pval threshold

[ci skip]

This build is based on
f1d1a88.

This commit was created by the following CI build and job:
https://github.com/biocypher/biochatter-paper/commit/f1d1a88d4ff5c035230d842bc20ffd57f02917da/checks
https://github.com/biocypher/biochatter-paper/actions/runs/7914660257

README.md

@@ -1,7 +1,7 @@
 # Output directory containing the formatted manuscript
 
 The [`gh-pages`](https://github.com/biocypher/biochatter-paper/tree/gh-pages) branch hosts the contents of this directory at <https://biocypher.github.io/biochatter-paper/>.
-The permalink for this webpage version is <https://biocypher.github.io/biochatter-paper/v/32a990970f754b4a632acac66c661aed6c8b01c6/>.
+The permalink for this webpage version is <https://biocypher.github.io/biochatter-paper/v/f1d1a88d4ff5c035230d842bc20ffd57f02917da/>.
 To redirect to the permalink for the latest manuscript version at anytime, use the link <https://biocypher.github.io/biochatter-paper/v/freeze/>.
 
 ## Files
@@ -35,4 +35,4 @@ Verifying timestamps with the `ots verify` command requires running a local bitc
 ## Source
 
 The manuscripts in this directory were built from
-[`32a990970f754b4a632acac66c661aed6c8b01c6`](https://github.com/biocypher/biochatter-paper/commit/32a990970f754b4a632acac66c661aed6c8b01c6).
+[`f1d1a88d4ff5c035230d842bc20ffd57f02917da`](https://github.com/biocypher/biochatter-paper/commit/f1d1a88d4ff5c035230d842bc20ffd57f02917da).

index.html

@@ -124,8 +124,8 @@
   <meta name="dc.date" content="2024-02-15" />
   <meta name="citation_publication_date" content="2024-02-15" />
   <meta property="article:published_time" content="2024-02-15" />
-  <meta name="dc.modified" content="2024-02-15T10:38:49+00:00" />
-  <meta property="article:modified_time" content="2024-02-15T10:38:49+00:00" />
+  <meta name="dc.modified" content="2024-02-15T10:44:30+00:00" />
+  <meta property="article:modified_time" content="2024-02-15T10:44:30+00:00" />
   <meta name="dc.language" content="en-UK" />
   <meta name="citation_language" content="en-UK" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -169,9 +169,9 @@
   <meta name="citation_fulltext_html_url" content="https://biocypher.github.io/biochatter-paper/" />
   <meta name="citation_pdf_url" content="https://biocypher.github.io/biochatter-paper/manuscript.pdf" />
   <link rel="alternate" type="application/pdf" href="https://biocypher.github.io/biochatter-paper/manuscript.pdf" />
-  <link rel="alternate" type="text/html" href="https://biocypher.github.io/biochatter-paper/v/32a990970f754b4a632acac66c661aed6c8b01c6/" />
-  <meta name="manubot_html_url_versioned" content="https://biocypher.github.io/biochatter-paper/v/32a990970f754b4a632acac66c661aed6c8b01c6/" />
-  <meta name="manubot_pdf_url_versioned" content="https://biocypher.github.io/biochatter-paper/v/32a990970f754b4a632acac66c661aed6c8b01c6/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://biocypher.github.io/biochatter-paper/v/f1d1a88d4ff5c035230d842bc20ffd57f02917da/" />
+  <meta name="manubot_html_url_versioned" content="https://biocypher.github.io/biochatter-paper/v/f1d1a88d4ff5c035230d842bc20ffd57f02917da/" />
+  <meta name="manubot_pdf_url_versioned" content="https://biocypher.github.io/biochatter-paper/v/f1d1a88d4ff5c035230d842bc20ffd57f02917da/manuscript.pdf" />
   <meta property="og:type" content="article" />
   <meta property="twitter:card" content="summary_large_image" />
   <link rel="icon" type="image/png" sizes="192x192" href="https://manubot.org/favicon-192x192.png" />
@@ -188,9 +188,9 @@ <h1 class="title">A Platform for the Biomedical Application of Large Language Mo
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://biocypher.github.io/biochatter-paper/v/32a990970f754b4a632acac66c661aed6c8b01c6/">permalink</a>)
+(<a href="https://biocypher.github.io/biochatter-paper/v/f1d1a88d4ff5c035230d842bc20ffd57f02917da/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/biocypher/biochatter-paper/tree/32a990970f754b4a632acac66c661aed6c8b01c6">biocypher/biochatter-paper@32a9909</a>
+from <a href="https://github.com/biocypher/biochatter-paper/tree/f1d1a88d4ff5c035230d842bc20ffd57f02917da">biocypher/biochatter-paper@f1d1a88</a>
 on February 15, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -410,7 +410,7 @@ <h3 id="benchmarking">Benchmarking</h3>
 Of note, while the newer version (0125) of gpt-3.5-turbo outperforms the previous version (0613) of gpt-4, version 0125 of gpt-4 shows a significant drop in performance.
 The performance of open-source models appears to depend on their quantisation level, i.e., the bit-precision used to represent the model’s parameters.
 For models that offer quantisation options, performance apparently plateaus or even decreases after the 4- or 5-bit mark (Figure <a href="#fig:benchmark">3</a> A).
-There is no apparent correlation between model size and performance (Pearson’s r = 0.171, p = 9.59e-05).</p>
+There is no apparent correlation between model size and performance (Pearson’s r = 0.171, p &lt; 0.001).</p>
 <p>To evaluate the benefit of BioChatter functionality, we compared the performance of models with and without the use of BioChatter’s prompt engine for KG querying.
 The models without prompt engine still have access to the BioCypher schema definition, which details the KG structure, but they do not use the multi-step procedure available through BioChatter.
 Consequently, the models without prompt engine show a lower performance in creating correct queries than the same models with prompt engine (0.444±0.11 vs. 0.818±0.11, unpaired t-test P &lt; 0.001, Figure <a href="#fig:benchmark">3</a> B).</p>