Papers

Language models now draft, classify and criticise inside research production, yet the artifacts they help produce carry little accountable history. Rather than detecting machine involvement afterwards, we specify an auditability discipline built at production time: git sealing with an anchor lineage, hash-bound provenance, red-line gates that refuse non-compliant artifacts and log every refusal, cross-model role separation, and programmatic assembly from registered sources. Adherence is instrumented by metric cards, each carrying a pre-registered blind spot and evidential standing, frozen before the prospective case it observes. In that case the observed project's pre-registered confirmatory test was executed under seal and returned No-Go, and that project's frozen stopping rule halted the work, against its own operators. A lower-graded retrospective case covers families whose machinery predates the protocol. Current observations are provisional; we release a package from which a third party can recompute every primary metric.

The academic publishing ecosystem is a vast, heterogeneous network of works, authors, institutions, journals, and topics. Traditional scientometrics reduces it to isolated tabular indicators (h-index, Impact Factor) that ignore topological context and are not designed to capture coordinated illegitimate practices. Building on our companion review, which proposed graph analysis of publishing integrity, this paper implements that approach. We define a heterogeneous multivariate graph model over OpenAlex open data (seven node types, seven edge types) and a methodology based on projections (citation and co-authorship networks), interpretable structural metrics, community detection, and three screening detectors of anomalous publishing patterns. We deliberately avoid binary classification: detectors return ranked candidates with explicit structural evidence for human assessment. On the institutional corpus of VSB - Technical University of Ostrava (2020-2025) with its one-hop citation neighbourhood, community detection recovers real research groups, centralities identify cross-disciplinary bridges, and the screenings flag dense co-authorship cliques, locally closed citation loops, and thematically isolated venues. On a second, venue-centric corpus with external ground truth (journals delisted by Scopus and DOAJ) and size-matched controls, a naive case-control design yields seemingly strong but spurious detectors (a prominence confound), whereas after matching the only robust signal is the breadth of disciplinary scope (AUC 0.70); an open graph-based prestige measure (PageRank over the journal citation network) tracks a JIF proxy while being an order of magnitude more resistant to citation gaming than count-based indicators. We release the method as the open-source library apnet with a reproducible CLI workflow and a web interface; the analysis runs on commodity hardware in minutes.

Predatory journals pose a significant challenge to the integrity of the Open Access (OA) publishing model by exploiting its framework for financial gain while bypassing essential editorial and peer-review standards. This study critically evaluates existing methodologies for identifying such journals, ranging from manual blacklist checks to advanced automated approaches utilizing machine learning. The analysis highlights critical limitations, including the lack of a universally accepted definition of predatory journals, over-reliance on binary classification systems (e.g., blacklists and whitelists), and issues with scalability, reliability and interpretability. To address these shortcomings, this paper introduces a novel methodology based on multivariate graph analysis. By modeling the academic publishing ecosystem as a network of interconnected entities (such as authors, articles, journals, and publishers), this approach provides broader insights into the dynamics of scholarly communication and could help identify illegitimate publishing practices by utilizing graph algorithms like centrality measures, community detection, and anomaly detection. The proposed framework aims to enhance the accuracy, scalability, and transparency of detection of illegitimate journals and publishing practices while fostering a more comprehensive understanding of the academic publishing landscape.

Over the past several years, LLM-powered chatbots and agents have become widely used as a tool for academic writing. LLM-assisted writing can be valuable by removing language barriers but at the same time causes concerns about misconduct and fraud. To inform policy decisions, it is necessary to monitor the prevalence of LLM-altered texts in scholarly publications. Despite some recent progress in this direction, no existing method can produce reliable estimates. Here we suggest and validate a new unbiased approach to estimate LLM usage in a corpus of texts based on changing word frequencies. We apply our method to the full texts of open-access biomedical papers from Pubmed Central, and show that by the end of 2025, 89% of papers show excess of LLM-associated vocabulary. We also find that LLMs are twice as likely to be used when writing a paragraph in the Discussion section (68%) compared to a paragraph in the Methods section (32%), but even inside the Methods section, the overall prevalence of LLM usage is over 50%. We believe that our estimates are crucial to shape future guidelines and policies.

