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arXiv2026

One Success Isn't Reliability: Thinkingbox, a Sandbox and Benchmark for Agents in Stateful Business Workflows

Recent agent benchmarks increasingly ground evaluation in executable environments, from code repair to web navigation, app APIs, and function calling. Yet completing consequential work beyond code requires more than producing a plausible response or valid tool call: agents must gather missing information over multiple turns, follow domain policies, coordinate dependent tools, and realize the correct persistent state transition without collateral effects. In this paper, we introduce Thinkingbox, a sandbox for tool-agent-user interaction that provides isolated MCP-compatible tool sessions, complete execution traces, and outcome evaluation over terminal backend state. Built on this sandbox, Thinkingbox-bench contains 507 policy-conditioned workflows across business scenarios, including retail, hospitality, auto insurance, neobank internal IT, and consulting IT/HR support. Each attempt is evaluated by task-specific executable checks that accept valid trajectories while rejecting wrong, missing, or extra effects; designated tasks additionally check required properties of the final response. Our experiments reveal that even the strongest proprietary and open-weight models show steep reliability drops: Claude Opus 5 falls from 66.50% pass@1 to 47.53% pass^20, and Kimi-K3 from 57.37% pass@1 to 17.60% pass^20. Moreover, many failed trials terminate cleanly after valid state-changing actions, so response- or tool-call-level signals poorly proxy end-to-end completion. Thinkingbox-bench reveals a large gap between occasionally finding a successful trajectory and reliably completing stateful business tasks. We release both Thinkingbox (https://github.com/microsoft/thinkingbox) and Thinkingbox-bench (https://github.com/microsoft/thinkingbox-data).

cs.CL↗

arXiv2026

Constructing Disambiguated Knowledge Bases from Large Language Models at Scale

Automated Knowledge Base Construction (AKBC) is a core NLP task, and recent work proposes generating knowledge bases directly from large language models (LLMs), treating the model itself as the knowledge source. However, LLMs natively possess no representation of entities, leading to duplicate entries as well as conflations. We propose GPTKB 2.0, a methodology for constructing disambiguated KBs directly from LLMs. GPTKB 2.0 incorporates on-the-fly disambiguation of entities, relations and classes, and is meticulously designed to satisfy both scalability and disambiguation accuracy. We analyze the central design decisions and characterize the trade-offs between accuracy, scale, and cost. We execute GPTKB 2.0 at scale, obtaining a materialized KB containing over 1M disambiguated entities and 38.4M triples. This represents the first million-scale LLM-native KB with explicit internal canonicalization of entities, relations, and classes, a significant departure from prior Wikimedia-centric works. GPTKB 2.0 is available at https://gptkb.org/.

cs.CL↗

arXiv2026

IBLTs Measure Before They Decode: Self-Sizing Set Reconciliation for Database Consistency Verification

Cross-system data replication pipelines cannot confirm end-to-end consistency from the local guarantees of each hop, so the two endpoints must be compared directly on a periodic basis. Once the rows of a fixed snapshot are normalized into fingerprints, the task reduces to finding the symmetric difference of the two sets. An Invertible Bloom Lookup Table (IBLT) reconciles the sets with communication that grows only with the difference cardinality $d$, independent of table size, but its capacity must be fixed while $d$ is still unknown. Across 41,603 production reconciliations over 90 days, nonzero $d$ spans about seven orders of magnitude, and no reliable empirical constant exists. We show that the count array of an IBLT has already measured $d$ before decoding. The measurement is in-band: it is carried by the recovery sketch itself and adds no bytes dedicated to estimation. A mapping-aware theorem extends the construction to Irregular, Rateless, and MET IBLTs. The protocol reads the estimate only after a decoding failure; we prove that the failure-conditioned lower quantile bounds the risk of underestimation, which gives the second-round capacity a configurable success-probability guarantee. The resulting self-sizing protocol attempts recovery with a small first-round sketch and stops on success; on failure it reads $d$, sizes the second round, and completes reconciliation in at most two rounds. Against a controlled oracle, communication is 1.29-1.47 times that of a scheme given $d$ in advance. Production workload characterization, relational-database replay, and a cross-city KV deployment confirm the end-to-end mechanism. In production on an Oracle-MySQL link, all completed runs succeeded within two rounds, over 90% on the 1-RTT fast path with a single 16 KB sketch.

