Learning Chain Of Thoughts Prompts for Predicting Entities, Relations, and even Literals on Knowledge Graphs

Knowledge graph embedding (KGE) models perform well on link prediction but struggle with unseen entities, relations, and especially literals, limiting their use in dynamic, heterogeneous graphs. In contrast, pretrained large language models (LLMs) generalize effectively through prompting. We reformulate link prediction as a prompt learning problem and introduce RALP, which learns string-based chain-of-thought (CoT) prompts as scoring functions for triples. Using Bayesian Optimization through MIPRO algorithm, RALP identifies effective prompts from fewer than 30 training examples without gradient access. At inference, RALP predicts missing entities, relations or whole triples and assigns confidence scores based on the learned prompt. We evaluate on transductive, numerical, and OWL instance retrieval benchmarks. RALP improves state-of-the-art KGE models by over 5% MRR across datasets and enhances generalization via high-quality inferred triples. On OWL reasoning tasks with complex class expressions (e.g., $\exists hasChild.Female$, $\geq 5 \; hasChild.Female$), it achieves over 88% Jaccard similarity. These results highlight prompt-based LLM reasoning as a flexible alternative to embedding-based methods. We release our implementation, training, and evaluation pipeline as open source: https://github.com/dice-group/RALP .

KG-Reasoner: A Reinforced Model for End-to-End Multi-Hop Knowledge Graph Reasoning

Large Language Models (LLMs) exhibit strong abilities in natural language understanding and generation, yet they struggle with knowledge-intensive reasoning. Structured Knowledge Graphs (KGs) provide an effective form of external knowledge representation and have been widely used to enhance performance in classical Knowledge Base Question Answering (KBQA) tasks. However, performing precise multi-hop reasoning over KGs for complex queries remains highly challenging. Most existing approaches decompose the reasoning process into a sequence of isolated steps executed through a fixed pipeline. While effective to some extent, such designs constrain reasoning flexibility and fragment the overall decision process, often leading to incoherence and the loss of critical intermediate information from earlier steps. In this paper, we introduce KG-Reasoner, an end-to-end framework that integrates multi-step reasoning into a unified "thinking" phase of a Reasoning LLM. Through Reinforcement Learning (RL), the LLM is trained to internalize the KG traversal process, enabling it to dynamically explore reasoning paths, and perform backtracking when necessary. Experiments on eight multi-hop and knowledge-intensive reasoning benchmarks demonstrate that KG-Reasoner achieves competitive or superior performance compared to the state-of-the-art methods. Codes are available at the repository: https://github.com/Wangshuaiia/KG-Reasoner.

Topology-Aware Reasoning over Incomplete Knowledge Graph with Graph-Based Soft Prompting

Large Language Models (LLMs) have shown remarkable capabilities across various tasks but remain prone to hallucinations in knowledge-intensive scenarios. Knowledge Base Question Answering (KBQA) mitigates this by grounding generation in Knowledge Graphs (KGs). However, most multi-hop KBQA methods rely on explicit edge traversal, making them fragile to KG incompleteness. In this paper, we proposed a novel graph-based soft prompting framework that shifts the reasoning paradigm from node-level path traversal to subgraph-level reasoning. Specifically, we employ a Graph Neural Network (GNN) to encode extracted structural subgraphs into soft prompts, enabling LLM to reason over richer structural context and identify relevant entities beyond immediate graph neighbors, thereby reducing sensitivity to missing edges. Furthermore, we introduce a two-stage paradigm that reduces computational cost while preserving good performance: a lightweight LLM first leverages the soft prompts to identify question-relevant entities and relations, followed by a more powerful LLM for evidence-aware answer generation. Experiments on four multi-hop KBQA benchmarks show that our approach achieves state-of-the-art performance on three of them, demonstrating its effectiveness. Code is available at the repository: https://github.com/Wangshuaiia/GraSP.

