Bayesian-Agent: Posterior-Guided Skill Evolution for LLM Agent Harnesses

LLM agents increasingly rely on external inference conditions: prompts, tools, memory, SOPs, skills, and harness feedback. These assets can improve task execution without changing model weights, but they are often revised by heuristic reflection or by reusing observed successes and failures as if counts alone were reliable belief. We introduce \textbf{Bayesian-Agent}, a native and cross-harness framework that treats reusable skills and SOPs as hypotheses about whether a frozen model will succeed under a particular prompt, context, and harness environment. Bayesian-Agent records verified trajectory evidence, maintains a feature-conditioned categorical posterior over each skill, and maps posterior state into inspectable actions such as patch, split, compress, retire, and explore. Model-facing prompts receive executable guardrails and failure-mode patches, while posterior summaries remain available for audit. With \texttt{deepseek-v4-flash}, incremental repair improves SOP-Bench from 80\% to 95\%, Lifelong AgentBench from 90\% to 100\%, and RealFin-Bench from 45\% to 65\%. We further evaluate Bayesian-Agent's native backend and optional GenericAgent, mini-swe-agent, and Claude Code backends. The results include positive, negative, saturated, and case-study settings, suggesting that agent skill evolution is best viewed as posterior-guided harness optimization rather than uncalibrated prompt accumulation. The source code is available at https://github.com/DataArcTech/Bayesian-Agent.

Conflicts Make Large Reasoning Models Vulnerable to Attacks

Large Reasoning Models (LRMs) have achieved remarkable performance across diverse domains, yet their decision-making under conflicting objectives remains insufficiently understood. This work investigates how LRMs respond to harmful queries when confronted with two categories of conflicts: internal conflicts that pit alignment values against each other and dilemmas, which impose mutually contradictory choices, including sacrificial, duress, agent-centered, and social forms. Using over 1,300 prompts across five benchmarks, we evaluate three representative LRMs - Llama-3.1-Nemotron-8B, QwQ-32B, and DeepSeek R1 - and find that conflicts significantly increase attack success rates, even under single-round non-narrative queries without sophisticated auto-attack techniques. Our findings reveal through layerwise and neuron-level analyses that safety-related and functional representations shift and overlap under conflict, interfering with safety-aligned behavior. This study highlights the need for deeper alignment strategies to ensure the robustness and trustworthiness of next-generation reasoning models. Our code is available at https://github.com/DataArcTech/ConflictHarm. Warning: This paper contains inappropriate, offensive and harmful content.

Towards Knowledgeable Deep Research: Framework and Benchmark

Deep Research (DR) requires LLM agents to autonomously perform multi-step information seeking, processing, and reasoning to generate comprehensive reports. In contrast to existing studies that mainly focus on unstructured web content, a more challenging DR task should additionally utilize structured knowledge to provide a solid data foundation, facilitate quantitative computation, and lead to in-depth analyses. In this paper, we refer to this novel task as Knowledgeable Deep Research (KDR), which requires DR agents to generate reports with both structured and unstructured knowledge. Furthermore, we propose the Hybrid Knowledge Analysis framework (HKA), a multi-agent architecture that reasons over both kinds of knowledge and integrates the texts, figures, and tables into coherent multimodal reports. The key design is the Structured Knowledge Analyzer, which utilizes both coding and vision-language models to produce figures, tables, and corresponding insights. To support systematic evaluation, we construct KDR-Bench, which covers 9 domains, includes 41 expert-level questions, and incorporates a large number of structured knowledge resources (e.g., 1,252 tables). We further annotate the main conclusions and key points for each question and propose three categories of evaluation metrics including general-purpose, knowledge-centric, and vision-enhanced ones. Experimental results demonstrate that HKA consistently outperforms most existing DR agents on general-purpose and knowledge-centric metrics, and even surpasses the Gemini DR agent on vision-enhanced metrics, highlighting its effectiveness in deep, structure-aware knowledge analysis. Finally, we hope this work can serve as a new foundation for structured knowledge analysis in DR agents and facilitate future multimodal DR studies.

