Qifeng Wu

Yuxin Wang, Jiahao Lu, Qifeng Wu et al.

Large Language Models (LLMs) have achieved remarkable performance in complex reasoning tasks through Chain-of-Thought (CoT) prompting. However, this approach often leads to ``over-thinking,'' where models generate unnecessarily long reasoning traces for simple queries and incur avoidable inference cost. While recent work has explored adaptive reasoning, existing methods typically make a single query-level decision about whether to reason. This overlooks the dynamic nature of multi-step tasks, where the need for explicit reasoning varies across intermediate stages. To address this limitation, we introduce AdaptR1, a Reinforcement Learning (RL) based framework for adaptive interleaved thinking in multi-hop Question Answering (QA). Unlike previous approaches that require Supervised Fine-Tuning (SFT) for cold-start initialization, AdaptR1 uses a fully RL-based strategy with a quality-gated efficiency reward to dynamically allocate reasoning budgets at each step. Under the Graph-R1 setting, AdaptR1 reduces average think tokens by 69.71\%, with a 90.35\% reduction on HotpotQA, while maintaining performance comparable to or better than standard baselines. Furthermore, our analysis reveals that overthinking in multi-hop reasoning is not uniformly distributed but occurs predominantly during the initial planning stages, highlighting the effectiveness of step-wise adaptive budget allocation.

Chunhan Li, Qifeng Wu, Jia-Hui Pan et al.

Text-to-image generation has advanced rapidly, but existing models still struggle with faithfully composing multiple objects and preserving their attributes in complex scenes. We propose coDrawAgents, an interactive multi-agent dialogue framework with four specialized agents: Interpreter, Planner, Checker, and Painter that collaborate to improve compositional generation. The Interpreter adaptively decides between a direct text-to-image pathway and a layout-aware multi-agent process. In the layout-aware mode, it parses the prompt into attribute-rich object descriptors, ranks them by semantic salience, and groups objects with the same semantic priority level for joint generation. Guided by the Interpreter, the Planner adopts a divide-and-conquer strategy, incrementally proposing layouts for objects with the same semantic priority level while grounding decisions in the evolving visual context of the canvas. The Checker introduces an explicit error-correction mechanism by validating spatial consistency and attribute alignment, and refining layouts before they are rendered. Finally, the Painter synthesizes the image step by step, incorporating newly planned objects into the canvas to provide richer context for subsequent iterations. Together, these agents address three key challenges: reducing layout complexity, grounding planning in visual context, and enabling explicit error correction. Extensive experiments on benchmarks GenEval and DPG-Bench demonstrate that coDrawAgents substantially improves text-image alignment, spatial accuracy, and attribute binding compared to existing methods.

Qifeng Wu, Zhengzhe Liu, Han Zhu et al.

This paper aims to retrieve proteins with similar structures and semantics from large-scale protein dataset, facilitating the functional interpretation of protein structures derived by structural determination methods like cryo-Electron Microscopy (cryo-EM). Motivated by the recent progress of vision-language models (VLMs), we propose a CLIP-style framework for aligning 3D protein structures with functional annotations using contrastive learning. For model training, we propose a large-scale dataset of approximately 200,000 protein-caption pairs with rich functional descriptors. We evaluate our model in both in-domain and more challenging cross-database retrieval on Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) dataset, respectively. In both cases, our approach demonstrates promising zero-shot retrieval performance, highlighting the potential of multimodal foundation models for structure-function understanding in protein biology.

Mostofa Rafid Uddin, Mahek Vora, Qifeng Wu et al.

Cryo-electron tomography (cryo-ET) provides direct 3D visualization of macromolecules inside the cell, enabling analysis of their in situ morphology. This morphology can be regarded as an SE(3)-invariant, denoised volumetric representation of subvolumes extracted from tomograms. Inferring morphology is therefore an inverse problem of estimating both a template morphology and its SE(3) transformation. Existing expectation-maximization based solution to this problem often misses rare but important morphologies and requires extensive manual hyperparameter tuning. Addressing this issue, we present a disentangled deep representation learning framework that separates SE(3) transformations from morphological content in the representation space. The framework includes a novel multi-choice learning module that enables this disentanglement for highly noisy cryo-ET data, and the learned morphological content is used to generate template morphologies. Experiments on simulated and real cryo-ET datasets demonstrate clear improvements over prior methods, including the discovery of previously unidentified macromolecular morphologies.

Xingjian Li, Qifeng Wu, Adithya S. Ubaradka et al.

Medical image segmentation is vital for clinical diagnosis, yet current deep learning methods often demand extensive expert effort, i.e., either through annotating large training datasets or providing prompts at inference time for each new case. This paper introduces a zero-shot and automatic segmentation pipeline that combines off-the-shelf vision-language and segmentation foundation models. Given a medical image and a task definition (e.g., "segment the optic disc in an eye fundus image"), our method uses a grounding model to generate an initial bounding box, followed by a visual prompt boosting module that enhance the prompts, which are then processed by a promptable segmentation model to produce the final mask. To address the challenges of domain gap and result verification, we introduce a test-time adaptation framework featuring a set of learnable adaptors that align the medical inputs with foundation model representations. Its hyperparameters are optimized via Bayesian Optimization, guided by a proxy validation model without requiring ground-truth labels. Our pipeline offers an annotation-efficient and scalable solution for zero-shot medical image segmentation across diverse tasks. Our pipeline is evaluated on seven diverse medical imaging datasets and shows promising results. By proper decomposition and test-time adaptation, our fully automatic pipeline not only substantially surpasses the previously best-performing method, yielding a 69\% relative improvement in accuracy (Dice Score from 42.53 to 71.81), but also performs competitively with weakly-prompted interactive foundation models.