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arXiv2026

X-DigCheck: Co-Evolving Application Profiles and Knowledge Graphs, Demonstrated on the RTI Documentation of Rupe Magna

We demonstrate X-DigCheck, a domain-independent environment for building and maintaining application profiles as they co-evolve with the data they describe. Profiles developed against a fixed ontology quickly drift from the schema they were meant to capture. X-DigCheck treats profile construction as a continuous ontology-data co-evolution loop: data are lifted into RDF against the profile, checked through competency questions and SHACL, and the resulting reports jointly drive revisions of the ontology, mappings, constraints, and graph. The loop is agnostic to the domain and to the pipeline that produces the graph. We validate and demonstrate the tool in the cultural heritage domain, on the construction of RupeMagna-RTI, the first Reflectance Transformation Imaging (RTI) specialisation of the Cultural Heritage Survey ODP (CHS-ODP), aligned with CIDOC-CRM/CRMdig, ArCo, CHAD-KG, and Getty AAT, with semRTI as the lifting pipeline of this use case. The demonstration lets visitors run one full turn of the loop -on the shipped Rupe Magna (Grosio, Italy) RTI survey, or on a profile and graph of their own -executing the competency-question and SHACL checks live and reading the bidirectional coverage report that flags modelling gaps and stale assumptions. The result is a portable co-evolution environment for profile engineering, together with a reusable RTI application profile produced through it. A screencast of the demonstration is available at https://zenodo.org/records/22210609.

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arXiv2026

Tree Databases

We propose a novel database model whose basic structure is a labeled, directed tree with node identities. Intuitively, the root of the tree is seen as an object (or entity), the non-root nodes as attributes of the object and the semantics of each attribute is represented by the unique path leading from the root to the attribute. We define a tree database to be a set of such trees. The trees of the database can be combined to produce new trees using a set of operations on trees that we define in the paper. The query language of our model offers two types of queries, traversal queries and analytic queries. A query (whether traversal or analytic) is always defined over a tree, which is either a tree in the database or a tree derived from other trees using tree operations. The operations on trees and the query language are both defined using a simple functional algebra whose operations are: restriction of a function, composition of functions, pairing of functions and Cartesian product of sets. A distinctive feature of our model is that traversal queries and analytic queries are both defined within the same formal framework; and in fact, traversal queries serve as the building blocks for analytic queries. This is in sharp contrast to the relational model, where analytic queries are defined outside the relational algebra, in the form of SQL Group-by queries. Therefore our model supports data access and data analysis within the same formal framework. We demonstrate the expressive power of our model by showing: (a) how our model can support inheritance in a seamless manner, (b) how one can define consistent relational databases on top of a tree database - with the tree database playing the role of an underlying semantic layer and (c) how a tree database can be used as a user-friendly interface for accessing and analyzing relational data.

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arXiv2026

VeriTS: Verifiable Model-Enhanced Time-Series Queries on Blockchain Systems

Every blockchain transaction carries a timestamp, and the chain imposes a total order. On-chain data therefore forms per-source time-series streams. However, existing systems support only basic lookups on blocks and transactions, and cannot answer time-series queries such as time-range retrieval and windowed aggregation. Offloading queries off-chain restores expressiveness, but the off-chain query layer is untrusted, so results must be verifiable. To this end, we propose VeriTS, the first verifiable time-series query framework for blockchain systems. It supports efficient range and aggregation queries. VeriTS maintains an off-chain query layer. In this layer, each stream is kept under one tree whose nodes carry authenticated aggregates, so the query index is itself the authenticated data structure. A light client thus verifies a windowed aggregate from a logarithmic number of authenticated nodes rather than from every record. VeriTS further answers error-tolerant queries from compact model representations of a stream, and extends the completeness and soundness guarantees to such approximate answers. As VeriTS never trusts the model behind a representation, a faulty or adversarial model can only widen an answer's certified interval, never falsify it. Experiments offer evidence that on windowed aggregation, VeriTS improves verification efficiency by more than two orders of magnitude over per-record proofs. On range retrieval, proofs shrink by up to 14.5x.

