Ontology
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QLoRA Fine-Tuning of Ministral LLM for Sequence-to-Function Protein Annotation
2026-09-21 13:09:59Demian Pavlyshenko, Bohdan PavlyshenkoAbstract
Functional annotation of newly sequenced proteins remains a bottleneck in molecular biology: the number of sequences in public repositories grows far faster than the capacity for manual curation. Most computational approaches consider annotation as multi-label classification over a fixed ontology, which constrains predictions to a predefined label set. In this work we study the the protein annotation as a sequence-to-text generation problem. We fine-tune the 3B-parameter Ministral 3 base model with QLoRA (4-bit NF4 quantization with low-rank adapters) on sequence annotation pairs. We assess predictions with an LLM-as-expert protocol: a GPT model prompted as a senior molecular-biology curator scores organism identification as binary and function annotation quality. We conclude that QLoRA-fine-tuned compact LLMs can generate curator-style annotations with genuine biological value for a substantial subset of proteins. We also discuss future directions in data quality, model scaling, and evidence grounding that are needed to make the approach sufficiently reliable for practical use.
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https://arxiv.org/abs/2609.24538
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Blind Thermodynamic Ontology Discovery from Anonymous Experiments
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Before a machine learning model can learn a thermodynamic equation of state, it must discover what its measurements represent: which channels scale with system size, which are intensive conjugates, how sectors pair through contact, and which potential governs stability. When sensors expose only an unknown linear mixture of extensive states and intensive responses, passive observations cannot disentangle physical quantities from coordinate artifacts. We formulate the problem of discovering this hidden thermodynamic ontology directly from anonymous controlled experiments. We present an operational identifiability theory and a constructive polynomial-time algorithm that extracts extensive and intensive scaling sectors from replication contrasts, recovers their dual cotangent pairing from thermal contact and reciprocity, verifies a globally admissible concave potential via discrete cyclic concavity, and determines an invariant matroid of reservoir ensembles. We prove that the residual observational equivalence is strictly (x, lambda) ~ (A x, a A^{-T} lambda + beta), establishing the sharp observational limit that no permitted experiment can break. Blind evaluations on van der Waals fluids and Curie-Weiss magnets confirm robust recovery under ill-conditioned mixing, correctly resolving anonymous Maxwell tie-lines while rejecting non-equilibrium continuations. External validation across six real fluids from the NIST WebBook demonstrates that operational ontology discovery transfers across real physical substances without coordinate leakage.
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https://arxiv.org/abs/2609.23387
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Discovering Physical Representation Languages
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Before a machine can discover a physical law, it must discover what its measurements are: which observations live on cells, which are intensive or extensive, which sectors are dual, and which distinctions are merely gauge. We introduce physical representation-language discovery, the problem of recovering this hidden ontology directly from anonymous controlled experiments. We give an identifiability theory and constructive polynomial-time procedure that recovers a carrier and differential sequence, measurement types and orientation twist, noninvertible refinement semantics, primal-dual Maxwell diagrams, and the residual equivalences that no permitted experiment can break. The theory turns material nuisance into a commutant, uses refinement to separate quantities from coordinates, and selects physics only after its representation has been recovered. For a certified finite experiment family, we prove an end-to-end two-stage measurement bound and a matching minimax rate in dimension, accuracy, and confidence. Blind Maxwell experiments recover complete primal/relative-dual ontologies on regular and unstructured carriers under jointly corrupted observations; an independent unstructured RLC system demonstrates that the result is not specific to Maxwell. The framework scales to tens of thousands of cells per carrier, while stress audits demonstrate robustness across severe physical regimes - including non-Markovian memory, nonlinearities, nonlocality, and complex constitutive hysteresis. A public FDTD audit demonstrates the emergence of anonymous curl structure from incomplete field data, while characterizing the informational prerequisites for complete recovery. The goal is to move scientific ML from learning laws in a human-supplied language to discovering the language in which laws become expressible, establishing exact theoretical limits on observational identifiability.
