Knowledge-Guided Manipulation Using Multi-Task Reinforcement Learning

This paper introduces Knowledge Graph based Massively Multi-task Model-based Policy Optimization (KG-M3PO), a framework for multi-task robotic manipulation in partially observable settings that unifies Perception, Knowledge, and Policy. The method augments egocentric vision with an online 3D scene graph that grounds open-vocabulary detections into a metric, relational representation. A dynamic-relation mechanism updates spatial, containment, and affordance edges at every step, and a graph neural encoder is trained end-to-end through the RL objective so that relational features are shaped directly by control performance. Multiple observation modalities (visual, proprioceptive, linguistic, and graph-based) are encoded into a shared latent space, upon which the RL agent operates to drive the control loop. The policy conditions on lightweight graph queries alongside visual and proprioceptive inputs, yielding a compact, semantically informed state for decision making. Experiments on a suite of manipulation tasks with occlusions, distractors, and layout shifts demonstrate consistent gains over strong baselines: the knowledge-conditioned agent achieves higher success rates, improved sample efficiency, and stronger generalization to novel objects and unseen scene configurations. These results support the premise that structured, continuously maintained world knowledge is a powerful inductive bias for scalable, generalizable manipulation: when the knowledge module participates in the RL computation graph, relational representations align with control, enabling robust long-horizon behavior under partial observability.

GRMLR: Knowledge-Enhanced Small-Data Learning for Deep-Sea Cold Seep Stage Inference

Deep-sea cold seep stage assessment has traditionally relied on costly, high-risk manned submersible operations and visual surveys of macrofauna. Although microbial communities provide a promising and more cost-effective alternative, reliable inference remains challenging because the available deep-sea dataset is extremely small ($n = 13$) relative to the microbial feature dimension ($p = 26$), making purely data-driven models highly prone to overfitting. To address this, we propose a knowledge-enhanced classification framework that incorporates an ecological knowledge graph as a structural prior. By fusing macro-microbe coupling and microbial co-occurrence patterns, the framework internalizes established ecological logic into a \underline{\textbf{G}}raph-\underline{\textbf{R}}egularized \underline{\textbf{M}}ultinomial \underline{\textbf{L}}ogistic \underline{\textbf{R}}egression (GRMLR) model, effectively constraining the feature space through a manifold penalty to ensure biologically consistent classification. Importantly, the framework removes the need for macrofauna observations at inference time: macro-microbe associations are used only to guide training, whereas prediction relies solely on microbial abundance profiles. Experimental results demonstrate that our approach significantly outperforms standard baselines, highlighting its potential as a robust and scalable framework for deep-sea ecological assessment.

AI-Supervisor: Autonomous AI Research Supervision via a Persistent Research World Model

Existing automated research systems operate as stateless, linear pipelines, generating outputs without maintaining a persistent understanding of the research landscape. They process papers sequentially, propose ideas without structured gap analysis, and lack mechanisms for agents to verify or refine each other's findings. We present AutoProf (Autonomous Professor), a multi-agent orchestration framework where specialized agents provide end-to-end AI research supervision driven by human interests, from literature review through gap discovery, method development, evaluation, and paper writing, via autonomous exploration and self-correcting updates. Unlike sequential pipelines, AutoProf maintains a continuously evolving Research World Model implemented as a Knowledge Graph, capturing methods, benchmarks, limitations, and unexplored gaps as shared memory across agents. The framework introduces three contributions: first, structured gap discovery that decomposes methods into modules, evaluates them across benchmarks, and identifies module-level gaps; second, self-correcting discovery loops that analyze why modules succeed or fail, detect benchmark biases, and assess evaluation adequacy; third, self-improving development loops using cross-domain mechanism search to iteratively address failing components. All agents operate under a consensus mechanism where findings are validated before being committed to the shared model. The framework is model-agnostic, supports mainstream large language models, and scales elastically with token budget from lightweight exploration to full-scale investigation.

