Yitian Zhou

Yitian Zhou, Gaétan Lelu, Boris Labbé et al.

Purpose. Ability to locate and track ultrasound images in the 3D operating space is of great benefit for multiple clinical applications. This is often accomplished by tracking the probe using a precise but expensive optical or electromagnetic tracking system. Our goal is to develop a simple and low cost augmented reality echography framework using a standard RGB-D Camera. Methods. A prototype system consisting of an Occipital Structure Core RGB-D camera, a specifically-designed 3D marker, and a fast point cloud registration algorithm FaVoR was developed and evaluated on an Ultrasonix ultrasound system. The probe was calibrated on a 3D-printed N-wire phantom using the software PLUS toolkit. The proposed calibration method is simplified, requiring no additional markers or sensors attached to the phantom. Also, a visualization software based on OpenGL was developed for the augmented reality application. Results. The calibrated probe was used to augment a real-world video in a simulated needle insertion scenario. The ultrasound images were rendered on the video, and visually-coherent results were observed. We evaluated the end-to-end accuracy of our AR US framework on localizing a cube of 5 cm size. From our two experiments, the target pose localization error ranges from 5.6 to 5.9 mm and from -3.9 to 4.2 degrees. Conclusion. We believe that with the potential democratization of RGB-D cameras integrated in mobile devices and AR glasses in the future, our prototype solution may facilitate the use of 3D freehand ultrasound in clinical routine. Future work should include a more rigorous and thorough evaluation, by comparing the calibration accuracy with those obtained by commercial tracking solutions in both simulated and real medical scenarios.

Zhenzhen Huang, Chaoning Zhang, Fachrina Dewi Puspitasari et al.

Large language models (LLMs) are increasingly utilized in various complex reasoning tasks due to their excellent instruction following capability. However, the model's performance is highly dependent on the open-ended characteristics of the users' input prompt. Natural prompts often do not follow proper syntactic rules, which creates ambiguous queries that yield multiple interpretations. Such ambiguous prompts confuse the model in choosing the correct reasoning paths to answer questions. Prior works address this challenge by applying query editing during the LLM inference process without explicitly solving the root cause of the ambiguity. To address this limitation, we propose a pre-inference prompt optimization mechanism via explicit prompt disambiguation. Particularly, we identify semantic risks in the prompt, check their multi-perspective consistency, and resolve any semantic conflicts that arise. Finally, we organize the resolved ambiguities in a logically structured manner as a clean input to the LLM. By explicitly resolving semantic ambiguity, our method can produce a more focused attention distribution to the semantically essential tokens. We also leverage small language models (SLMs) as the main executor of prompt disambiguation to benefit from their efficient computation. Through comprehensive experiments on multiple benchmarks, we demonstrate that our method improves reasoning performance by 2.5 points at a cost of only \$0.02. Our study promotes explicit prompt disambiguation as an effective prompt optimization method without disturbing the internal mechanism of LLM inference.

Jiaquan Zhang, Qigan Sun, Chaoning Zhang et al.

Enhancing the reasoning capability of large language models (LLMs) remains a core challenge in natural language processing. The Chain-of-Thought (CoT) paradigm dominates practical applications for its single-round efficiency, yet its reasoning chains often exhibit logical gaps. While multi-round paradigms like Graph-of-Thoughts (GoT), Tree-of-Thoughts (ToT), and Atom of Thought (AoT) achieve strong performance and reveal effective reasoning structures, their high cost limits practical use. To address this problem, this paper proposes a topology-based method for optimizing reasoning chains. The framework embeds essential topological patterns of effective reasoning into the lightweight CoT paradigm. Using persistent homology, we map CoT, ToT, and GoT into a unified topological space to quantify their structural features. On this basis, we design a unified optimization system: a Topological Optimization Agent diagnoses deviations in CoT chains from desirable topological characteristics and simultaneously generates targeted strategies to repair these structural deficiencies. Compared with multi-round reasoning methods like ToT and GoT, experiments on multiple datasets show that our approach offers a superior balance between reasoning accuracy and efficiency, showcasing a practical solution to ``single-round generation with multi-round intelligence''.

Shuxu Chen, Yitian Zhou, Jiaquan Zhang et al.