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https://arxiv.org/abs/2609.23381
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Graph Memory for LLM Agents: At What Cost? A Comparative Evaluation of Query, Ingest, and Update Performance Across Graph Database Engines
2026-09-20 03:04:30Donald Nguyen, Gurbinder Gill, Hadi Ahmadi, Christopher J. RossbachAbstract
Graph databases are frequently positioned as categorically necessary for connected-data workloads, yet the systems dimension along which they actually differ - query planning, indexing, and data-readiness cost - is rarely isolated from vendor framing. We construct a synthetic, biomedical-shaped property graph (1.02 million nodes, 5.34 million total node and edge rows) and a twenty-query workload spanning neighborhood lookups, bounded paths, set intersections, anti-joins, grouped aggregation, top-k ranking, temporal filters, full scans, and relational joins. We benchmark Corvic AI - a purpose-built columnar query engine underlying Corvic's ontology management layer ("memories")- against seven purpose-built or graph-extension database systems (LoraDB, Ladybug, DuckPGQ, Memgraph, Neo4j, HugeGraph, and FalkorDB) at three graph scales spanning three orders of magnitude. We report query latency geomeans, bulk-ingest throughput, point-update latency, and answer correctness for each system, and we derive a simple total-cost-of-ownership model that expresses the ingest/query trade-off as a function of query volume. Our central finding is that no system in this sample is categorically fastest: a native graph engine (Ladybug) outperforms Corvic AI on narrow, bounded-neighborhood shapes, while Corvic AI is faster on shapes that scan or join a large fraction of the graph, and a system implementing graph query syntax via SQL/PGQ (DuckPGQ) is measurably slower purely due to query-plan choice. The dominant cost differential in our data is not query latency but the cost of making data queryable at all: bulk-ingest throughput varies by three orders of magnitude across engines (5.0k-4.3M rows/s), a gap that a simple crossover-point calculation shows dominates total cost for any workload with fewer than roughly 105 queries per data refresh.
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https://arxiv.org/abs/2609.23315
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Integrating knowledge from case reports: a medical ontology based multimodal information system with structured summary
2026-09-17 06:41:18Shuyu Guo, Lan Huang, Yichen Liu, Hanbin Ma, Tian BaiAbstract
Published medical case reports serve as a crucial medical information carrier, documenting discoveries in rare diseases, diagnostic methods, and innovative treatments. Despite the wealth of clinical knowledge in millions of case reports in the public medicine literature database (PubMed), accessing relevant information efficiently is hindered by the limitations of traditional keyword-based retrieval tools on unstructured and diverse case reports. To address the above issues, we introduce a comprehensive multimodal information system for case reports integrating structured clinical summaries of patients including medical images and biomedical named entities from 52949 open-access case reports published from 2000 to 2021. The multimodal essential information is organized in a well-structured medical ontology. Also, a powerful interface for searching and browsing case reports is designed to assist junior clinicians in retrieving cases effectively and improving the identification and diagnosis of rare diseases.
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https://arxiv.org/abs/2609.19775
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Large Language Model Agents for Evidence Based Genetic Disease Severity Classification
2026-09-17 01:56:38Tohid Ghasemnejad, Ahmadreza Argha, Mark Grosser, John Wang, Min Yang, Thantrira Porntaveetus, Tony Roscioli, Nigel H. Lovell, Mahmoud Aarabi, Hamid Alinejad-RoknyAbstract
Disease severity classification for genetic conditions is subjective and labor-intensive, creating bottlenecks in genomic screening, where commercial panels vary widely in size and overlap. We developed an autonomous AI agent integrating Reasoning and Acting (ReAct) with Retrieval-Augmented Generation (RAG) to classify 10,211 Human Phenotype Ontology terms. It uses American College of Medical Genetics (ACMG)-endorsed severity guidelines and American College of Obstetricians and Gynecologists (ACOG) quality-of-life criteria to retrieve PubMed literature, generate interpretable reasoning chains, and independently verify claims. At the phenotype level, using expert-curated cohorts, the agent achieved 93.55% accuracy (MCC 0.9237) with 82.6% to 91.4% of claims supported by direct evidence or valid inferences. Gene-level severity was aggregated across 8,738 pairs, identifying 3,283 autosomal recessive pairs with severe or profound presentations. External validation showed 95.2% concordance with Mackenzie's Mission gene list. This system enables standardized panel design by providing reliable, automated classification supported by direct evidence.