Continual Pretraining on Encrypted Synthetic Data for Privacy-Preserving LLMs

Preserving privacy in sensitive data while pretraining large language models on small, domain-specific corpora presents a significant challenge. In this work, we take an exploratory step toward privacy-preserving continual pretraining by proposing an entity-based framework that synthesizes encrypted training data to protect personally identifiable information (PII). Our approach constructs a weighted entity graph to guide data synthesis and applies deterministic encryption to PII entities, enabling LLMs to encode new knowledge through continual pretraining while granting authorized access to sensitive data through decryption keys. Our results on limited-scale datasets demonstrate that our pretrained models outperform base models and ensure PII security, while exhibiting a modest performance gap compared to models trained on unencrypted synthetic data. We further show that increasing the number of entities and leveraging graph-based synthesis improves model performance, and that encrypted models retain instruction-following capabilities with long retrieved contexts. We discuss the security implications and limitations of deterministic encryption, positioning this work as an initial investigation into the design space of encrypted data pretraining for privacy-preserving LLMs. Our code is available at https://github.com/DataArcTech/SoE.

GraphSearch: An Agentic Deep Searching Workflow for Graph Retrieval-Augmented Generation

Graph Retrieval-Augmented Generation (GraphRAG) enhances factual reasoning in LLMs by structurally modeling knowledge through graph-based representations. However, existing GraphRAG approaches face two core limitations: shallow retrieval that fails to surface all critical evidence, and inefficient utilization of pre-constructed structural graph data, which hinders effective reasoning from complex queries. To address these challenges, we propose \textsc{GraphSearch}, a novel agentic deep searching workflow with dual-channel retrieval for GraphRAG. \textsc{GraphSearch} organizes the retrieval process into a modular framework comprising six modules, enabling multi-turn interactions and iterative reasoning. Furthermore, \textsc{GraphSearch} adopts a dual-channel retrieval strategy that issues semantic queries over chunk-based text data and relational queries over structural graph data, enabling comprehensive utilization of both modalities and their complementary strengths. Experimental results across six multi-hop RAG benchmarks demonstrate that \textsc{GraphSearch} consistently improves answer accuracy and generation quality over the traditional strategy, confirming \textsc{GraphSearch} as a promising direction for advancing graph retrieval-augmented generation.

KnowCoder-V2: Deep Knowledge Analysis

Deep knowledge analysis tasks always involve the systematic extraction and association of knowledge from large volumes of data, followed by logical reasoning to discover insights. However, to solve such complex tasks, existing deep research frameworks face three major challenges: 1) They lack systematic organization and management of knowledge; 2) They operate purely online, making it inefficient for tasks that rely on shared and large-scale knowledge; 3) They cannot perform complex knowledge computation, limiting their abilities to produce insightful analytical results. Motivated by these, in this paper, we propose a \textbf{K}nowledgeable \textbf{D}eep \textbf{R}esearch (\textbf{KDR}) framework that empowers deep research with deep knowledge analysis capability. Specifically, it introduces an independent knowledge organization phase to preprocess large-scale, domain-relevant data into systematic knowledge offline. Based on this knowledge, it extends deep research with an additional kind of reasoning steps that perform complex knowledge computation in an online manner. To enhance the abilities of LLMs to solve knowledge analysis tasks in the above framework, we further introduce \textbf{\KCII}, an LLM that bridges knowledge organization and reasoning via unified code generation. For knowledge organization, it generates instantiation code for predefined classes, transforming data into knowledge objects. For knowledge computation, it generates analysis code and executes on the above knowledge objects to obtain deep analysis results. Experimental results on more than thirty datasets across six knowledge analysis tasks demonstrate the effectiveness of \KCII. Moreover, when integrated into the KDR framework, \KCII can generate high-quality reports with insightful analytical results compared to the mainstream deep research framework.

Select2Reason: Efficient Instruction-Tuning Data Selection for Long-CoT Reasoning

A practical approach to activate long chain-of-thoughts reasoning ability in pre-trained large language models is to perform supervised fine-tuning on instruction datasets synthesized by strong Large Reasoning Models such as DeepSeek-R1, offering a cost-effective alternative to reinforcement learning. However, large-scale instruction sets with more than 100k samples incur significant training overhead, while effective strategies for automatic long-CoT instruction selection still remain unexplored. In this work, we propose Select2Reason, a novel and efficient instruction-tuning data selection framework for long-CoT reasoning. From the perspective of emergence of rethinking behaviors like self-correction and backtracking, we investigate common metrics that may determine the quality of long-CoT reasoning instructions. Select2Reason leverages a quantifier to estimate difficulty of question and jointly incorporates a reasoning trace length-based heuristic through a weighted scheme for ranking to prioritize high-utility examples. Empirical results on OpenR1-Math-220k demonstrate that fine-tuning LLM on only 10% of the data selected by Select2Reason achieves performance competitive with or superior to full-data tuning and open-source baseline OpenR1-Qwen-7B across three competition-level and six comprehensive mathematical benchmarks. Further experiments highlight the scalability in varying data size, efficiency during inference, and its adaptability to other instruction pools with minimal cost.