AgenticAI-DialogGen: Topic-Guided Conversation Generation for Fine-Tuning and Evaluating Short- and Long-Term Memories of LLMs

Recent advancements in Large Language Models (LLMs) have improved their ability to process extended conversational contexts, yet fine-tuning and evaluating short- and long-term memories remain difficult due to the absence of datasets that encode both short- and long-term conversational history. Existing conversational datasets lack memory grounding, overlook topic continuity, or rely on costly human annotation. To address these gaps, we introduce AgenticAI-DialogGen, a modular agent-based framework that generates persona-grounded and topic-guided conversations without human supervision. The framework uses LLM agents to extract knowledge graphs, identify topics, build speaker personas, and simulate topic-guided conversations from unstructured conversations. A QA module generates memory-grounded Question Answer (QA) pairs drawn from short- and long-term conversational histories. We also generated a new dataset entitled, TopicGuidedChat (TGC), where long-term memory is encoded as speaker-specific knowledge graphs and short-term memory as newly generated topic-guided conversations. Evaluations depict that AgenticAI-DialogGen yields higher conversational quality and LLMs fine-tuned on TGC dataset achieve improved performance on memory-grounded QA tasks.

QuarkMedSearch: A Long-Horizon Deep Search Agent for Exploring Medical Intelligence

As agentic foundation models continue to evolve, how to further improve their performance in vertical domains has become an important challenge. To this end, building upon Tongyi DeepResearch, a powerful agentic foundation model, we focus on the Chinese medical deep search scenario and propose QuarkMedSearch, systematically exploring a full-pipeline approach spanning medical multi-hop data construction, training strategies, and evaluation benchmarks to further push and assess its performance upper bound in vertical domains. Specifically, for data synthesis, to address the scarcity of deep search training data in the medical domain, we combine a large-scale medical knowledge graph with real-time online exploration to construct long-horizon medical deep search training data; for post-training, we adopt a two-stage SFT and RL training strategy that progressively enhances the model's planning, tool invocation, and reflection capabilities required for deep search, while maintaining search efficiency; for evaluation, we collaborate with medical experts to construct the QuarkMedSearch Benchmark through rigorous manual verification. Experimental results demonstrate that QuarkMedSearch achieves state-of-the-art performance among open-source models of comparable scale on the QuarkMedSearch Benchmark, while also maintaining strong competitiveness on general benchmarks.

Policy-Invisible Violations in LLM-Based Agents

LLM-based agents can execute actions that are syntactically valid, user-sanctioned, and semantically appropriate, yet still violate organizational policy because the facts needed for correct policy judgment are hidden at decision time. We call this failure mode policy-invisible violations: cases in which compliance depends on entity attributes, contextual state, or session history absent from the agent's visible context. We present PhantomPolicy, a benchmark spanning eight violation categories with balanced violation and safe-control cases, in which all tool responses contain clean business data without policy metadata. We manually review all 600 model traces produced by five frontier models and evaluate them using human-reviewed trace labels. Manual review changes 32 labels (5.3%) relative to the original case-level annotations, confirming the need for trace-level human review. To demonstrate what world-state-grounded enforcement can achieve under favorable conditions, we introduce Sentinel, an enforcement framework based on counterfactual graph simulation. Sentinel treats every agent action as a proposed mutation to an organizational knowledge graph, performs speculative execution to materialize the post-action world state, and verifies graph-structural invariants to decide Allow/Block/Clarify. Against human-reviewed trace labels, Sentinel substantially outperforms a content-only DLP baseline (68.8% vs. 93.0% accuracy) while maintaining high precision, though it still leaves room for improvement on certain violation categories. These results demonstrate what becomes achievable once policy-relevant world state is made available to the enforcement layer.

