Yingfang Yuan
Publications
Scaling with Confidence: Calibrating Confidence of LLMs for Adaptive Test Time Scaling
Training large language models (LLMs) with reinforcement learning (RL) has significantly advanced their performance on reasoning and question-answering tasks. However, prevailing RL reward designs typically prioritize response correctness, neglecting to incentivize models to express their confidence accurately. This leads to a critical problem: performance gains are often accompanied by poor calibration between confidence and accuracy, misleading models to overconfidently hallucinate when uncertain. To address this limitation, we propose $\textbf{C}$orrectness and $\textbf{C}$onfidence $\textbf{C}$alibration $\textbf{R}$einforcement $\textbf{L}$earning ($\textbf{C3RL}$), a novel RL algorithm integrating correctness, calibration and dataset-informed reference accuracy rewards together. Comprehensive evaluation across 8 text and multimodal datasets demonstrates that C3RL enhances calibration without sacrificing accuracy, outperforming the current state-of-the-art method in both performance and calibration metrics. Utilizing the well-calibrated verbalized confidence from C3RL, we further introduce $\textbf{C}$onfidence-based $\textbf{A}$daptive Test Time $\textbf{S}$caling ($\textbf{CAS}$), an adjustable inference-time strategy that allocates computational resources based on response confidence. Experiments show that CAS surpasses majority voting on both in-domain and out-of-domain datasets while reducing the inference budget by up to 12.33 times. We believe the synergy of C3RL and CAS paves the way for deploying more reliable and resource-efficient LLMs. The code, data and models will be released.
Towards Trustworthy Report Generation: A Deep Research Agent with Progressive Confidence Estimation and Calibration
As agent-based systems continue to evolve, deep research agents are capable of automatically generating research-style reports across diverse domains. While these agents promise to streamline information synthesis and knowledge exploration, existing evaluation frameworks-typically based on subjective dimensions-fail to capture a critical aspect of report quality: trustworthiness. In open-ended research scenarios where ground-truth answers are unavailable, current evaluation methods cannot effectively measure the epistemic confidence of generated content, making calibration difficult and leaving users susceptible to misleading or hallucinated information. To address this limitation, we propose a novel deep research agent that incorporates progressive confidence estimation and calibration within the report generation pipeline. Our system leverages a deliberative search model, featuring deep retrieval and multi-hop reasoning to ground outputs in verifiable evidence while assigning confidence scores to individual claims. Combined with a carefully designed workflow, this approach produces trustworthy reports with enhanced transparency. Experimental results and case studies demonstrate that our method substantially improves interpretability and significantly increases user trust.
STProtein: predicting spatial protein expression from multi-omics data
The integration of spatial multi-omics data from single tissues is crucial for advancing biological research. However, a significant data imbalance impedes progress: while spatial transcriptomics data is relatively abundant, spatial proteomics data remains scarce due to technical limitations and high costs. To overcome this challenge we propose STProtein, a novel framework leveraging graph neural networks with multi-task learning strategy. STProtein is designed to accurately predict unknown spatial protein expression using more accessible spatial multi-omics data, such as spatial transcriptomics. We believe that STProtein can effectively addresses the scarcity of spatial proteomics, accelerating the integration of spatial multi-omics and potentially catalyzing transformative breakthroughs in life sciences. This tool enables scientists to accelerate discovery by identifying complex and previously hidden spatial patterns of proteins within tissues, uncovering novel relationships between different marker genes, and exploring the biological "Dark Matter".