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https://arxiv.org/abs/2609.19569
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Hyperbolic Graph Representation Learning for Differential Diagnosis on Biomedical Knowledge Graphs
2026-09-16 11:11:46Pietro Miotto, Lucia Mellini, Tommaso Marzi, Cesare Alippi, Elena Casiraghi, Alberto Paccanaro, Giorgio Valentini, Mauricio Soto-GomezAbstract
Biomedical knowledge graphs combine ontology-derived hierarchies with transversal associations among heterogeneous entities such as phenotypes, diseases, genes, proteins, and patients. This hybrid structure raises the question of whether hyperbolic embeddings, which naturally capture tree-like organization, remain useful beyond purely hierarchical graphs. We present a preliminary study of hyperbolic graph representation learning for Mendelian-disease differential diagnosis on a patient-integrated biomedical graph. Experiments on isolated ontology subgraphs show that hyperbolic models achieve strong performance in substantially lower dimensions than Euclidean baselines. We then evaluate the models on a link-prediction task that ranks candidate diseases for each patient. Results suggest that hyperbolic embeddings can exploit biomedical hierarchical structure while supporting diagnostic reasoning over heterogeneous patient-level graphs.
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https://arxiv.org/abs/2609.18481
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Too Good to Be Real? Diagnosing and Reducing the Gap Between AI Preference and Real User Engagement
2026-09-16 08:04:14Xinglang Zhang, Yuanmeng Xiang, Yunyao Zhang, Zeliang Chen, Junqing Yu, Zikai SongAbstract
Large language models are increasingly used to generate and evaluate online content, yet it remains unclear whether the qualities they associate with higher engagement match what real users respond to. We study this question using 1.17 million answers to 25,978 questions from Zhihu, Quora, and Reddit, comparing real platform answers and AI-generated answers across four within-question engagement levels. We introduce Ontological Preference Measurement, which represents answers along three dimensions: logic, affect, and expression. We find a systematic gap between AI preference and real user engagement: as target engagement increases, LLMs add more explicit logical structure, while real user engagement is more strongly associated with affective and expressive salience. We call this tendency logic overbinding. Based on this diagnosis, we propose Ontology-Masked Reasoning Autoencoding (OMRA), a controlled intervention that masks and reconstructs over-explained spans while preserving stance, factual content, and coherence. Across four LLM families, OMRA reduces the measured gap by an average of 54.4%. In human evaluation, OMRA wins 62.4% of pairwise preference judgments against matched real platform answers, even though the real answers are more often judged to be human-written.
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https://arxiv.org/abs/2609.18282
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SNOMED CT Concept Recommendation from Masked Clinical Context
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Standardizing clinical language to SNOMED CT supports interoperability, analytics, and reusable phenotyping, but concept recommendation remains difficult when relevant concepts are rare or absent from training data. We present a masked-concept recommendation benchmark using the SNOMED CT Entity Linking Challenge v1.2.1 data derived from MIMIC-IV-Note. The dataset contains 75,491 annotations across 272 discharge summaries, with 204 notes used for training and 68 for historical testing. For each unique note-concept pair, the target mention is masked from a local clinical context and the system ranks SNOMED CT concepts observed during training. We compare a popularity baseline, sparse TF-IDF concept prototypes, dense latent semantic analysis embeddings, sparse-dense fusion, retrieved-note evidence, and a retrieval-augmented hybrid. Sparse TF-IDF performs best, achieving Recall@1 of 14.81%, Recall@10 of 33.43%, MRR of 0.2114, and nDCG@10 of 0.2297. Retrieval augmentation does not improve this baseline, with Recall@10 of 31.99% and MRR of 0.1937. Performance is strongly affected by concept frequency: Recall@10 is 7.74% for concepts appearing in only one or two training notes versus 43.90% for concepts appearing in more than ten. In addition, 9.66% of test note-concept pairs contain concepts unseen during training. These findings show that local lexical context and terminology coverage are major determinants of recommendation quality in low-resource settings and provide a reproducible baseline for future ontology-grounded and biomedical-encoder retrieval systems.