Modeling Co-Pilots for Text-to-Model Translation

There is growing interest in leveraging large language models (LLMs) for text-to-model translation and optimization tasks. This paper aims to advance this line of research by introducing \textsc{Text2Model} and \textsc{Text2Zinc}. \textsc{Text2Model} is a suite of co-pilots based on several LLM strategies with varying complexity, along with an online leaderboard. \textsc{Text2Zinc} is a cross-domain dataset for capturing optimization and satisfaction problems specified in natural language, along with an interactive editor with built-in AI assistant. While there is an emerging literature on using LLMs for translating combinatorial problems into formal models, our work is the first attempt to integrate \textit{both} satisfaction and optimization problems within a \textit{unified architecture} and \textit{dataset}. Moreover, our approach is \textit{solver-agnostic} unlike existing work that focuses on translation to a solver-specific model. To achieve this, we leverage \textsc{MiniZinc}'s solver-and-paradigm-agnostic modeling capabilities to formulate combinatorial problems. We conduct comprehensive experiments to compare execution and solution accuracy across several single- and multi-call strategies, including; zero-shot prompting, chain-of-thought reasoning, intermediate representations via knowledge-graphs, grammar-based syntax encoding, and agentic approaches that decompose the model into sequential sub-tasks. Our co-pilot strategies are competitive, and in parts improve, recent research in this domain. Our findings indicate that while LLMs are promising they are not yet a push-button technology for combinatorial modeling. We contribute \textsc{Text2Model} co-pilots and leaderboard, and \textsc{Text2Zinc} and interactive editor to open-source to support closing this performance gap.

GAM: Hierarchical Graph-based Agentic Memory for LLM Agents

To sustain coherent long-term interactions, Large Language Model (LLM) agents must navigate the tension between acquiring new information and retaining prior knowledge. Current unified stream-based memory systems facilitate context updates but remain vulnerable to interference from transient noise. Conversely, discrete structured memory architectures provide robust knowledge retention but often struggle to adapt to evolving narratives. To address this, we propose GAM, a hierarchical Graph-based Agentic Memory framework that explicitly decouples memory encoding from consolidation to effectively resolve the conflict between rapid context perception and stable knowledge retention. By isolating ongoing dialogue in an event progression graph and integrating it into a topic associative network only upon semantic shifts, our approach minimizes interference while preserving long-term consistency. Additionally, we introduce a graph-guided, multi-factor retrieval strategy to enhance context precision. Experiments on LoCoMo and LongDialQA indicate that our method consistently outperforms state-of-the-art baselines in both reasoning accuracy and efficiency.

Knowledge Is Not Static: Order-Aware Hypergraph RAG for Language Models

Retrieval-augmented generation (RAG) enhances large language models by grounding outputs in retrieved knowledge. However, existing RAG methods including graph- and hypergraph-based approaches treat retrieved evidence as an unordered set, implicitly assuming permutation invariance. This assumption is misaligned with many real-world reasoning tasks, where outcomes depend not only on which interactions occur, but also on the order in which they unfold. We propose Order-Aware Knowledge Hypergraph RAG (OKH-RAG), which treats order as a first-class structural property. OKH-RAG represents knowledge as higher-order interactions within a hypergraph augmented with precedence structure, and reformulates retrieval as sequence inference over hyperedges. Instead of selecting independent facts, it recovers coherent interaction trajectories that reflect underlying reasoning processes. A learned transition model infers precedence directly from data without requiring explicit temporal supervision. We evaluate OKH-RAG on order-sensitive question answering and explanation tasks, including tropical cyclone and port operation scenarios. OKH-RAG consistently outperforms permutation-invariant baselines, and ablations show that these gains arise specifically from modeling interaction order. These results highlight a key limitation of set-based retrieval: effective reasoning requires not only retrieving relevant evidence, but organizing it into structured sequences.

Towards Autonomous Mechanistic Reasoning in Virtual Cells

Large language models (LLMs) have recently gained significant attention as a promising approach to accelerate scientific discovery. However, their application in open-ended scientific domains such as biology remains limited, primarily due to the lack of factually grounded and actionable explanations. To address this, we introduce a structured explanation formalism for virtual cells that represents biological reasoning as mechanistic action graphs, enabling systematic verification and falsification. Building upon this, we propose VCR-Agent, a multi-agent framework that integrates biologically grounded knowledge retrieval with a verifier-based filtering approach to generate and validate mechanistic reasoning autonomously. Using this framework, we release VC-TRACES dataset, which consists of verified mechanistic explanations derived from the Tahoe-100M atlas. Empirically, we demonstrate that training with these explanations improves factual precision and provides a more effective supervision signal for downstream gene expression prediction. These results underscore the importance of reliable mechanistic reasoning for virtual cells, achieved through the synergy of multi-agent and rigorous verification.