Purpose: Keyphrases are statistically and semantically important textual units that can also attract readers' attention during comprehension. However, existing keyphrase extraction (KPE) studies mainly focus on improving textual representation while largely overlooking human reading behavior. This study examines whether lightweight webcam-based eye-tracking features can improve KPE from Chinese academic abstracts in Library and Information Science (LIS). Methodology: To address the limited availability of eye-tracking data for Chinese academic reading, we developed a lightweight webcam-based data collection platform using the open-source SearchGazer library and constructed the Chinese LIS Eye-Tracking Corpus (CLIS-ET). Three character-level eye-tracking features, first fixation duration (FFD), fixation number (FN), and total fixation duration (TFD), were incorporated into KPE models to evaluate their effects on extraction performance. Findings: Eye-tracking features consistently improved KPE performance. The combination of FN and TFD achieved the best results on the Att-BiLSTM+CRF model, indicating that readers' fixation behavior provides useful signals for identifying keyphrases in academic abstracts. Originality/value: This study introduces a cost-effective webcam-based eye-tracking approach for KPE and presents CLIS-ET, a Chinese academic eye-tracking corpus containing FFD, FN, and TFD features. The results demonstrate the value of incorporating human reading behavior into keyphrase extraction. Dataset and code: https://github.com/yan-xinyi/ET_AKE and https://github.com/yan-xinyi/Reading_ET_System.

Scholar assessment plays a fundamental role in faculty recruitment, funding allocation, academic promotion, and talent discovery. Existing scholar assessment methods predominantly rely on bibliometric indicators and reputation proxies, while recent large language model (LLM)-based approaches mainly focus on evaluating individual research papers rather than comprehensively assessing scholars. We argue that scholar assessment should be formulated as an evidence-driven reasoning problem that jointly considers intrinsic research quality and externally verifiable scholarly behavior. To this end, we propose HexEval, an evidence-driven hexagonal framework for multidimensional scholar assessment. HexEval explicitly organizes scholar assessment into two complementary evidence layers. The intrinsic layer evaluates anonymized representative works along three dimensions, namely research rigor, methodological innovation, and scientific contribution, whereas the external layer characterizes scholars through knowledge translation, research coherence, and academic impact using heterogeneous evidence collected from GitHub, Lens, OpenAlex, and other publicly verifiable sources. Instead of producing opaque aggregate scores, HexEval preserves intermediate evidence, dimension-specific rationales, and verification signals throughout the evaluation process, enabling interpretable and auditable scholar profiles. Experiments across all six dimensions show dimension-dependent agreement with human or external reference criteria: structured calibration improves absolute agreement for intrinsic quality, while the external modules recover broad trajectory and ordinal impact signals. These results support evidence-driven reasoning over heterogeneous scholarly evidence as a promising paradigm for auditable AI-assisted scholar assessment, while exposing the coverage and attribution limitations of public scholarly data.

Large Language Models (LLMs) are being considered for research evaluation, raising concerns about the introduction of AI bias. This study investigates whether ChatGPT research quality scores differ by first-author gender using 89,744 journal articles from the UK Research Excellence Framework (REF) 2021. Author information was withheld from ChatGPT to avoid direct gender bias. Nevertheless, male first-authored papers had slightly higher ChatGPT scores in most Units of Assessment (UoAs), especially in health, science and engineering-related subjects, and this pattern was often stronger for ChatGPT than for REF scores, based on a departmental-level proxy. Rank-based ChatGPT gains relative to REF scores were also more favourable for male first-authored papers in most UoAs, although the differences were generally small. Gender differences were not evident for solo research in the social sciences, arts and humanities, however. The male-favouring pattern for first-authored research was not explained by gender differences in writing styles, at least as reflected in abstract complexity. Some ChatGPT-REF differences may also reflect the departmental averaging process used to generate the REF proxy scores. Average ChatGPT scores may differ by first-author gender indirectly through other factors, such as field, topic, method, journal context or authorship structure. Thus, this is an additional reason to be cautious with AI-based research evaluation.

