Update manuscript to address issues: #1 #2 #3 #4 #5 #6 #7 #8 #9

_quarto.yml

@@ -15,6 +15,7 @@ format:
   # docx: 
   #   notebook-links: false
   agu-pdf: 
+    dpi: 200
     notebook-links: false
     header-includes:
       - \usepackage{annotate-equations}

docs/_tex/references.bib

@@ -132,6 +132,8 @@ @article{
   title={GPT-4 Technical Report},
   url={http://arxiv.org/abs/2303.08774},
   DOI={10.48550/arXiv.2303.08774},
+	journal={arXiv},
+  year={2024},
 author={OpenAI and Achiam, Josh and Adler, Steven and Agarwal, Sandhini and Ahmad, Lama and Akkaya, Ilge and Aleman, Florencia Leoni and Almeida, Diogo and Altenschmidt, Janko and Altman, Sam and et al.} }
 
 @article{
@@ -192,13 +194,17 @@ @article{
   title={BiomedGPT: A Unified and Generalist Biomedical Generative Pre-trained Transformer for Vision, Language, and Multimodal Tasks},
   url={http://arxiv.org/abs/2305.17100},
   DOI={10.48550/arXiv.2305.17100},
+	journal={arXiv},
+  year={2023},
 author={Zhang, Kai and Yu, Jun and Yan, Zhiling and Liu, Yixin and Adhikarla, Eashan and Fu, Sunyang and Chen, Xun and Chen, Chen and Zhou, Yuyin and Li, Xiang and et al.} }
 
 @article{
   boltonBioMedLM7BParameter2024,
   title={BioMedLM: A 2.7B Parameter Language Model Trained On Biomedical Text},
   url={http://arxiv.org/abs/2403.18421},
   DOI={10.48550/arXiv.2403.18421},
+	journal={arXiv},
+  year={2024},
 author={Bolton, Elliot and Venigalla, Abhinav and Yasunaga, Michihiro and Hall, David and Xiong, Betty and Lee, Tony and Daneshjou, Roxana and Frankle, Jonathan and Liang, Percy and Carbin, Michael and et al.} }
 
 @article{
@@ -233,34 +239,44 @@ @article{
   title={Towards Accurate Differential Diagnosis with Large Language Models},
   url={http://arxiv.org/abs/2312.00164},
   DOI={10.48550/arXiv.2312.00164},
+	journal={arXiv},
+  year={2023},
 author={McDuff, Daniel and Schaekermann, Mike and Tu, Tao and Palepu, Anil and Wang, Amy and Garrison, Jake and Singhal, Karan and Sharma, Yash and Azizi, Shekoofeh and Kulkarni, Kavita and et al.} }
 
 @article{
   singhalExpertLevelMedicalQuestion2023,
   title={Towards Expert-Level Medical Question Answering with Large Language Models},
   url={http://arxiv.org/abs/2305.09617},
   DOI={10.48550/arXiv.2305.09617},
+	journal={arXiv},
+  year={2023},
 author={Singhal, Karan and Tu, Tao and Gottweis, Juraj and Sayres, Rory and Wulczyn, Ellery and Hou, Le and Clark, Kevin and Pfohl, Stephen and Cole-Lewis, Heather and Neal, Darlene and et al.} }
 
 @article{
   oneilPhenomicsAssistantInterface2024,
   title={Phenomics Assistant: An Interface for LLM-based Biomedical Knowledge Graph Exploration},
   url={https://www.biorxiv.org/content/10.1101/2024.01.31.578275v1},
   DOI={10.1101/2024.01.31.578275},
+	journal={bioRxiv},
+  year={2024},
 author={O’Neil, Shawn T. and Schaper, Kevin and Elsarboukh, Glass and Reese, Justin T. and Moxon, Sierra A. T. and Harris, Nomi L. and Munoz-Torres, Monica C. and Robinson, Peter N. and Haendel, Melissa A. and Mungall, Christopher J.} }
 
 @article{
   labrakBioMistralCollectionOpenSource2024,
   title={BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains},
   url={http://arxiv.org/abs/2402.10373},
   DOI={10.48550/arXiv.2402.10373},
+	journal={arXiv},
+  year={2024},
 author={Labrak, Yanis and Bazoge, Adrien and Morin, Emmanuel and Gourraud, Pierre-Antoine and Rouvier, Mickael and Dufour, Richard} }
 
