Mengdi Liu

Keliang Li, Yansong Li, Hongze Shen et al.

The dense, temporal nature of video presents a profound challenge for automated analysis. Despite the use of powerful Vision-Language Models, prevailing methods for video understanding are limited by the inherent disconnect between reasoning and perception: they rely on static, pre-processed information and cannot actively seek raw evidence from video as their understanding evolves. To address this, we introduce LensWalk, a flexible agentic framework that empowers a Large Language Model reasoner to control its own visual observation actively. LensWalk establishes a tight reason-plan-observe loop where the agent dynamically specifies, at each step, the temporal scope and sampling density of the video it observes. Using a suite of versatile, Vision-Language Model based tools parameterized by these specifications, the agent can perform broad scans for cues, focus on specific segments for fact extraction, and stitch evidence from multiple moments for holistic verification. This design allows for progressive, on-demand evidence gathering that directly serves the agent's evolving chain of thought. Without requiring any model fine-tuning, LensWalk delivers substantial, plug-and-play performance gains on multiple model recipes, boosting their accuracy by over 5\% on challenging long-video benchmarks like LVBench and Video-MME. Our analysis reveals that enabling an agent to control how it sees is key to unlocking more accurate, robust, and interpretable video reasoning.

Mengdi Liu, Qiang Li, Weizhi Nie et al.

Type A Aortic Dissection (TAAD) is a life-threatening cardiovascular emergency that demands rapid and precise preoperative evaluation. While key anatomical and pathological features are decisive for surgical planning, current research focuses predominantly on improving segmentation accuracy, leaving the reliable, quantitative extraction of clinically actionable features largely under-explored. Furthermore, constructing comprehensive TAAD datasets requires labor-intensive, expert level pixel-wise annotations, which is impractical for most clinical institutions. Due to significant domain shift, models trained on a single center dataset also suffer from severe performance degradation during cross-institutional deployment. This study addresses a clinically critical challenge: the accurate extraction of key TAAD clinical features during cross-institutional deployment in the total absence of target-domain annotations. To this end, we propose an unsupervised domain adaptation (UDA)-driven framework for the automated extraction of TAAD clinical features. The framework leverages limited source-domain labels while effectively adapting to unlabeled data from target domains. Tailored for real-world emergency workflows, our framework aims to achieve stable cross-institutional multi-class segmentation, reliable and quantifiable clinical feature extraction, and practical deployability independent of high-cost annotations. Extensive experiments demonstrate that our method significantly improves cross-domain segmentation performance compared to existing state-of-the-art approaches. More importantly, a reader study involving multiple cardiovascular surgeons confirms that the automatically extracted clinical features provide meaningful assistance for preoperative assessment, highlighting the practical utility of the proposed end-to-end segmentation-to-feature pipeline.

Kai Zhuang, Jiawei Zhang, Yumou Liu et al.

Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma. Whether treating sequences as a specialized language, risking the loss of functional motif information, or as a separate modality, introducing formidable alignment challenges, current strategies fundamentally limit their reasoning capacity. We challenge this sequence-centric paradigm by positing that a more effective strategy is to provide Sci-LLMs with high-level structured context derived from established bioinformatics tools, thereby bypassing the need to interpret low-level noisy sequence data directly. Through a systematic comparison of leading Sci-LLMs on biological reasoning tasks, we tested three input modes: sequence-only, context-only, and a combination of both. Our findings are striking: the context-only approach consistently and substantially outperforms all other modes. Even more revealing, the inclusion of the raw sequence alongside its high-level context consistently degrades performance, indicating that raw sequences act as informational noise, even for models with specialized tokenization schemes. These results suggest that the primary strength of existing Sci-LLMs lies not in their nascent ability to interpret biomolecular syntax from scratch, but in their profound capacity for reasoning over structured, human-readable knowledge. Therefore, we argue for reframing Sci-LLMs not as sequence decoders, but as powerful reasoning engines over expert knowledge. This work lays the foundation for a new class of hybrid scientific AI agents, repositioning the developmental focus from direct sequence interpretation towards high-level knowledge synthesis. The code is available at https://github.com/opendatalab-raiser/CoKE.