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https://arxiv.org/abs/2609.17855
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Extracting ontology-compliant knowledge from scientific text describing irradiated materials using large language models
2026-09-15 15:05:57Marco Luca Sbodio, Marcos Mart\'inez Galindo, Vanessa Lopez, Blanca Biel, Pablo Canca, Pedro Delgado, Jes\'us I. Mendieta-Moreno, Raphael Tack, Maria J. CaturlaAbstract
The quest for new materials increasingly relies on predictive models and comprehensive simulations that span scales from atomic to macroscopic levels. However, essential data necessary for these models and simulations are often embedded in scientific literature as unstructured text, limiting reusability and posing challenges for researchers seeking to leverage existing knowledge effectively. While extracting structured data from unstructured text using large language models is gaining popularity, traditional methods typically generate key-value pairs data with straightforward schemas. In contrast, we introduce eolas, a modular pipeline that uses large language models to automatically transform scientific documents into knowledge graphs aligned with a specified ontology. We demonstrate eolas effectiveness in extracting useful information for scientists studying materials designed to endure the extreme temperatures and radiation levels found in fusion reactors. While a human expert might spend between thirty to ninety minutes extracting relevant data from an article, eolas can generate high-quality knowledge graphs in just a few minutes. These are presented in a tabular format with faceted navigation for easy human validation. Additionally, we introduce the first benchmark dataset designed to assess large language models capabilities in constructing knowledge graphs within the domain of irradiated materials. The analysis of 168 experiments using our dataset, various large language models and prompting techniques provides key insights that we summarize into practical guidelines for effectively extracting knowledge graphs aligned with an input ontology.
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https://arxiv.org/abs/2609.17291
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Symbolic Separation: Grounding Deep Agents in Knowledge Graphs for Trustworthy Operational Data Analytics
2026-09-15 12:38:43Baibek Davletiyarov, Junaid Ahmed Khan, Andrea BartoliniAbstract
Generative AI promises natural language access to the massive numerical telemetry of data centers and Industry 4.0 installations, yet text-to-query and tool-using agents stay unreliable: even frontier models answer little more than half of real-world database questions, and far fewer of the multi-step, operational ones, because the LLM must compose how heterogeneous sources relate and hallucinates the relations, not just the fields. We propose symbolic separation: a deep agent reasons freely but may act on data only through an ontology-constrained Virtual Knowledge Graph with deterministic pre-execution validation. Unlike a tool API's interface contract, this domain-semantic contract turns a complex question into one validated graph traversal instead of LLM-inferred joins. Instantiated as the Neurosymbolic Deep Analyst and evaluated on 49.9 TB of superconputer telemetry against a rigid workflow and a non-symbolic ablation, it raises end-to-end task success from 43% to 86%, prevents silent data-integrity errors that no syntactic check catches, and cuts token cost by 2.4x, letting a smaller on-premise model outperform a larger one.
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https://arxiv.org/abs/2609.17107
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EvoOntology: A Self-Evolving Ontology Layer for Data Agents
2026-09-14 15:59:24Meiduo Chong, Shaolei Zhang, Ju Fan, Xiaoyong DuAbstract
Data agents aim to fulfill natural-language instructions over heterogeneous data, including tables, files, and databases. However, data agents face a challenging agent-data gap: heterogeneous data resides outside the agent, while the agent can access it (e.g., column names and file paths) only through generic tools. Existing approaches either let agents directly explore raw data sources or inject manually constructed semantic layers into prompts. However, neither scales well to large heterogeneous data sources nor adapts to different agent behaviors. In this paper, we introduce EvoOntology, a self-evolving ontology layer for data agents. EvoOntology encapsulates the ontology as an MCP server comprising a schema layer, a content layer, and a tool layer, enabling agents to actively query and interact with the ontology at runtime. To this end, we introduce a builder agent for autonomous ontology construction and a self-evolution loop that continuously refines the ontology through attribution-guided typed edits that are accepted only after a backbone-conditional paired evaluation. Experiments on three well-adopted data-agent benchmarks with four LLM backbones demonstrate that EvoOntology consistently outperforms strong baselines and existing semantic-layer approaches, effectively bridging the agent-data gap and enabling more effective interaction with heterogeneous data. Code: this https URL
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https://arxiv.org/abs/2609.15779
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From Ideas to Actions: A Public-Data Decision-Support Toolchain Across the Venture Lifecycle
2026-09-14 08:40:08Lei Qu (Shanghai Xing Yun Zhi Li AI Institute)Abstract
Founders face two linked decisions: whether to pursue an idea before founding, and which operating actions and capital partners fit afterward. We present a public-data decision-support toolchain combining time-bounded proposal profiling, market and moat checks, and deterministic aggregation with auditable investor-company event chains for retrospective analysis. Pre-founding: (a) After threshold selection on 198 development companies, the frozen pipeline achieves F0.5=0.5357 [0.412, 0.655] on an independent, row-disjoint 198-company validation sample. On the combined 396 rows, the Full Pipeline scores 0.6301 versus 0.2734 for a paired Raw LLM baseline. Post-stratification of 1,027 completed cases in a separate scale cohort yields 0.6506 [0.598, 0.707]; the run remains incomplete. A 377-row composition-matched check yields 0.6573. (b) The AI-inference study identifies distribution-layer businesses as a replicable path to independent profitability with a limited revenue ceiling, and frontier-model ownership as a path to capital-market upside at exceptional capital cost. Post-founding: (a) Public sources support auditable event-chain analysis. (b) In the chip-company study, sustained product, customer, and supply-chain progress is associated with better observed outcomes; financing alone does not establish operating progress. (c) Financing comprises 79% of confirmed visible post-investment actions. Evidence tentatively favors acquisition-experienced strategic corporate investors for acquisition-oriented founders and financing-led institutional VCs with fewer observed control events for independence-oriented founders. Findings are developmental and observational, not causal guarantees or investment advice. We release shared ontology, provenance-bearing EventChain data, schemas, benchmarks, and executable skills for audit, reuse, and extension.
