Jingyi Ren

Weitao Li, Hao Zhou, Xuanyu Lei et al.

Reinforcement learning with verifiable rewards (RLVR) has become central to LLM reasoning, but its outcome-level rewards can make models more willing to give confident answers when evidence or reasoning is unreliable. Existing SFT or RL methods mainly teach LLMs to refuse or express uncertainty at the response level, which can overfit abstention behavior rather than improve reasoning reliability. To address this limitation, we propose Cognitive Pairwise Training (CPT), a cognitive mid-training alignment stage that turns pairwise comparisons over reasoning traces into a reusable alignment signal. By learning to distinguish trustworthy from flawed reasoning, CPT encourages the model to internalize a reasoning-quality discrimination boundary rather than memorize surface refusal patterns. Across five model scales and three model families, CPT improves the reasoning--metacognition trade-off. At 14B, CPT+RL outperforms the standard SFT+RL pipeline by +2.2 math-average points and +5.2 abstention-F1 points. Further analyses show that CPT improves trace quality and exhibits strong robustness and scalability across evaluation and training settings. Code and models are released at https://github.com/Tsinghua-dhy/CPT.

Ruida Hu, Chao Peng, Jingyi Ren et al.

In this work, we introduce CodeRepoQA, a large-scale benchmark specifically designed for evaluating repository-level question-answering capabilities in the field of software engineering. CodeRepoQA encompasses five programming languages and covers a wide range of scenarios, enabling comprehensive evaluation of language models. To construct this dataset, we crawl data from 30 well-known repositories in GitHub, the largest platform for hosting and collaborating on code, and carefully filter raw data. In total, CodeRepoQA is a multi-turn question-answering benchmark with 585,687 entries, covering a diverse array of software engineering scenarios, with an average of 6.62 dialogue turns per entry. We evaluate ten popular large language models on our dataset and provide in-depth analysis. We find that LLMs still have limitations in question-answering capabilities in the field of software engineering, and medium-length contexts are more conducive to LLMs' performance. The entire benchmark is publicly available at https://github.com/kinesiatricssxilm14/CodeRepoQA.

Sheng Yu, Zheng Yuan, Jun Xia et al. · tsinghua

Biomedical knowledge graphs (BioMedKGs) are essential infrastructures for biomedical and healthcare big data and artificial intelligence (AI), facilitating natural language processing, model development, and data exchange. For decades, these knowledge graphs have been developed via expert curation; however, this method can no longer keep up with today's AI development, and a transition to algorithmically generated BioMedKGs is necessary. In this work, we introduce the Biomedical Informatics Ontology System (BIOS), the first large-scale publicly available BioMedKG generated completely by machine learning algorithms. BIOS currently contains 4.1 million concepts, 7.4 million terms in two languages, and 7.3 million relation triplets. We present the methodology for developing BIOS, including the curation of raw biomedical terms, computational identification of synonymous terms and aggregation of these terms to create concept nodes, semantic type classification of the concepts, relation identification, and biomedical machine translation. We provide statistics on the current BIOS content and perform preliminary assessments of term quality, synonym grouping, and relation extraction. The results suggest that machine learning-based BioMedKG development is a viable alternative to traditional expert curation.

Shufa Wei, Xiaolong Xu, Xianbiao Qi et al.

Large Language Models (LLMs) have demonstrated exceptional capabilities across various natural language processing tasks. Yet, many of these advanced LLMs are tailored for broad, general-purpose applications. In this technical report, we introduce AcademicGPT, designed specifically to empower academic research. AcademicGPT is a continual training model derived from LLaMA2-70B. Our training corpus mainly consists of academic papers, thesis, content from some academic domain, high-quality Chinese data and others. While it may not be extensive in data scale, AcademicGPT marks our initial venture into a domain-specific GPT tailored for research area. We evaluate AcademicGPT on several established public benchmarks such as MMLU and CEval, as well as on some specialized academic benchmarks like PubMedQA, SCIEval, and our newly-created ComputerScienceQA, to demonstrate its ability from general knowledge ability, to Chinese ability, and to academic ability. Building upon AcademicGPT's foundation model, we also developed several applications catered to the academic area, including General Academic Question Answering, AI-assisted Paper Reading, Paper Review, and AI-assisted Title and Abstract Generation.