Scientific named entity recognition (SciNER) plays a crucial role in information extraction and knowledge discovery from scientific texts. Recently, large language models (LLMs) have demonstrated the capacity to achieve competitive SciNER performance with minimal human effort. Existing research highlights the importance of incorporating candidate entity type information for accurate entity recognition and classification by LLMs. However, when too many candidate entity types are provided in the prompt, LLMs struggle to accurately recognize and label entities in scientific texts, where entity types are more complex than in general domains. To address this challenge, we propose TdSciNER, a type-driven approach that effectively leverages entity type information to enhance SciNER performance. In TdSciNER, we first design an entity type filter model to identify the most likely entity types present in a given sentence. Subsequently, we introduce an auxiliary multi-class entity typing task within a multi-task learning framework alongside SciNER to obtain richer contextual representations. Then, we develop a novel demonstration selection strategy based on sentence similarity and entity type diversity to activate the in-context learning capabilities of LLMs, thereby improving entity recognition accuracy across diverse scientific domains. Experiments on three datasets demonstrate that our method achieves performance comparable to fully supervised models. Further analysis validates that each entity type-driven component in TdSciNER contributes to the improvement of SciNER performance. This work provides valuable insights for future advancements in SciNER and broader information extraction tasks in scientific text mining.

In this paper, we introduce StatCite, a large-scale citation network dataset covering publications in statistics and data science from 1981 to 2025. The dataset contains 189,101 research articles collected from 62 representative journals and provides bibliographic metadata, including title, author list, publisher, published year, abstract, keywords, and reference list. Based on the collected publications, we construct four complementary citation-based networks, namely the paper citation network, the co-citation network, the bibliographic coupling network, and the journal citation network. To illustrate the utility of the dataset, we present descriptive analyses of the constructed networks and investigate the community structure of the paper citation network. The results show that StatCite preserves key structural characteristics commonly observed in large-scale citation networks and captures several major research areas in statistics and data science. By integrating multiple network representations with rich textual metadata, StatCite provides a valuable resource for statistical analysis, knowledge discovery, and data-driven studies of scientific literature.

The increasing specialization of scientific research challenges existing classification systems, which provide effective representations of broad disciplines and research topics but often fail to capture the fine-grained conceptual structure of contemporary science. Author keywords offer greater specificity, but their fragmentation, redundancy, and terminological variability limit their use as stable units of knowledge organization. We introduce SCALE (Scientific Concept Aggregation via LLMs and Embeddings), a framework that extends the OpenAlex taxonomy with a new level of scientific Concepts below Topics. Rather than treating keywords as isolated descriptors, SCALE organizes semantically related terms into coherent and interpretable conceptual units and integrates them within the existing disciplinary hierarchy. The framework combines scientific text embeddings, large language models, and graph-based community detection to construct this additional layer at scale. The resulting taxonomy enables scientific literature to be read through an intermediate conceptual level between broad research topics and individual documents. This perspective provides a more detailed representation of how scientific knowledge is structured, specialized, and connected across disciplines. By transforming heterogeneous author terminology into reusable hierarchical units, SCALE offers a foundation for fine-grained scholarly classification, scientometric analysis, research monitoring, and future ontology development.

We analyzed a curated climate–health bibliographic corpus of 22,695 multi-labeled records from 2007–2023 to characterize growth, thematic concentration, and evolving methods. Annual publication counts rose sharply, with multiple change-points indicating phase-structured expansion; Negative Binomial models estimated roughly 10–11% year-over-year growth. Exposure–health co-occurrence departed strongly from independence, with canonical hazard–outcome dyads (e.g., extreme heat with heat-related impacts; floods/hurricanes with mental health) occurring far more often than expected even after accounting for marginal term popularity. A hierarchical logistic model for asthma-tagged records showed strong alignment with air-pollution-related exposures (including ozone and particulate matter) and relative under-representation of generic heat/temperature terms. Methodologically, modeling timescales shifted toward longer horizons over time, while at least one legacy method tag declined. Finally, we detected time- and geography-dependent annotation completeness, including decreased exposure-term coding in recent years, underscoring the need to model missingness when interpreting temporal trends.