Fractal Graph Contrastive Learning

While Graph Contrastive Learning (GCL) has attracted considerable attention in the field of graph self-supervised learning, its performance heavily relies on data augmentations that are expected to generate semantically consistent positive pairs. Existing strategies typically resort to random perturbations or local structure preservation, yet lack explicit control over global structural consistency between augmented views. To address this limitation, we propose Fractal Graph Contrastive Learning (FractalGCL), a theory-driven framework that leverages fractal self-similarity to enforce global topological coherence. FractalGCL introduces two key innovations: a renormalisation-based augmentation that generates structurally aligned positive views via box coverings; and a fractal-dimension-aware contrastive loss that aligns graph embeddings according to their fractal dimensions. While combining the two innovations markedly boosts graph-representation quality, it also adds non-trivial computational overhead. To mitigate the computational overhead of fractal dimension estimation, we derive a one-shot estimator by proving that the dimension discrepancy between original and renormalised graphs converges weakly to a centred Gaussian distribution. This theoretical insight enables a reduction in dimension computation cost by an order of magnitude, cutting overall training time by approximately 61%. The experiments show that FractalGCL not only delivers state-of-the-art results on standard benchmarks but also outperforms traditional baselines on traffic networks by an average margin of about remarkably 7%. Codes are available at (https://anonymous.4open.science/r/FractalGCL-0511).

Synthesize-on-Graph: Knowledgeable Synthetic Data Generation for Continue Pre-training of Large Language Models

Large Language Models (LLMs) have achieved remarkable success but remain data-inefficient, especially when learning from small, specialized corpora with limited and proprietary data. Existing synthetic data generation methods for continue pre-training focus on intra-document content and overlook cross-document knowledge associations, limiting content diversity and depth. We propose Synthetic-on-Graph (SoG), a synthetic data generation framework that incorporates cross-document knowledge associations for efficient corpus expansion. SoG constructs a context graph by extracting entities and concepts from the original corpus, representing cross-document associations, and employing a graph walk strategy for knowledge-associated sampling. This enhances synthetic data diversity and coherence, enabling models to learn complex knowledge structures and handle rare knowledge. To further improve synthetic data quality, we integrate Chain-of-Thought (CoT) and Contrastive Clarifying (CC) synthetic, enhancing reasoning processes and discriminative power. Experiments show that SoG outperforms the state-of-the-art (SOTA) method in a multi-hop document Q&A dataset while performing comparably to the SOTA method on the reading comprehension task datasets, which also underscores the better generalization capability of SoG. Our work advances synthetic data generation and provides practical solutions for efficient knowledge acquisition in LLMs, especially in domains with limited data availability.

LongFaith: Enhancing Long-Context Reasoning in LLMs with Faithful Synthetic Data

Despite the growing development of long-context large language models (LLMs), data-centric approaches relying on synthetic data have been hindered by issues related to faithfulness, which limit their effectiveness in enhancing model performance on tasks such as long-context reasoning and question answering (QA). These challenges are often exacerbated by misinformation caused by lack of verification, reasoning without attribution, and potential knowledge conflicts. We propose LongFaith, a novel pipeline for synthesizing faithful long-context reasoning instruction datasets. By integrating ground truth and citation-based reasoning prompts, we eliminate distractions and improve the accuracy of reasoning chains, thus mitigating the need for costly verification processes. We open-source two synthesized datasets, LongFaith-SFT and LongFaith-PO, which systematically address multiple dimensions of faithfulness, including verified reasoning, attribution, and contextual grounding. Extensive experiments on multi-hop reasoning datasets and LongBench demonstrate that models fine-tuned on these datasets significantly improve performance. Our ablation studies highlight the scalability and adaptability of the LongFaith pipeline, showcasing its broad applicability in developing long-context LLMs.