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.

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.

A practical approach to activate long chain-of-thoughts reasoning ability in large language models is to perform supervised fine-tuning on instruction datasets synthesized by strong large reasoning models, offering a cost-effective alternative to reinforcement learning. However, large-scale instruction sets incur significant training overhead, while effective strategies for automatic data selection still remain unexplored. 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 metrics that may determine the quality of long-CoT instructions. Select2Reason leverages a difficulty-aware reward model to estimate the learning value of questions 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 our method achieves performance competitive with or superior to full-data tuning and open-source baseline across nine competition-level mathematical benchmarks and four broader reasoning tasks. Further experiments highlight the scalability in varying data size, efficiency during inference, and adaptability to other instruction pools of Select2Reason with minimal cost.

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.

The Knowledge Graph Completion (KGC) task aims to infer the missing entity from an incomplete triple. Existing embedding-based methods rely solely on triples in the KG, which is vulnerable to specious relation patterns and long-tail entities. On the other hand, text-based methods struggle with the semantic gap between KG triples and natural language. Apart from triples, entity contexts (e.g., labels, descriptions, aliases) also play a significant role in augmenting KGs. To address these limitations, we propose KGR3, a context-enriched framework for KGC. KGR3 is composed of three modules. Firstly, the Retrieval module gathers supporting triples from the KG, collects plausible candidate answers from a base embedding model, and retrieves context for each related entity. Then, the Reasoning module employs a large language model to generate potential answers for each query triple. Finally, the Re-ranking module combines candidate answers from the two modules mentioned above, and fine-tunes an LLM to provide the best answer. Extensive experiments on widely used datasets demonstrate that KGR3 consistently improves various KGC methods. Specifically, the best variant of KGR3 achieves absolute Hits@1 improvements of 12.3% and 5.6% on the FB15k237 and WN18RR datasets.

The escalating complexity of modern codebases has intensified the need for code retrieval systems capable of interpreting cross-component change intents—a capability fundamentally absent in conventional function-level search paradigms. While recent research has improved alignment between queries and code snippets, retrieving contextually relevant code for certain change request remains underexplored. To bridge this gap, we present RepoAlignBench, the first benchmark designed to evaluate repository-level code retrieval for change request-driven scenarios, encompassing 52k columns. The benchmark shifts the paradigm from function-centric retrieval to holistic repository analysis. In addition, we propose ReflectCode, an adversarial reflection-augmented dual-tower architecture featuring disentangled code_encoder and doc_encoder towers. Our framework dynamically integrates syntactic patterns, function dependency, and semantic expansion intent through LLM. Comprehensive evaluations demonstrate that ReflectCode achieves 12.2% Top-5 Accuracy and 7.1% Recall improvements over state-of-the-art baselines.