Optional Knowledge-Graph Layer

An optional, LLM-gated stage lifts the corpus from bibliometrics to hypothesis-level evidence. For each record, a local language model (Ollama, default model gemma3:4b) extracts structured assertions — each encoding a direction (supports / contradicts / neutral), a confidence score, and a short natural-language justification — against the 6 hypotheses declared in configuration. Assertions are serialized as RDF-compatible nanopublications [kuhn2016decentralized] and scored by a citation-weighted evidence function.

Assertion Model

Each assertion \(a\) encodes:

• Direction: \(\text{supports}\), \(\text{contradicts}\), or \(\text{neutral}\) with respect to a hypothesis \(H\)
• Confidence: a score \(c_a \in [0, 1]\) from the LLM
• Citation weight: \(\log(1 + n_{\text{cites}})\), where \(n_{\text{cites}}\) is the citation count of the asserting paper

The evidence score for hypothesis \(H\) is:

\[\text{score}(H) = \frac{\sum_{a \in A(H)^+} c_a \cdot \log(1 + n_{\text{cites}}(a)) - \sum_{a \in A(H)^-} c_a \cdot \log(1 + n_{\text{cites}}(a))} {\sum_{a \in A(H)} c_a \cdot \log(1 + n_{\text{cites}}(a))}\]

where \(A(H)^+\) is the set of supporting assertions and \(A(H)^-\) the contradicting ones. The score ranges from \(-1\) (all evidence contradicts) to \(+1\) (all evidence supports).

Incremental Extraction

Assertion extraction is incremental and resumable: assertions are appended to nanopublications.jsonl at configurable checkpoint intervals (default: 50 papers). On restart, already-processed papers are skipped automatically, so a long extraction run that is interrupted can resume without re-processing. The --clear-assertions flag discards previous results for a fresh start.

Gating and Defaults

This stage is optional and gated by language-model availability. With no language model configured, the hypothesis evidence scores read pending; with Ollama configured (as in this instance, with 127 assertions extracted), scores are populated from citation-weighted assertion extraction. The hypotheses themselves — their names and scope — come from configuration and are reported regardless of whether the scoring stage has run.

The hypotheses explored in this instance are: H1 Wakefulness Efficacy; H2 Cognitive Enhancement; H3 Low Abuse Liability; H4 Dopaminergic Mechanism; H5 Off-label Psychiatric Utility; H6 Tolerability.