CORTEX: High-Quality Cross-Domain Organization of Web-Scale Corpora through Ontological Corpus Graph

Ontology learning (OL) aims to automatically construct structured knowledge models from text, yet progress remains fragmented across methods, domains, and evaluation practices. Despite decades of research, OL lacks a shared infrastructure for systematic evaluation and ontology access. This absence has hindered progress and fragmented research, leaving the central challenges of OL largely unaddressed. We introduce OntoLearner, a modular, cross-domain, and first-of-its-kind framework that unifies ontology access, large language model (LLM)-driven learning pipelines, and standardized benchmarking. OntoLearner releases 180 machine-readable ontologies spanning 22 domains and provides pipeline-ready datasets with train/dev/test splits for three core OL tasks: term typing, taxonomy discovery, and non-taxonomic relation extraction. Using this infrastructure, we conduct a large-scale empirical study of OL, evaluating 22 retrieval models and 12 LLMs across domains and tasks. The results converge on a finding that reframes the central challenge of OL: failure modes scale with ontological complexity rather than model size or architectural sophistication. The primary bottleneck is not model capability, but a structural mismatch between how models encode knowledge and how ontologies organize it. These findings establish that effective OL is reachable through the cross-domain, multi-task benchmarking enabled by OntoLearner. OntoLearner is open-source (MIT license) at https://github.com/sciknoworg/OntoLearner/.

Adapting small instruction-tuned models to specialized domains often relies on supervised fine-tuning (SFT) on curated instruction-response examples, which is expensive to collect at scale. Synthetic training examples generated by a teacher LLM from a domain corpus can reduce this cost, but existing pipelines can produce homogenized outputs and do not consistently capture cross-passage or cross-document dependencies. We introduce EmbGen, a synthetic data generation pipeline that decomposes a corpus into entity-description pairs, reassembles them using semantic structure inferred from embedding similarity, and then generates question-answer (QA) pairs via proximity, intra-cluster, and inter-cluster sampling with cluster-specialized system prompts. We evaluate EmbGen against EntiGraph, InstructLab and Knowledge-Instruct on three datasets of varied semantic heterogeneity, under fixed token budgets (5 and 20 million tokens). We use lexical overlap metrics, an LLM-as-a-judge rubric, and Binary Accuracy, a composed metric combining Factual Accuracy and Completeness for evaluation. EmbGen improves Binary Accuracy on the most heterogeneous dataset by 12.5% at 5M and 88.9% at 20M tokens budget, relative to the strongest baseline, while remaining competitive across other datasets with lower heterogeneity.

Dominant web data curation pipelines for pretraining collapse document quality into a single composite score, systematically missing high-value content along dimensions the scorer underweights. We present a taxonomy-driven framework that recovers this value by filtering along semantically meaningful dimensions that composite scores fail to capture. First, building on the ESSENTIAL-WEB taxonomy, we introduce two novel dimensions: timeliness and cultural specificity, both of which show low pairwise NMI with existing ones. We annotate 14M documents using Qwen2.5 32B and distill into a lightweight 0.5B model. To enable rapid corpus-wide annotation, we additionally train a 73M multi-task MLP on E5 embeddings, achieving 50x inference throughput. Second, to navigate the combinatorial explosion of filter configurations, we introduce a compute-efficient two-pass framework: Pass 1 identifies the strongest dimension signals at small scale; Pass 2 constructs and evaluates conjunctive and disjunctive compound filters from the top performers - identifying high-performing configurations at a fraction of full scaling-law cost. Applying the selected filters to deprioritized web data, taxonomy-filtered subsets outperform their unfiltered baselines and even surpass the highest-quality tier. On mid-tier data, our best filter improves over its unfiltered baseline by 12.1% on reasoning, 9.5% on coding, and 2.0% on knowledge benchmarks, exceeding unfiltered top-tier data by 6.7% on reasoning and 13.7% on coding. Furthermore, filtered data from two tiers below the typical production threshold improves by 22.3% on reasoning and 19.5% on coding over its unfiltered baseline, surpassing top-tier data on coding benchmarks. These results establish that vast latent value remains locked in deprioritized web data, and that multi-dimensional taxonomy filtering is a principled, compute-efficient key to unlocking it.