HGNet: Scalable Foundation Model for Automated Knowledge Graph Generation from Scientific Literature

Automated knowledge graph (KG) construction is essential for navigating the rapidly expanding body of scientific literature. However, existing approaches struggle to recognize long multi-word entities, often fail to generalize across domains, and typically overlook the hierarchical nature of scientific knowledge. While general-purpose large language models (LLMs) offer adaptability, they are computationally expensive and yield inconsistent accuracy on specialized tasks. As a result, current KGs are shallow and inconsistent, limiting their utility for exploration and synthesis. We propose a two-stage framework for scalable, zero-shot scientific KG construction. The first stage, Z-NERD, introduces (i) Orthogonal Semantic Decomposition (OSD), which promotes domain-agnostic entity recognition by isolating semantic "turns" in text, and (ii) a Multi-Scale TCQK attention mechanism that captures coherent multi-word entities through n-gram-aware attention heads. The second stage, HGNet, performs relation extraction with hierarchy-aware message passing, explicitly modeling parent, child, and peer relations. To enforce global consistency, we introduce two complementary objectives: a Differentiable Hierarchy Loss to discourage cycles and shortcut edges, and a Continuum Abstraction Field (CAF) Loss that embeds abstraction levels along a learnable axis in Euclidean space. This is the first approach to formalize hierarchical abstraction as a continuous property within standard Euclidean embeddings, offering a simpler alternative to hyperbolic methods. We release SPHERE (https://github.com/basiralab/SPHERE), a multi-domain benchmark for hierarchical relation extraction. Our framework establishes a new state of the art on SciERC, SciER, and SPHERE, improving NER by 8.08% and RE by 5.99% on out-of-distribution tests. In zero-shot settings, gains reach 10.76% for NER and 26.2% for RE.

Cross-Slice Knowledge Transfer via Masked Multi-Modal Heterogeneous Graph Contrastive Learning for Spatial Gene Expression Inference

While spatial transcriptomics (ST) has advanced our understanding of gene expression in tissue context, its high experimental cost limits its large-scale application. Predicting ST from pathology images is a promising, cost-effective alternative, but existing methods struggle to capture complex cross-slide spatial relationships. To address the challenge, we propose SpaHGC, a multi-modal heterogeneous graph-based model that captures both intra-slice and inter-slice spot-spot relationships from histology images. It integrates local spatial context within the target slide and cross-slide similarities computed from image embeddings extracted by a pathology foundation model. These embeddings enable inter-slice knowledge transfer, and SpaHGC further incorporates Masked Graph Contrastive Learning to enhance feature representation and transfer spatial gene expression knowledge from reference to target slides, enabling it to model complex spatial dependencies and significantly improve prediction accuracy. We conducted comprehensive benchmarking on seven matched histology-ST datasets from different platforms, tissues, and cancer subtypes. The results demonstrate that SpaHGC significantly outperforms the existing nine state-of-the-art methods across all evaluation metrics. Additionally, the predictions are significantly enriched in multiple cancer-related pathways, thereby highlighting its strong biological relevance and application potential.

CoCR-RAG: Enhancing Retrieval-Augmented Generation in Web Q&A via Concept-oriented Context Reconstruction

Retrieval-augmented generation (RAG) has shown promising results in enhancing Q&A by incorporating information from the web and other external sources. However, the supporting documents retrieved from the heterogeneous web often originate from multiple sources with diverse writing styles, varying formats, and inconsistent granularity. Fusing such multi-source documents into a coherent and knowledge-intensive context remains a significant challenge, as the presence of irrelevant and redundant information can compromise the factual consistency of the inferred answers. This paper proposes the Concept-oriented Context Reconstruction RAG (CoCR-RAG), a framework that addresses the multi-source information fusion problem in RAG through linguistically grounded concept-level integration. Specifically, we introduce a concept distillation algorithm that extracts essential concepts from Abstract Meaning Representation (AMR), a stable semantic representation that structures the meaning of texts as logical graphs. The distilled concepts from multiple retrieved documents are then fused and reconstructed into a unified, information-intensive context by Large Language Models, which supplement only the necessary sentence elements to highlight the core knowledge. Experiments on the PopQA and EntityQuestions datasets demonstrate that CoCR-RAG significantly outperforms existing context-reconstruction methods across these Web Q&A benchmarks. Furthermore, CoCR-RAG shows robustness across various backbone LLMs, establishing itself as a flexible, plug-and-play component adaptable to different RAG frameworks.