Jingyi Ren, Ante Wang, Yunghwei Lai et al.

Reliable Large Language Models (LLMs) should abstain when confidence is insufficient. However, prior studies often treat refusal as a generic "I don't know'', failing to distinguish input-level ambiguity (data uncertainty) from capability limitations (model uncertainty). This lack of distinction limits downstream action decisions like requesting clarification or invoking external tools. In this work, we introduce UA-Bench, a benchmark of over 3,500 questions drawn from six datasets spanning knowledge-intensive and reasoning-intensive tasks, designed to evaluate explicit uncertainty attribution. An evaluation of 18 frontier LLMs shows that even state-of-the-art models struggle to reliably discriminate between data uncertainty and model uncertainty, and that high answer accuracy does not necessarily imply strong uncertainty attribution ability. To narrow this gap, we propose a lightweight data synthesis and reinforcement learning strategy. Experiments on both Qwen3-4B-Instruct-2507 and Qwen3-8B in thinking mode show that the proposed method improves uncertainty attribution while preserving answer accuracy. Our code and data are publicly available now.

Junkai Li, Yunghwei Lai, Weitao Li et al.

The recent rapid development of large language models (LLMs) has sparked a new wave of technological revolution in medical artificial intelligence (AI). While LLMs are designed to understand and generate text like a human, autonomous agents that utilize LLMs as their "brain" have exhibited capabilities beyond text processing such as planning, reflection, and using tools by enabling their "bodies" to interact with the environment. We introduce a simulacrum of hospital called Agent Hospital that simulates the entire process of treating illness, in which all patients, nurses, and doctors are LLM-powered autonomous agents. Within the simulacrum, doctor agents are able to evolve by treating a large number of patient agents without the need to label training data manually. After treating tens of thousands of patient agents in the simulacrum (human doctors may take several years in the real world), the evolved doctor agents outperform state-of-the-art medical agent methods on the MedQA benchmark comprising US Medical Licensing Examination (USMLE) test questions. Our methods of simulacrum construction and agent evolution have the potential in benefiting a broad range of applications beyond medical AI.

Jingyi Ren, Yekun Xu, Xiaolong Wang et al.

Retrieval-Augmented Generation (RAG) delivers substantial value in knowledge-intensive applications. Many recent works use reinforcement learning (RL) to elicit strong reasoning in RAG generators. However, two key challenges remain unresolved: (1) Transparency: most prior methods do not explicitly indicate which references are actually used during the reasoning that leads to the final answer, limiting interpretability and visibility; (2) Stability: the KL divergence estimator used in existing RL-based approaches may cause gradient spikes, leading to unstable training. To address these challenges, we propose Adaptive-Rewarded Evidence Navigation Agent (ARENA), a transparent and robust RAG generator framework trained via RL with designed rewards. Based on our structured protocol, KL divergence stabilization, and adaptive reward calculation modules, ARENA enables the RAG generator to identify key evidence, perform structured reasoning, and generate answers with interpretable decision traces. Applied to Qwen2.5-7B-Instruct and Llama3.1-8B-Instruct, extensive experiments across multiple baselines show 10-30% accuracy improvements on three multi-hop QA datasets, comparable to advanced closed-source LLMs (e.g., OpenAI o1, DeepSeek R1). Further analyses show that ARENA generalizes well to unseen datasets and tasks. Our models and codes are publicly released.

Xiaoyun Liang, Jingyi Ren, Jiayi Qi et al.

Large Language Models (LLMs) have become increasingly integral to enhancing developer productivity, particularly in code generation, comprehension, and repair tasks. However, fine-tuning these models with high-quality, real-world data is challenging due to privacy concerns and the lack of accessible, labeled datasets. In this paper, we present DialogAgent, an automated tool for generating synthetic training data that closely mimics real developer interactions within Integrated Development Environments (IDEs). DialogAgent enables the production of diverse, high-fidelity query-response pairs by simulating multi-turn dialogues and contextual behaviors observed in real-world programming scenarios. The tool significantly reduces the reliance on manual data generation, increasing efficiency by 4.8 times compared to traditional methods. Our experiments and online deployment demonstrate substantial improvements in model performance for code-related question-answering tasks: the acceptance rate of responses generated by our in-house model is improved by 33%, after training on synthesized data generated by DialogAgent.