 @article{
   noriCanGeneralistFoundation2023,
   title={Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine},
   url={http://arxiv.org/abs/2311.16452},
   DOI={10.48550/arXiv.2311.16452},
+	journal={arXiv},
+  year={2023},
 author={Nori, Harsha and Lee, Yin Tat and Zhang, Sheng and Carignan, Dean and Edgar, Richard and Fusi, Nicolo and King, Nicholas and Larson, Jonathan and Li, Yuanzhi and Liu, Weishung and et al.} }
 
 @inbook{
@@ -324,13 +340,17 @@ @article{
   title={Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning},
   url={http://arxiv.org/abs/2304.02711},
   DOI={10.48550/arXiv.2304.02711},
+	journal={arXiv},
+  year={2023},
 author={Caufield, J. Harry and Hegde, Harshad and Emonet, Vincent and Harris, Nomi L. and Joachimiak, Marcin P. and Matentzoglu, Nicolas and Kim, HyeongSik and Moxon, Sierra A. T. and Reese, Justin T. and Haendel, Melissa A. and et al.} }
 
 @article{
   panLargeLanguageModels2023,
   title={Large Language Models and Knowledge Graphs: Opportunities and Challenges},
   url={http://arxiv.org/abs/2308.06374},
   DOI={10.48550/arXiv.2308.06374},
+	journal={arXiv},
+  year={2023},
 author={Pan, Jeff Z. and Razniewski, Simon and Kalo, Jan-Christoph and Singhania, Sneha and Chen, Jiaoyan and Dietze, Stefan and Jabeen, Hajira and Omeliyanenko, Janna and Zhang, Wen and Lissandrini, Matteo and et al.} }
 
 @article{
@@ -380,6 +400,8 @@ @article{
   title={Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)},
   url={http://arxiv.org/abs/2312.10904},
   DOI={10.48550/arXiv.2312.10904},
+	journal={arXiv},
+  year={2023},
 author={Toro, Sabrina and Anagnostopoulos, Anna V. and Bello, Sue and Blumberg, Kai and Cameron, Rhiannon and Carmody, Leigh and Diehl, Alexander D. and Dooley, Damion and Duncan, William and Fey, Petra and et al.} }
 
 @article{
@@ -402,32 +424,42 @@ @article{
   title={Efficient Estimation of Word Representations in Vector Space},
   url={http://arxiv.org/abs/1301.3781},
   DOI={10.48550/arXiv.1301.3781},
+	journal={arXiv},
+  year={2013},
 author={Mikolov, Tomas and Chen, Kai and Corrado, Greg and Dean, Jeffrey} }
 
 @article{
   weiLongformFactualityLarge2024,
   title={Long-form factuality in large language models},
   url={http://arxiv.org/abs/2403.18802},
+  journal={arXiv},
+  year={2024},
 author={Wei, Jerry and Yang, Chengrun and Song, Xinying and Lu, Yifeng and Hu, Nathan and Huang, Jie and Tran, Dustin and Peng, Daiyi and Liu, Ruibo and Huang, Da and et al.} }
 
 @article{
   janikAspectsHumanMemory2024,
   title={Aspects of human memory and Large Language Models},
   url={http://arxiv.org/abs/2311.03839},
   DOI={10.48550/arXiv.2311.03839},
+	journal={arXiv},
+  year={2024},
 author={Janik, Romuald A.} }
 
 @article{
   marcinkevicsInterpretabilityExplainabilityMachine2023,
   title={Interpretability and Explainability: A Machine Learning Zoo Mini-tour},
   url={http://arxiv.org/abs/2012.01805},
   DOI={10.48550/arXiv.2012.01805},
+  journal={arXiv},
+  year={2023},
 author={Marcinkevičs, Ričards and Vogt, Julia E.} }
 
 @article{murphyIdentificationCellTypespecific2023,
 	title = {Identification of cell type-specific gene targets underlying thousands of rare diseases and subtraits},
 	author = {Murphy, Kitty B. and Gordon-Smith, Robert and Chapman, Jai and Otani, Momoko and Schilder, Brian M. and Skene, Nathan G.},
 	doi = {10.1101/2023.02.13.23285820},
+	journal={medRxiv},
+  year={2023},
 	langid = {en}
 }