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https://arxiv.org/abs/2609.15219
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Natural Language Knowledge Graph Query Execution: Leveraging Controlled Semantics in the LLM Context Window
2026-09-13 16:36:40Blake G. FitchAbstract
Large Language Model (LLM) applications often transfer domain concepts into the model's context informally, through prompt prose, schema dumps, and examples. We show that for database queries, data model concepts pass to LLMs more effectively through representations whose vocabulary terms carry declared, machine-readable semantics (controlled semantics). NLKGQ is a working system and reusable framework that does this for data modeled in a knowledge graph. A formal OWL ontology serves as the transfer mechanism, concentrating the meaning of the data into semantically precise tokens the model can use directly. In a single LLM call, NLKGQ places in the context a system prompt instructing on SPARQL, the complete domain OWL ontology, and a domain-specific prompt addition, together with the user's natural language query. The model then generates the SPARQL query directly, zero-shot. Where the native vocabulary of an existing database or federation of databases is opaque, a wrapper ontology substitutes clean terms and a runtime rewriter restores the native forms. Evaluating on DBLP-QuAD 2.0 showed that its scores depend on the graph snapshot, the endpoint used, and the wording of its machine-generated questions, so we propose DBLP-QuAD 3.1, which maintains the intent of 2.0 while making reference results deterministic, revising reference SPARQL where needed, and rewriting the natural language questions, with a frontier model, to state each reference query's intent clearly and completely. We evaluate on the DBLP-QuAD 2.0 benchmark (57.6% Match under deterministic re-scoring), DBLP-QuAD 3.1 (89.9% Match on 1,000 questions), SemOpenAlex (98% Match against a published baseline's 86% on the identical test set), and neuroimaging metadata (100%).
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https://arxiv.org/abs/2609.14652
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ORDER: A Fictitious-World Benchmark for Domain-Adaptive Embodied AI
2026-09-13 07:21:22Sai Krishna Reddy Sathi, Anuj TiwariAbstract
Adapting language models to new domains via continual pre-training raises a basic evaluation problem: if the training corpus overlaps with what the model already knows, performance gains cannot be cleanly attributed to new learning rather than pre-existing knowledge. This matters most for knowledge-intensive, task-light (KHTL) robot deployments - pharmaceutical dispensing, hazardous-material handling, facility-specific protocols, where the physical task is simple but the governing rules are proprietary and safety-critical, and where extensive live testing is costly or unsafe. We introduce ORDER (Ontology-driven Decision-making for Embodied Reasoning), a benchmark built on a fictitious world: a 342,069-token synthetic corpus defining a self-consistent physics that cannot appear in any model's pre-training data. ORDER pairs a 500-question knowledge test (ORDER-BENCH) with a harder compositional task, ORDER-SPATIAL: ordering objects for safe manipulation across both familiar and entirely novel scenes. GPT-4.1 without adaptation scores below chance on ORDER-SPATIAL (Kendall's tau = 0.441), showing its priors actively conflict with the invented physics. After continual pre-training, small models improve substantially on both familiar and novel scenes alike evidence of genuine world-model induction rather than memorization. We then carry this through to a robot pipeline: models that answer the knowledge test well often cannot produce valid, executable plans without a further skill-adaptation stage, after which small, fully offline models outperform GPT-4.1 even when GPT-4.1 is given retrieval access to the same rules (Kendall's tau = 0.848 vs. 0.606), on a full perception-to-execution loop demonstrated on a simulated iiwa7 arm with human-in-the-loop correction. Throughout, ORDER-SPATIAL performance, not knowledge-test accuracy is what predicts real plan quality.