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arXiv2026

Diachronic Hypergraphs for Orchestrated Multi-Agent Multimodal Memory Curation

Multi-agent systems solve tasks through collaboration, tool use, multimodal reasoning, and orchestration, but each agent operates within a knowledge boundary defined by its observations, context, and resources. Memory must preserve and transfer evidence, role specific context, decisions, procedures, and experience across interactions, not only outcomes. Vector and graph memories flatten these structures into embeddings or dyadic traces, obscuring events involving agents, tools, documents, errors, and evidence. This limits knowledge sharing, tracing, reuse, revision, and orchestration. We present MAGE, a hypergraph based multimodal database designed as a memory engine for MAS. MAGE stores agents, messages, tools, errors, procedures, documents, entities, decisions, and evidence in a heterogeneous temporal hypergraph, preserving high order collaborative events as reusable memory. It supports decision driven updates, role aware retrieval, validation, lifecycle management, and budget bounded context packing. By delivering knowledge to agents and orchestrators, MAGE expands their knowledge boundaries without modifying the models. Experiments show MAGE outperforms on various memory baselines.

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arXiv2026

sheval: An RDF data shapes evaluation tool and test-suite for recursive shapes

Two different languages have been developed to validate RDF data based on the concept of a shape: ShEx and SHACL. In each language it is possible to define a shape that refers to itself, which is called a recursive shape. While in the case of ShEx, the semantics of recursive shapes is well defined and is part of the specification, in the case of SHACL, the semantics of recursive shapes is left to the implementation of the different SHACL engines. Consequently, the different SHACL engines show different behaviours when confronted with recursive shapes. In this paper we present sheval: an evaluation framework consisting of a tool and a test suite that can be used to compare the behaviour of different shapes technologies when confronted with recursive definitions. The tool has been used to evaluate and understand the differences in the implementation of recursive shapes in ShEx and SHACL. It provides a framework for testing and comparing the behaviour of different shape engines, helping to identify inconsistencies and potential issues, and providing a basis for further research and development in the field of shape-based validation of RDF data.

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arXiv2026

Large-scale spatial variable gene atlas for spatial transcriptomics

Spatial variable genes (SVGs) reveal critical information about tissue architecture, cellular interactions, and disease microenvironments. As spatial transcriptomics (ST) technologies proliferate, accurately identifying SVGs across diverse platforms, tissue types, and disease contexts has become both a major opportunity and a significant computational challenge. Here, we present a comprehensive benchmarking study of 20 state-of-the-art SVG detection methods using human slides from STimage-1K4M, a large-scale resource of ST data comprising 662 slides from more than 18 tissue types. We evaluate each method across a range of biologically and technically meaningful criteria, including recovery of pathologist-annotated domain-specific markers, cross-slide reproducibility, scalability to high-resolution data, and robustness to technical variation. Our results reveal marked differences in performance depending on tissue type, spatial resolution, and study design. Beyond benchmarking, we construct the first cross-tissue atlas of SVGs, enabling comparative analysis of spatial gene programs across cancer and normal tissues. We observe similarities between pairs of tissues that reflect developmental and functional relationships, such as high overlap between thymus and lymph node, and uncover spatial gene programs associated with metastasis, immune infiltration, and tissue-of-origin identity in cancer. Together, our work defines a framework for evaluating and interpreting spatial gene expression and establishes a reference resource for the ST community.