Zhangyang Gao, Hao Wang, Cheng Tan et al.

This study investigates the current landscape and future directions of protein foundation model research. While recent advancements have transformed protein science and engineering, the field lacks a comprehensive benchmark for fair evaluation and in-depth understanding. Since ESM-1B, numerous protein foundation models have emerged, each with unique datasets and methodologies. However, evaluations often focus on limited tasks tailored to specific models, hindering insights into broader generalization and limitations. Specifically, researchers struggle to understand the relationships between tasks, assess how well current models perform across them, and determine the criteria in developing new foundation models. To fill this gap, we present PFMBench, a comprehensive benchmark evaluating protein foundation models across 38 tasks spanning 8 key areas of protein science. Through hundreds of experiments on 17 state-of-the-art models across 38 tasks, PFMBench reveals the inherent correlations between tasks, identifies top-performing models, and provides a streamlined evaluation protocol. Code is available at \href{https://github.com/biomap-research/PFMBench}{\textcolor{blue}{GitHub}}.

Mengdi Liu, Xiaoxue Cheng, Zhangyang Gao et al.

Designing protein sequences that fold into a target 3D structure, known as protein inverse folding, is a fundamental challenge in protein engineering. While recent deep learning methods have achieved impressive performance by recovering native sequences, they often overlook the one-to-many nature of the problem: multiple diverse sequences can fold into the same structure. This motivates the need for a generative model capable of designing diverse sequences while preserving structural consistency. To address this trade-off, we introduce ProtInvTree, the first reward-guided tree-search framework for protein inverse folding. ProtInvTree reformulates sequence generation as a deliberate, step-wise decision-making process, enabling the exploration of multiple design paths and exploitation of promising candidates through self-evaluation, lookahead, and backtracking. We propose a two-stage focus-and-grounding action mechanism that decouples position selection and residue generation. To efficiently evaluate intermediate states, we introduce a jumpy denoising strategy that avoids full rollouts. Built upon pretrained protein language models, ProtInvTree supports flexible test-time scaling by expanding the search depth and breadth without retraining. Empirically, ProtInvTree outperforms state-of-the-art baselines across multiple benchmarks, generating structurally consistent yet diverse sequences, including those far from the native ground truth.

Qibo Chen, Weizhong Jin, Jianyue Ge et al.

Recent research on universal object detection aims to introduce language in a SoTA closed-set detector and then generalize the open-set concepts by constructing large-scale (text-region) datasets for training. However, these methods face two main challenges: (i) how to efficiently use the prior information in the prompts to genericise objects and (ii) how to reduce alignment bias in the downstream tasks, both leading to sub-optimal performance in some scenarios beyond pre-training. To address these challenges, we propose a strong universal detection foundation model called CP-DETR, which is competitive in almost all scenarios, with only one pre-training weight. Specifically, we design an efficient prompt visual hybrid encoder that enhances the information interaction between prompt and visual through scale-by-scale and multi-scale fusion modules. Then, the hybrid encoder is facilitated to fully utilize the prompted information by prompt multi-label loss and auxiliary detection head. In addition to text prompts, we have designed two practical concept prompt generation methods, visual prompt and optimized prompt, to extract abstract concepts through concrete visual examples and stably reduce alignment bias in downstream tasks. With these effective designs, CP-DETR demonstrates superior universal detection performance in a broad spectrum of scenarios. For example, our Swin-T backbone model achieves 47.6 zero-shot AP on LVIS, and the Swin-L backbone model achieves 32.2 zero-shot AP on ODinW35. Furthermore, our visual prompt generation method achieves 68.4 AP on COCO val by interactive detection, and the optimized prompt achieves 73.1 fully-shot AP on ODinW13.