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https://arxiv.org/abs/2609.22285
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Surprising Effectiveness of Self-Demonstrations in Enhancing Schema-Ontology Mapping with LLMs
2026-09-12 07:42:55Siddhesh Thombre, Manasi Patwardhan, Sunita SarawagiAbstract
Integrating heterogeneous relational databases into a centralized ontology remains a persistent challenge in enterprise knowledge representation, primarily due to semantic heterogeneity, cryptic schema naming, missing metadata, and the abstraction gap between relational schemas and ontological models. Although large language models (LLMs) offer strong semantic reasoning capabilities, we show that directly applying them through one-shot prompting or naive multi-stage pipelines leads to poor performance for schema-ontology mapping. This paper presents a self-demonstration-driven approach that combines a neuro-symbolic task decomposition with a novel mechanism for automatically generating pattern-guided, dependency-aware demonstrations to address this integration challenge. Our approach incorporates two key strategies to achieve substantial accuracy gains over existing LLM-based schema integration methods: (i) a neuro-symbolic decomposition of the task into cascaded sub-tasks, where symbolic constraints structure the search space and LLMs perform semantic reasoning within each focused sub-task, and (ii) self-generated demonstrations guided by domain-agnostic patterns to supervise each sub-task. Experiments on three of the most challenging scenarios from the RODI benchmark show that our approach achieves state-of-the-art performance, substantially outperforming (25 percentage points F1 improvements) both traditional schema-to-ontology mapping techniques and recent LLM-based schema-to-ontology and schema matching approaches. Ablation studies further reveal the significant benefits of pattern-guided self-demonstrations and the complementary benefits of neuro-symbolic task decomposition.
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https://arxiv.org/abs/2609.13776
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HemaHier: Chain-Conditioned Ordinal Hierarchies for Lineage-Aware Bone-Marrow Cytology
2026-09-11 13:30:20Afshin Bozorgpour, Peter Sch\"uffler, Edgar Jost, Dorit MerhofAbstract
Bone-marrow cytology is inherently structured: each cell belongs to a hematopoietic lineage, and many cell types lie on ordered maturation trajectories. Standard flat classifiers ignore this structure, treating a mild same-lineage confusion the same as a severe cross-lineage mistake and predicting only discrete labels. We propose HemaHier, an ordinal-hierarchical prediction head for a frozen or lightly adapted cytology foundation model. Its central component is a chain-conditioned maturity score that reads a single maturity value under a per-chain query, supervised only on biologically valid healthy chains, while dysplastic and off-chain cell types remain classes but are excluded from maturity supervision. Fine and lineage predictions are coupled through a shared posterior that guarantees hierarchical consistency, and a staged objective first stabilizes recognition, then adds lineage and maturity supervision. On three bone-marrow datasets under a shared ontology, HemaHier achieves competitive recognition while reducing biologically severe errors and adding a within-lineage maturity ordering that flat classifiers lack. Code is available at this https URL.
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https://arxiv.org/abs/2609.12835
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From Document Silos to Process Intelligence: A Multi-Layer Knowledge Graph for CMC Process Development
2026-09-10 12:59:04Reza Amirmoshiri, Faryad Sahneh, Yasser JangjouAbstract
Chemistry, Manufacturing and Controls (CMC) process development generates an enormous body of technical information across a multi-stage, knowledge-intensive continuum from drug discovery to commercial manufacturing. This knowledge is traditionally fragmented across functions and heterogeneous formats, causing traceability gaps and significant knowledge-management costs during technology transfer and regulatory filing. We present a modular agentic-AI platform that converts a heterogeneous corpus of process-development documents into a queryable, dual-layer knowledge graph. A base knowledge layer builds a lexical graph with a Document-Section-Chunk hierarchy through lossless ingestion of digital, scanned, handwritten, and multilingual documents, while an intelligence layer extracts ontology-aligned entities and bridges cross-document concepts through a provenance-anchored domain graph. LLM agents operate across both layers, selecting the retrieval path best suited to each question. We evaluate the lexical layer with a novel three-tier protocol measuring the deployment-fidelity of a retrieval-augmented generation (RAG) system on proprietary data, demonstrated on 505 questions curated from 38 development reports of a Sanofi small-molecule program. Tier-1 multiple-choice accuracy of 95% signals strong platform reliability; the stricter Tier-2 LLM-judge pass rate of 85%, which degrades on comparative and corpus-wide questions, reveals a failure taxonomy that Tier-1 accuracy alone fails to capture. A router agent selects between layers according to question type. We anticipate this protocol will enable future designers of agentic platforms to assess their systems against nonpublic databases, and that graph-based architectures will see broader adoption in pharma as a means of transforming fragmented document repositories into structured process intelligence.