stat.AP↗

arXiv2026

QDAG: Declarative Composition of Reusable Analytics Methodologies at LinkedIn

Production analytics products often depend on reusable methodologies: multi-step definitions such as headcount growth, top-skill growth, or differentially-private impression distributions. Although these methodologies define business-critical numbers, they are commonly implemented as imperative glue around OLAP queries, service calls, joins, transformations, and conditional logic. As a result, teams duplicate orchestration code, definitions drift across products, and methodologies are difficult to test or analyze. We present QDAG, a production system at LinkedIn that represents an analytics methodology as a declarative directed acyclic graph of typed steps. Nodes may execute Apache Pinot queries, downstream service calls, in-memory SQLite joins, jq transformations, conditionals, differentially-private aggregations, or calls to other QDAGs. The engine evaluates graphs demand-driven, memoized, pruned, and parallelized in the per-request analytics mid-tier. QDAG is deployed across more than 500 hosts and over 100 production use cases, adding roughly 10 ms median orchestration overhead and under 50 ms at the 99th percentile. Our experience shows that making methodologies declarative improves reuse, testability, and cross-product consistency while preserving interactive latency.

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arXiv2026

UnespDataLens-RM: A Reference Model for Analytical Data Engineering with Governance, Quality, Provenance, and Reproducibility

The growing reliance on data in analytical processes and evidence-based decision-making has reinforced the importance of Data Engineering in building pipelines capable of integrating, transforming, validating, and delivering data from heterogeneous sources. However, the reliability of analytical assets depends not only on data processing capabilities but also on mechanisms for governance, quality assurance, provenance, traceability, versioning, and reproducibility throughout their lifecycle. These responsibilities are commonly addressed by different models, frameworks, and operational practices, resulting in methodological fragmentation across the analytical data lifecycle. To address this gap, this article proposes UnespDataLens-RM, a technology-independent reference model that integrates technical-operational processes and cross-cutting capabilities within a unified structure for Analytical Data Engineering. The model aims to support the specification, organization, and evolution of analytical pipelines by incorporating governance, quality, provenance, traceability, and reproducibility from the design stage. Developed following the Design Science Research approach, UnespDataLens-RM comprises eight technical-operational modules, eight cross-cutting modules, complementary dimensions, and a formalized set of artifacts, metrics, and validation criteria. The resulting specification offers a conceptual and methodological framework for future instantiations and empirical evaluations of analytical pipelines designed to be more governable, documented, traceable, auditable, and reproducible.

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arXiv2026

SmartANN: Object Causal Modeling Boosts Approximate Nearest Neighbor Diagnosis and Auto-Design

Approximate Nearest Neighbor (ANN) algorithms achieve high efficiency through interdependent phases across index construction and query execution. This coupling allows upstream performance loss to propagate downstream, affecting execution behavior and measurable outputs. Existing component-level analyses mainly compare isolated design choices, while end-to-end benchmarks report aggregate metrics; neither traces loss propagation across dependent phases, hindering root-cause attribution and automated redesign. We present SmartANN, a framework based on the object causal model (OCM) for ANN bottleneck attribution and automated redesign. SmartANN represents an ANN workflow as eight ordered, replaceable objects and diagnoses them with a sequential diagnose-and-replace loop. At each iteration, it identifies the first object deviating from expected behavior or output as a bottleneck. Because an upstream bottleneck can obscure downstream ones, SmartANN replaces it with a test oracle when available, or with an implementation producing a better outcome, then continues downstream diagnosis. From the diagnosed bottlenecks and failure causes, SmartANN composes compatible actions from a pluggable action library to generate an optimized end-to-end ANN design. We instantiate SmartANN for IVF-PQ and HNSW, covering partition-and-quantization and graph-based ANN families. Experiments on eight real-world datasets show that SmartANN improves Recall by 0.24--74.20%, and increases QPS by 28.8--256.5% at comparable Recall, with low diagnosis and auto-design overhead. The code is available at https://github.com/zhouyutong20/SmartANN.