Large language models (LLMs) can leave small stylistic traces in text written with their help. The most discussed is the em-dash (U+2014), especially the unspaced form word—word, which is normal in typeset English prose but unusual in U.S. press writing, where AP style calls for spaced dashes. This study asks whether that trace is measurable in congressional press releases. In a preregistered design (OSF: 10.17605/OSF.IO/U5NEY), 146,239 scraper-sourced releases from 480 House and Senate offices (2021-2025, the open congress-press dataset) were analyzed: density of unspaced prose-form em-dashes per 1,000 characters of cleaned text, Poisson/negative-binomial models with a length offset, clustering by office. Density stayed within 0.10-0.12 per 1,000 characters through 2021-2024, then rose to 0.217 in 2025, more than twice the four-year baseline; the share of releases with such an em-dash rose from ~13% to 24.8%. The primary frequency ratio (2023-2025 vs 2021-2022) was 1.55 (95% CI 1.28-1.93; exact registered cut-off: 1.528), just above the prespecified 1.5x threshold. The rise was net-new (hyphen density stable), held within authors (75.6% of 262 continuous offices increased; p ~ 1e-16) and in a closed panel of 224 offices, and survived falsification tests: three placebo cut-offs were null, the pipeline showed no step at the 2024/2025 boundary, and continuing offices carried the rise. A segmented regression finds no step at the ChatGPT cut-off but a clear post-period acceleration; the 2025 rise is symmetric across parties and chambers. Because the registered validation gate was formally breached, the full preregistered decision rule was not met; the interpretation (broad diffusion of LLM-assisted writing as the models matured) is offered as exploratory. The em-dash remains a population-level marker, not a per-release authorship detector, and the design supports no causal claim.

Scientific Knowledge Graphs (SKGs) rely on increasingly complex and heterogeneous semantic models, whose reuse and interoperability require ontologies and other semantic artefacts to be understandable by both machines and humans. However, existing ontology documentation tools provide limited support for modern reuse-oriented modelling practices, where entities are distributed across imported modules and enriched through cross-module annotations. This paper presents the new version of LODE, a re-engineered and extensible framework for generating human-readable documentation of semantic artefacts. LODE preserves the established single-page, W3C Recommendation-style documentation paradigm of its legacy predecessor, and introduces a modular architecture that separates artefact interpretation (Reader), internal representation (Model), and rendering (Viewer). Served as a web service, LODE supports the documentation of OWL ontologies and enables additional documentation features (e.g., entity stand-alone documentation, RDF entity provenance, Markdown rendering). We demonstrate the applicability of LODE through the documentation of the Scientific Knowledge Graph Interoperability Framework ontology (SKG-O), showing how it improves the accessibility and reuse of modular scientific knowledge graph models.

Retrieval-augmented generation (RAG) has become a common architecture for connecting large language models to enterprise knowledge. Most RAG systems retrieve unstructured documents (PDFs, wiki pages, support tickets) and feed them to an LLM for summarization or question answering. A growing class of enterprise agents, however, must query structured data: relational databases, data warehouses, and analytics APIs where the answer is a computed result, not a retrieved passage. Structured-data querying forces decisions that a document-RAG pipeline never has to make. We group them into seven dimensions: retrieval semantics, authorization, intent recognition, entity resolution, evaluation, failure modes, and latency. For each dimension, we characterize the baseline assumption, explain its limitation for structured data, and describe a generic architectural pattern. As supporting evidence, a controlled synthetic study shows that a staged agent built on this framework eliminates the authorization violations of a direct translate-and-execute baseline under controlled conditions. The primary result is a design-oriented framework, an evaluation protocol, and a set of open problems for governed structured-data agents.

The personal archive of Konstantin Tsiolkovsky (1857-1935) is held as fond 555 of the Archive of the Russian Academy of Sciences. The archive scanned the fond and published the images, but with no queryable catalogue, no full-text search and no dataset: the holdings can only be browsed one page at a time. This paper describes a machine-readable catalogue of all 2,019 files and 51,008 scans, a dating for 1,969 files taken from the archive's own descriptions, a page-level classification of every scan into handwriting and typescript, and a machine transcription of the fond in full: all 2,019 files and all 51,008 scans. It also reports a way to measure handwritten-text-recognition accuracy in an archive with no ground truth. Archives of the typewriter era often preserve one text twice, as manuscript and as a typed copy; transcribing both and comparing isolates the reading error, since source and pipeline are identical and only page difficulty differs. Across 1,759 such pairs from 224 files, two readings of a handwritten page agree on a median 37% of words and share a longest verbatim run of a median 10 words; the median is unchanged from the 294 pairs of the first version, on a sample six times larger. On two files that also have a published edition the estimate can be checked against ground truth: it is unbiased to within a percentage point and ranks pages as the truth does (rank correlation 0.92 where the edition is a faithful witness). This bounds use: two variants of one work here share 19% of words, below the rate at which two readings of a single page agree, so the redactions cannot be collated word by word at this quality. That negative result is reported as such, and the constraint is built into the tool.

