthermore, we enhance D-Flow's capacity by integrating protein language models (PLMs) with structural awareness through a lightweight structural adapter that injects structural representations into PLM embeddings. This enables D-Flow to learn conformational priors in the D-peptide chemical space and to accommodate the chiral selectivity of binding sites, thereby mitigating the scarcity of D-peptide data. A two-stage training pipeline and a control toolkit enable D-Flow to transition from general protein design to targeted binder design while preserving pre-training knowledge. Results on the PepMerge benchmark show D-Flow's effectiveness. D-peptides generated by D-Flow align more closely with native sequences and structures, with sequence identity improving by 10.2% over the best baseline, and the top affinity score reaching 24.31%. Overall, D-Flow shows potential for D-peptide design, facilitating the development of bioorthogonal and stable molecular tools and diagnostics. Code is available at https://github.com/smiles724/PeptideDesign.

Kiran Ramnath, Kang Zhou, Sheng Guan et al.

Since the advent of large language models (LLMs), prompt engineering has been a crucial step for eliciting desired responses for various Natural Language Processing (NLP) tasks. However, prompt engineering remains an impediment for end users due to rapid advances in models, tasks, and associated best practices. To mitigate this, Automatic Prompt Optimization (APO) techniques have recently emerged that use various automated techniques to help improve the performance of LLMs on various tasks. In this paper, we present a comprehensive survey summarizing the current progress and remaining challenges in this field. We provide a formal definition of APO, a 5-part unifying framework, and then proceed to rigorously categorize all relevant works based on their salient features therein. We hope to spur further research guided by our framework.

Darren Yow-Bang Wang, Zhengyuan Shen, Soumya Smruti Mishra et al.

Structured outputs are essential for large language models (LLMs) in critical applications like agents and information extraction. Despite their capabilities, LLMs often generate outputs that deviate from predefined schemas, significantly hampering reliable application development. We present SLOT (Structured LLM Output Transformer), a model-agnostic approach that transforms unstructured LLM outputs into precise structured formats. While existing solutions predominantly rely on constrained decoding techniques or are tightly coupled with specific models, SLOT employs a fine-tuned lightweight language model as a post-processing layer, achieving flexibility across various LLMs and schema specifications. We introduce a systematic pipeline for data curation and synthesis alongside a formal evaluation methodology that quantifies both schema accuracy and content fidelity. Our results demonstrate that fine-tuned Mistral-7B model with constrained decoding achieves near perfect schema accuracy (99.5%) and content similarity (94.0%), outperforming Claude-3.5-Sonnet by substantial margins (+25 and +20 percentage points, respectively). Notably, even compact models like Llama-3.2-1B can match or exceed the structured output capabilities of much larger proprietary models when equipped with SLOT, enabling reliable structured generation in resource-constrained environments.

Pengfei Guo, Can Zhao, Dong Yang et al.

Generating 3D CT volumes from descriptive free-text inputs presents a transformative opportunity in diagnostics and research. In this paper, we introduce Text2CT, a novel approach for synthesizing 3D CT volumes from textual descriptions using the diffusion model. Unlike previous methods that rely on fixed-format text input, Text2CT employs a novel prompt formulation that enables generation from diverse, free-text descriptions. The proposed framework encodes medical text into latent representations and decodes them into high-resolution 3D CT scans, effectively bridging the gap between semantic text inputs and detailed volumetric representations in a unified 3D framework. Our method demonstrates superior performance in preserving anatomical fidelity and capturing intricate structures as described in the input text. Extensive evaluations show that our approach achieves state-of-the-art results, offering promising potential applications in diagnostics, and data augmentation.

Jiyao Liu, Jinjie Wei, Wanying Qu et al.

Medical Image Quality Assessment (IQA) serves as the first-mile safety gate for clinical AI, yet existing approaches remain constrained by scalar, score-based metrics and fail to reflect the descriptive, human-like reasoning process central to expert evaluation. To address this gap, we introduce MedQ-Bench, a comprehensive benchmark that establishes a perception-reasoning paradigm for language-based evaluation of medical image quality with Multi-modal Large Language Models (MLLMs). MedQ-Bench defines two complementary tasks: (1) MedQ-Perception, which probes low-level perceptual capability via human-curated questions on fundamental visual attributes; and (2) MedQ-Reasoning, encompassing both no-reference and comparison reasoning tasks, aligning model evaluation with human-like reasoning on image quality. The benchmark spans five imaging modalities and over forty quality attributes, totaling 2,600 perceptual queries and 708 reasoning assessments, covering diverse image sources including authentic clinical acquisitions, images with simulated degradations via physics-based reconstructions, and AI-generated images. To evaluate reasoning ability, we propose a multi-dimensional judging protocol that assesses model outputs along four complementary axes. We further conduct rigorous human-AI alignment validation by comparing LLM-based judgement with radiologists. Our evaluation of 14 state-of-the-art MLLMs demonstrates that models exhibit preliminary but unstable perceptual and reasoning skills, with insufficient accuracy for reliable clinical use. These findings highlight the need for targeted optimization of MLLMs in medical IQA. We hope that MedQ-Bench will catalyze further exploration and unlock the untapped potential of MLLMs for medical image quality evaluation.

Naixing Xu, Qian Li, Xu Wang et al.

Knowledge graph (KG) embedding methods map entities and relations into continuous vector spaces, improving performance in tasks like link prediction and question answering. With rising privacy concerns, machine unlearning (MU) has emerged as a critical AI technology, enabling models to eliminate the influence of specific data. Existing MU approaches often rely on data obfuscation and adjustments to training loss but lack generalization across unlearning tasks. This paper introduces MetaEU, a Meta-Learning-Based Knowledge Graph Embedding Unlearning framework. MetaEU leverages meta-learning to unlearn specific embeddings, mitigating their impact while preserving model performance on remaining data. Experiments on benchmark datasets demonstrate its effectiveness in KG embedding unlearning.