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arXiv2026

What Eviction Destroys: A Restore-Counterfactual Audit of Forgetting in Agent Memory

Agent memory systems must discard stored information when their history exceeds a fixed token budget. Existing budget-accuracy frontiers quantify the resulting loss in accuracy, but do not distinguish irreversible losses caused by eviction from recoverable retrieval failures. We introduce the restore counterfactual, a per-question paired intervention that reinstates the question's gold evidence in the read-time context and reruns the same reader. Combining the change in correctness with whether the evidence was retained after eviction classifies each oracle-answerable error as recoverable, irreversible, or residual; in the residual case, the answer remains incorrect after restoration. We evaluate FIFO, random, redundancy-aware, and LLM-importance eviction on LongMemEval-S at three budgets and under two retrieval regimes, using GPT-4o-mini as the primary reader and judge and GPT-5.4-mini as a robustness reader. Under top-k retrieval at an 80k-token budget, the irreversible share among errors corrected by restoration is 0.67-0.73 for FIFO, random, and redundancy-aware eviction, compared with 0.60 for LLM-importance. At 8k tokens, it reaches 1.00 for all four policies. Recoverable errors occur under top-k retrieval at 80k tokens but are absent under forced-gold injection by construction, so budget-accuracy results are not directly comparable unless the retrieval regime is reported. An exploratory matched-accuracy analysis detects no difference in irreversible rate among accuracy-matched policy pairs at a resolution of 1.2-6 percentage points. The same analysis detects the deliberately destructive control. To our knowledge, this is the first per-item, per-question restore-counterfactual audit of eviction for external agent-memory stores on a standard conversational benchmark.

cs.CL↗

arXiv2026

WiDiff: Extracting Changes from Wikidata's Edit History

Knowledge graphs have become a key resource for integrating heterogeneous data and powering downstream tasks such as question answering, entity linking, and semantic search. They are built and maintained incrementally, either (i) fully automated, e.g., YAGO, (ii) semiautomatically with community oversight, e.g., DBpedia, or (iii) manually through collaborative editing, e.g., Wikidata. Understanding the evolution of knowledge graphs is essential as changes may reflect real-world updates, error corrections, or noise introduced by vandalism, all of which affect the reliability of downstream applications. Among openly available knowledge graphs, Wikidata is the most challenging case to study evolution, with over 120 million entities edited by humans and bots and an edit history spanning more than a decade. Although Wikidata exposes change data in various formats (e.g., periodic dumps and real-time event streams), none support analytical queries over the complete edit history. Therefore, we present WiDiff, a tool that extracts changes from Wikidata's complete edit history and provides a unified interface for large-scale analytical queries over it.

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arXiv2026

MAD-LEO: A Maneuver-Annotated Orbital Dataset for LEO Satellites with Tiered Multi-Source Evidence

With the rapid development of aerospace technology and the large-scale deployment of low Earth orbit (LEO) constellations, the risk of orbital collisions has increased, creating a growing demand for reliable observations of satellite maneuvers. However, public datasets containing real maneuver records remain scarce. We present MAD-LEO, a Maneuver-Annotated orbital Dataset for LEO satellites. The mission-reported subset contains 1,134 maneuver events from eleven geodetic and altimetry satellites spanning 1992 to 2026, with labels taken directly from mission-published maneuver histories. Each event is checked against two-line element (TLE) data, precise orbit products, and satellite laser ranging (SLR) observations, with evidence tiers assigned according to data availability. The operational subset pairs operator-published ephemerides for 6,785 Starlink satellites with cataloged TLE records over a continuous 107-hour period. Technical validation across seven machine-readable experiment suites confirms the cross-source consistency of the labels and the evidence products.

astro-ph.EP↗

arXiv2026

OntoKG-EQ: A provenance-grounded, competency-question-governed knowledge graph for auditable analyst querying