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https://arxiv.org/abs/2609.11493
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Fortunate Recall: Ontology-Driven Memory Lifecycle Management for Persistent Coherence in LLMs
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Current LLM memory systems treat all personal facts identically, so stores grow without bound while retrieval precision degrades. The core challenge is lifecycle management: which memories should persist, which should be replaced, and at what rate, conditioned on the behavioral type of each fact. Fortunate Recall (FR) is a composable policy layer that classifies personal facts into a 10+1 behavioral ontology and applies category-specific lifecycle policies (differential temporal decay, slot-key supersession, event-time validity, and category-aware retrieval routing) as deterministic functions over LLM-extracted metadata. FR-Bank, our infrastructure-independent implementation, reaches a 76.9% pass rate on LifecycleBench, a new 516-question temporal-disambiguation benchmark, ahead of Mem0, A-MEM, Memory-R1, and MemoryOS (61% to 70.5%), and 75.2% on the full LongMemEval-S under the canonical Wu et al. judge protocol, so lifecycle policies impose no measurable cost on standard retrieval. A pre-registered ablation locates the gains: replacing the typed layer with three generic lifecycle primitives leaves correctness statistically unchanged (-1.7pp, 95% CI [-6.0, +2.7]), so the generic lifecycle metadata carries the correctness advantage, while the behavioral ontology carries calibration, halving downstream confabulation (12.0% vs 24.2%, p<0.001). End-to-end, FR-Bank cuts confabulation from Mem0's 45.1% to 22.4% over answered queries and from 32.2% to 13.0% over all queries while answering more of them correctly (31.2% vs 18.6%); the ranking replicates on the open-weight Kimi K2.5. The decomposition transfers to BEAM, an independently built benchmark: 46.8% correct vs Mem0's 32.9% over 280 questions, with the ontology's benefit concentrated in contradiction resolution and saturating near seven policy clusters. The ontology, benchmark, and code are released.
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https://arxiv.org/abs/2609.10413
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OntologyAligner: Ontology-Aligned Retrieval and Hierarchy-Guided Large Language Model Reranking for Biomedical Ontology Normalization
2026-09-09 11:30:25Jie Song, Zhichuan Xu, Ziyu Lu, Meng Xiao, Cheng Bi, Yuxin Zhang, Xin Zheng, Xiaoran Li, Qiongfang Cao, Hao Yang, Bairong ShenAbstract
Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical data. This task remains challenging because lexical variation and subtle distinctions among hierarchically related concepts can obscure concept boundaries. We present OntologyAligner, a three-stage framework that combines ontology-aligned retrieval, large language model candidate reranking, and selective hierarchy-guided refinement. We also construct PhenoNormBench, a unified benchmark comprising 13,390 samples from seven Human Phenotype Ontology datasets. OntologyAligner achieved state-of-the-art performance on HPO normalization, with 88.78% Macro Top-1 Accuracy and 86.75% Micro Top-1 Accuracy, exceeding the strongest baseline by 4.85 and 5.07 percentage points, respectively. Ablation analyses showed complementary contributions from all three stages, and sensitivity analyses demonstrated stability across candidate-set sizes and model backbones. Applications to MONDO, MEDIC, and NCBITaxon further established portability to other ontologies. OntologyAligner offers a generalizable framework for accurate mapping of biomedical text to structured ontology concepts. PhenoNormBench and the code are publicly available at this https URL.
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https://arxiv.org/abs/2609.10055
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