Qibo Chen, Weizhong Jin, Shuchang Li et al.

Text prompts are crucial for generalizing pre-trained open-set object detection models to new categories. However, current methods for text prompts are limited as they require manual feedback when generalizing to new categories, which restricts their ability to model complex scenes, often leading to incorrect detection results. To address this limitation, we propose a novel visual prompt method that learns new category knowledge from a few labeled images, which generalizes the pre-trained detection model to the new category. To allow visual prompts to represent new categories adequately, we propose a statistical-based prompt construction module that is not limited by predefined vocabulary lengths, thus allowing more vectors to be used when representing categories. We further utilize the category dictionaries in the pre-training dataset to design task-specific similarity dictionaries, which make visual prompts more discriminative. We evaluate the method on the ODinW dataset and show that it outperforms existing prompt learning methods and performs more consistently in combinatorial inference.

Mengdi Liu, Zhangyang Gao, Hong Chang et al.

Understanding how genes influence phenotype across species is a fundamental challenge in genetic engineering, which will facilitate advances in various fields such as crop breeding, conservation biology, and personalized medicine. However, current phenotype prediction models are limited to individual species and expensive phenotype labeling process, making the genotype-to-phenotype prediction a highly domain-dependent and data-scarce problem. To this end, we suggest taking images as morphological proxies, facilitating cross-species generalization through large-scale multimodal pretraining. We propose the first genotype-to-phenotype diffusion model (G2PDiffusion) that generates morphological images from DNA considering two critical evolutionary signals, i.e., multiple sequence alignments (MSA) and environmental contexts. The model contains three novel components: 1) a MSA retrieval engine that identifies conserved and co-evolutionary patterns; 2) an environment-aware MSA conditional encoder that effectively models complex genotype-environment interactions; and 3) an adaptive phenomic alignment module to improve genotype-phenotype consistency. Extensive experiments show that integrating evolutionary signals with environmental context enriches the model's understanding of phenotype variability across species, thereby offering a valuable and promising exploration into advanced AI-assisted genomic analysis.

Hongjia Wu, Mengdi Liu

Driven by the visions of Internet of Things and 5G communications, recent years have seen a paradigm shift in personal mobile devices, from smartphones towards wearable devices. Wearable devices come in many different forms targeting different application scenarios. Among these, the fitness wearable devices (FWDs) are proven to be one of the forms that intrigue the market and occupy an increasing trend in terms of the market share. Nevertheless, although the fitness wearable devices nowadays are functionally self-contained based on the advanced sensor, computation, and communicative technologies, there is still a large gap to truly satisfy the target customer group, i.e., accessible to and usable by a larger quantity of users. This fuels the research area on applying the universal design principles to fitness wearable devices. In this survey, we first present the background of FWDs and show the acceptance and adaption challenges of the corresponding user groups. We then review the universal design principle and how it and its relative approaches could be used in FWDs. Further, we collect the available FWDs that bear the universal design principles in their development circles. Last, we open up the discussion based on the surveyed literature and provide the insight of potential future work.

Mengdi Liu, Guangquan Xu

Cold Start (CS) and sparse evaluation problems dramatically degrade recommendation performance in large-scale recommendation systems such as Taobao and eBay. We name this degradation as the sparse trust problem, which will cause the decrease of the recommendation accuracy rate. To address this problem we propose a novel sparse trust mining method, which is based on the Roundtable Gossip Algorithm (RGA). First, we define the relevant representation of sparse trust, which provides a research idea to solve the problem of sparse evidence in the large-scale recommendation system. Based on which the RGA is proposed for mining latent sparse trust relationships between entities in large-scale recommendation systems. Second, we propose an efficient and simple anti-sparsification method, which overcomes the disadvantages of random trust relationship propagation and Grade Inflation caused by different users have different standard for item rating. Finally, the experimental results show that our method can effectively mine new trust relationships and mitigate the sparse trust problem.