Jingyi Ren

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.

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.

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.

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.