Higher-order network datasets are dispersed across publications, institutional archives, and software-specific collections, making them difficult to discover, compare, and reuse. We introduce the Aachen Higher-Order Repository of Networks (AHORN), a curated repository of standardized higher-order network datasets derived from publicly released sources. Each dataset entry links a converted dataset to its source, metadata, citation guidance, conversion code, and version history. The repository supports browsable and machine-readable discovery, revision-specific downloads, format validation, and exports for interoperable reuse. We describe the repository architecture, curation workflow, access tools, and the coverage and limitations of the catalog snapshot analyzed in this article.

As language models move from drafting prose to running literature-search agents with tool calls, fabricated references are becoming easier to catch and constrain. The harder failure begins after every candidate is real: different models may still select the same narrow subset, producing citation monoculture without any single citation being wrong. We isolate this effect on 120 real papers. Eleven models from three vendors choose at most ten papers from uniformly random panels of thirty, with real titles and abstracts but fabricated authors, reassigned years, and hidden venues and citation counts. Each run is compared with indifferent selection on the same panel and realized budget. All eleven models concentrate sharply: the top decile receives 23.3-30.2% of citations against 15.6% under the null, one component explains 68-73% of variation across their preference maps, and cross-vendor agreement nearly matches within-vendor agreement. Formalizing the task as fixed-budget subset selection, we turn these patterns into identifiable mechanisms: an exchangeability bound rejects a mapless selector for every model, a spectral decomposition explains why the best cross-fitted mixture still retains 55% of the excess, and a rarity theorem predicts the recursive competition effect we verify within panels. Controlled paraphrase, content-slot crossover, and design resampling attribute about 90% of GPT-5 mini's map variance to paper content. Eight domain experts selecting from the same blinded panels under the same cap show no comparable shared preference, while model concentration persists in selection-only mode. Even when every reference is real and every paper is equally visible, current language models impose a common content-level filter on scientific attention. Equalizing retrieval or mixing vendors is therefore insufficient; the shared preference map itself must be changed.

The Loggia dei Lanzi in the Piazza della Signoria is one of Florence's most prominent structures visited by millions every year. Its construction history spans multiple centuries of modification. This paper presents the results of a thermal imaging campaign conducted in December 2025, using a FLIR T1020 HD camera, revealing hidden architectural features including walled-up openings and material transitions beneath the plaster surface. The favorable winter ambient conditions provided a feature-rich benchmark upon which to compare the results of enhancement algorithms and artificial intelligence models. We evaluate the application of AI-based image enhancement to thermal heritage documentation through a comparison of three tiers of image resolution in a photogrammetric Structure-from-Motion (SfM) pipeline: native resolution, FLIR's hardware-based pixel-shifted super-resolution (UltraMax), and state of the art AI-upscaled imagery models. We quantify the effect of each resolution tier on feature detection and tie-point generation, assessing whether the additional detail produced by super-resolution, whether hardware or AI-derived, translates into meaningfully denser and more accurate 3D thermal models. Our results contribute to the emerging intersection of artificial intelligence and heritage thermography by providing a direct comparison of hardware microscanning and AI super-resolution within a thermal photogrammetric workflow for cultural heritage. All datasets are made publicly available and accessible within an interactive 3D archival framework, and integrated into a custom citywide extended reality overlay application.

Scientific impact is multidimensional: overall influence, current popularity, early citation momentum, and field-relative performance each capture a distinct facet of a publication's impact. Yet, in practice, these dimensions are often reduced to a single metric, such as citation count. Open solutions for computing multiple complementary impact indicators at scale remain scarce, particularly for citation graphs as large as those provided by major scholarly databases. We introduce BIP! Ranker, an open-source, Spark-based library for computing citation-based impact indicators at scale, capable of processing citation networks with billions of citations among hundreds of millions of publications.