Agentic Personas for Adaptive Scientific Explanations with Knowledge Graphs

AI explanation methods often assume a static user model, producing non-adaptive explanations regardless of expert goals, reasoning strategies, or decision contexts. Knowledge graph-based explanations, despite their capacity for grounded, path-based reasoning, inherit this limitation. In complex domains such as scientific discovery, this assumption fails to capture the diversity of cognitive strategies and epistemic stances among experts, preventing explanations that foster deeper understanding and informed decision-making. However, the scarcity of human experts limits the use of direct human feedback to produce adaptive explanations. We present a reinforcement learning approach for scientific explanation generation that incorporates agentic personas, structured representations of expert reasoning strategies, that guide the explanation agent towards specific epistemic preferences. In an evaluation of knowledge graph-based explanations for drug discovery, we tested two personas that capture distinct epistemic stances derived from expert feedback. Results show that persona-driven explanations match state-of-the-art predictive performance while persona preferences closely align with those of their corresponding experts. Adaptive explanations were consistently preferred over non-adaptive baselines (n = 22), and persona-based training reduces feedback requirements by two orders of magnitude. These findings demonstrate how agentic personas enable scalable adaptive explainability for AI systems in complex and high-stakes domains.

The Semantic Ladder: A Framework for Progressive Formalization of Natural Language Content for Knowledge Graphs and AI Systems

Semantic data and knowledge infrastructures must reconcile two fundamentally different forms of representation: natural language, in which most knowledge is created and communicated, and formal semantic models, which enable machine-actionable integration, interoperability, and reasoning. Bridging this gap remains a central challenge, particularly when full semantic formalization is required at the point of data entry. Here, we introduce the Semantic Ladder, an architectural framework that enables the progressive formalization of data and knowledge. Building on the concept of modular semantic units as identifiable carriers of meaning, the framework organizes representations across levels of increasing semantic explicitness, ranging from natural language text snippets to ontology-based and higher-order logical models. Transformations between levels support semantic enrichment, statement structuring, and logical modelling while preserving semantic continuity and traceability. This approach enables the incremental construction of semantic knowledge spaces, reduces the semantic parsing burden, and supports the integration of heterogeneous representations, including natural language, structured semantic models, and vector-based embeddings. The Semantic Ladder thereby provides a foundation for scalable, interoperable, and AI-ready data and knowledge infrastructures.

GraphRAG for Engineering Diagrams: ChatP&ID Enables LLM Interaction with P&IDs

Large Language Models (LLMs) combined with Retrieval-Augmented Generation (RAG) and knowledge graphs offer new opportunities for interacting with engineering diagrams such as Piping and Instrumentation Diagrams (P&IDs). However, directly processing raw images or smart P&ID files with LLMs is often costly, inefficient, and prone to hallucinations. This work introduces ChatP&ID, an agentic framework that enables grounded and cost-effective natural-language interaction with P&IDs using Graph Retrieval-Augmented Generation (GraphRAG), a paradigm we refer to as GraphRAG for engineering diagrams. Smart P&IDs encoded in the DEXPI standard are transformed into structured knowledge graphs, which serve as the basis for graph-based retrieval and reasoning by LLM agents. This approach enables reliable querying of engineering diagrams while significantly reducing computational cost. Benchmarking across commercial LLM APIs (OpenAI, Anthropic) demonstrates that graph-based representations improve accuracy by 18% over raw image inputs and reduce token costs by 85% compared to directly ingesting smart P&ID files. While small open-source models still struggle to interpret knowledge graph formats and structured engineering data, integrating them with VectorRAG and PathRAG improves response accuracy by up to 40%. Notably, GPT-5-mini combined with ContextRAG achieves 91% accuracy at a cost of only $0.004 per task. The resulting ChatP&ID interface enables intuitive natural-language interaction with complex engineering diagrams and lays the groundwork for AI-assisted process engineering tasks such as Hazard and Operability Studies (HAZOP) and multi-agent analysis.

Ontology-Compliant Knowledge Graphs

Ontologies can act as a schema for constructing knowledge graphs (KGs), offering explainability, interoperability, and reusability. We explore \emph{ontology-compliant} KGs, aiming to build both internal and external ontology compliance. We discuss key tasks in ontology compliance and introduce our novel term-matching algorithms. We also propose a \emph{pattern-based compliance} approach and novel compliance metrics. The building sector is a case study to test the validity of ontology-compliant KGs. We recommend using ontology-compliant KGs to pursue automatic matching, alignment, and harmonisation of heterogeneous KGs.