Analysts in emerging equity markets keep answering the same questions. Did fundamentals match the market's response? How does the local currency co-move with returns? Which firms outperform sector and benchmark, and which disclosures coincide with abnormal trading? These answers come from ad-hoc spreadsheets that are hard to reproduce, audit, or trust. We present OntoKG-EQ, a knowledge-based system that makes such queries reproducible, evidence-linked, temporally explicit, valid, and inspectable. It couples a bounded, competency-question-governed core ontology with a provenance-aware knowledge graph in which every class, property, shape, and metric is justified by one of five frozen questions. The system materialises market data into the graph, computes the metrics, validates its structure against declarative shape constraints, answers each competency question with a graph query, derives typed findings, and generates an explanation tracing each result to its observations, evidence, sources, and provenance. We evaluate on curated datasets from three emerging markets (Pakistan, Malaysia, Indonesia). Once each market's data is mapped into the common schema, the ontology, shapes, queries, and rules are reused unchanged. A relational-database baseline shows the graph changes no analytics. Its value is governance, provenance, and self-explaining structure. Because answers are rendered deterministically from the validated graph, their consistency with it is guaranteed by construction. Used as a reference, the system measures how consistently eight open language models transcribe the same evidence (provenance coverage 0.00 to 1.00). A study with a 17-participant convenience panel finds the evidence bundle significantly increased perceived trust and completeness. Code and data are openly released.

cs.ET↗

arXiv2026

SQLMorph: Query Mutation and Fine-Grained Metrics for Text-to-SQL Evaluation

Text-to-SQL systems translate natural language queries into executable SQL, democratizing access to structured data. Despite recent advances driven by large language models (LLMs), evaluation remains a major bottleneck: public benchmarks fail to capture the complexity of enterprise schema, while building private evaluation sets is costly and nondeterministic, making evaluation results difficult to reproduce. To address this issue, we present SQLMorph, a framework for Text-to-SQL evaluation via query mutation. SQLMorph introduces two techniques to automatically generate and expand evaluation sets: Join Query Expansion (JQE), which systematically increases structural complexity through valid join additions, and Textual Query Augmentation (TQA), which generates controlled natural language perturbations to assess robustness to linguistic variation. JQE and TQA create targeted choke points to challenge specific system components. When applied to state-of-the-art systems, JQE increases query coverage and reveals accuracy degradation as the number of joins grows. Meanwhile, TQA shows that linguistic brittleness induced by heavy abbreviation can reduce accuracy by up to 17%. Beyond evaluation sets, SQLMorph introduces a family of execution-level metrics that address the limitations of current binary measures, such as Execution Accuracy. We define Execution Precision (EXP) and Execution Recall (EXR) to quantify the fraction of correct and recovered results, respectively, and combine them via F1 for unified scoring. Our experiments show that these relaxed metrics enable fine-grained analysis of over- and under-prediction, revealing differences across systems that binary metrics obscure. Together, SQLMorph's query mutation and fine-grained metrics support debugging and better align Text-to-SQL evaluation practices with real-world deployments.

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arXiv2026

Factorized and Vectorized Execution: Optimizing Analytical and Semantic Queries over Relations

Many-to-many joins are central to analytical and semantic workloads such as fraud detection, network analysis, and recommendation, where insights arise from relationships between entities. These workloads often suffer from an explosion of intermediate results, sometimes orders of magnitude larger than the inputs. Factorized representations address this problem by exploiting conditional independence among attributes to encode intermediates more compactly. In some cases, they can reduce the output size asymptotically below the worst-case output size. However, adopting factorization in modern vectorized query processors remains challenging: factorized representations are hierarchical, whereas vectorized execution is built around flat, block-oriented processing. Prior approaches either rely on full materialization or support only restricted factorization layouts, sacrificing much of the benefits of both factorization and vectorization. We present FFX, a novel engine for Fast Factorized eXecution. FFX is the first pipelined engine to support arbitrary factorization schemes while preserving full vectorization. The engine introduces packed factorized vectors and operators that maintain cache-friendly, contiguous layouts. Beyond analytics, FFX also co-optimizes semantic operators by serializing factorized intermediates into compact prompts for large language models (LLMs), substantially reducing token usage and inference cost while maintaining output quality and, in some cases, improving it. Together, these contributions enable efficient execution of join-heavy analytical queries, including queries augmented with semantic operators.

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