Chain-of-Thought (CoT) prompting has emerged as a simple and effective way to elicit step-by-step solutions from large language models (LLMs). However, CoT reasoning can be unstable across runs on long, multi-step problems, leading to inconsistent answers for unchanged task. Most prior work focuses on improving the forward reasoning chain within a single pass, with less attention to iterative and contrastive correction. To address this gap, we propose CAP-CoT, a Cycle Adversarial Prompt optimization framework designed to improve both CoT reasoning accuracy and stability of a single deployed solver. In each cycle, a forward solver generates candidate reasoning chains, an adversarial challenger constructs plausible but deliberately flawed chains using targeted error strategies, and a feedback agent contrasts the two chains and produces step-aligned structured feedback. This feedback closes the optimization loop in two directions, including updating the solver prompt based on errors exposed by the challenger, and updating the challenger prompt to generate increasingly targeted errors in subsequent cycles. Unlike safety-oriented adversarial prompting such as jailbreak or prompt-injection attacks, our adversarial component is task-semantic and aims to expose logical vulnerabilities in reasoning chains. Experiments across six benchmarks and four LLM backbones demonstrate that within two to three adversarial prompt optimization cycles, CAP-CoT consistently reduces variability across runs while improving reasoning accuracy and robustness to prompt perturbations.

Yitian Zhou, Chaoning Zhang, Jiaquan Zhang et al.

Long-context large language models remain computationally expensive to run and often fail to reliably process very long inputs, which makes context compression an important component of many systems. Existing compression approaches typically rely on trained compressors, dense retrieval-style selection, or heuristic trimming, and they often struggle to jointly preserve task relevance, topic coverage, and cross-sentence coherence under a strict token budget. To address this, we propose a training-free and model-agnostic compression framework that selects a compact set of sentences guided by structural graph priors. Our method constructs a sparse hybrid sentence graph that combines mutual k-NN semantic edges with short-range sequential edges, extracts a topic skeleton via clustering, and ranks sentences using an interpretable score that integrates task relevance, cluster representativeness, bridge centrality, and a cycle coverage cue. A budgeted greedy selection with redundancy suppression then produces a readable compressed context in original order. Experimental results on four datasets show that our approach is competitive with strong extractive and abstractive baselines, demonstrating larger gains on long-document benchmarks.

Yutong Li, Yitian Zhou, Xudong Wang et al.

Large language models (LLMs) have demonstrated impressive capabilities in natural language understanding and generation, including multi-step reasoning such as mathematical proving. However, existing approaches often lack an explicit and dynamic mechanism to structurally represent and evolve intermediate reasoning states, which limits their ability to perform context-aware theorem selection and iterative conclusion generation. To address these challenges, we propose GraphMind, a novel dynamic graph-based framework that integrates the graph neural network (GNN) with LLMs to iteratively select theorems and generate intermediate conclusions for multi-step reasoning. Our method models the reasoning process as a heterogeneous evolving graph, where nodes represent conditions, theorems, and conclusions, while edges capture logical dependencies between nodes. By encoding the current reasoning state with GNN and leveraging semantic matching for theorem selection, our framework enables context-aware, interpretable, and structured reasoning in a closed-loop manner. Experiments on various question-answering (QA) datasets demonstrate that our proposed GraphMind method achieves consistent performance improvements and significantly outperforms existing baselines in multi-step reasoning, validating the effectiveness and generalizability of our approach.

Antoine Honoré, Borja Rodríguez Gálvez, Yoomi Park et al.

Variant effect predictors (VEPs) aim to assess the functional impact of protein variants, traditionally relying on multiple sequence alignments (MSAs). This approach assumes that naturally occurring variants are fit, an assumption challenged by pharmacogenomics, where some pharmacogenes experience low evolutionary pressure. Deep mutational scanning (DMS) datasets provide an alternative by offering quantitative fitness scores for variants. In this work, we propose a transformer-based matrix variational auto-encoder (matVAE) with a structured prior and evaluate its performance on 33 DMS datasets corresponding to 26 drug target and ADME proteins from the ProteinGym benchmark. Our model trained on MSAs (matVAE-MSA) outperforms the state-of-the-art DeepSequence model in zero-shot prediction on DMS datasets, despite using an order of magnitude fewer parameters and requiring less computation at inference time. We also compare matVAE-MSA to matENC-DMS, a model of similar capacity trained on DMS data, and find that the latter performs better on supervised prediction tasks. Additionally, incorporating AlphaFold-generated structures into our transformer model further improves performance, achieving results comparable to DeepSequence trained on MSAs and finetuned on DMS. These findings highlight the potential of DMS datasets to replace MSAs without significant loss in predictive performance, motivating further development of DMS datasets and exploration of their relationships to enhance variant effect prediction.