Symposium 2025 - Revision history

Jeetvora: /* Agenda */

2025-07-31T13:39:57Z

Agenda

← Older revision		Revision as of 13:39, 31 July 2025
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	\|11:15am		\|11:15am
	\|BiomarkerKB		\|BiomarkerKB
	\|~~TBA~~ + 5 min Q/A		\|Lupus Discovery Project + 5 min Q/A
	\|Nathan Ressom, Ana Vohralikova, Mathias Belay (15 min)		\|Nathan Ressom, Ana Vohralikova, Mathias Belay (15 min)
	\|-		\|-

Jeetvora: /* Agenda */

2025-07-31T13:24:10Z

Agenda

← Older revision		Revision as of 13:24, 31 July 2025
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	\|-		\|-
	\|'''12:30pm'''		\|'''12:30pm'''
	\| colspan="3" \| '''LUNCH (90 mins)'''		\| colspan="3" \| '''LUNCH Ross 505 (90 mins)'''
	\|-		\|-
	\| colspan="4" \| ''Group 2 Moderator : Rene Ranzinger''		\| colspan="4" \| ''Group 2 Moderator : Rene Ranzinger''

Lorikrammer at 13:19, 31 July 2025

2025-07-31T13:19:01Z

← Older revision		Revision as of 13:19, 31 July 2025
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	The HIVE lab symposium will held in person at The George Washington University, Washington DC with an option to join virtually.		The HIVE lab symposium will held in person at The George Washington University, Washington DC with an option to join virtually.

	In Person - Ross ~~637~~, Ross Hall, School of Health and Medical Sciences, The George Washington University, Washington DC ([https://maps.app.goo.gl/PHQmZacA4hWDvTCh6 MAP])		In Person - Ross 643, Ross Hall, School of Health and Medical Sciences, The George Washington University, Washington DC ([https://maps.app.goo.gl/PHQmZacA4hWDvTCh6 MAP])

	Virtual - Zoom		Virtual - Zoom

Jeetvora: /* Agenda */

2025-07-31T03:35:15Z

Agenda

← Older revision		Revision as of 03:35, 31 July 2025
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	\|-		\|-
	\|''3:45pm''		\|''3:45pm''
	\| colspan="3" \|''Break (15mins)''		\| colspan="3" \|''<nowiki>Certificate Distribution \| Photo \| Break (15mins)</nowiki>''
	\|-		\|-
	\|4:00pm		\|4:00pm

Jeetvora at 03:13, 31 July 2025

2025-07-31T03:13:28Z

← Older revision		Revision as of 03:13, 31 July 2025
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	\|'''All (30 min)'''		\|'''All (30 min)'''
	\|-		\|-
	\|12:30pm		\|'''12:30pm'''
	\| colspan="3" \| '''LUNCH (90 mins)'''		\| colspan="3" \| '''LUNCH (90 mins)'''
	\|-		\|-
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	\| colspan="2" \|'''<nowiki>Open Q and A \| Closing Remarks</nowiki>'''		\| colspan="2" \|'''<nowiki>Open Q and A \| Closing Remarks</nowiki>'''
	\|'''<nowiki>All (20 min) \| Raja Mazumder</nowiki>'''		\|'''<nowiki>All (20 min) \| Raja Mazumder</nowiki>'''
			\|-
			\|''3:45pm''
			\| colspan="3" \|''Break (15mins)''
			\|-
			\|4:00pm
			\| colspan="2" \|'''Guest Lecture: Crafting a Strong LinkedIn Profile and Resume'''
			\|'''Sara Orrick (Senior Career Consultant (45 Mins)'''
	\|}		\|}

Jeetvora at 14:48, 29 July 2025

2025-07-29T14:48:15Z

← Older revision		Revision as of 14:48, 29 July 2025
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	\|3:10pm		\|3:10pm
	\|GlycoSiteMiner		\|GlycoSiteMiner
	\|~~TBA~~		\|Categorization of glycan names
	\|(15 min)		\|Filmawit Zeru (15 min)
	\|-		\|-
	\|'''3:25pm'''		\|'''3:25pm'''
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	=== Glycobiology Web Development ===		=== Glycobiology Web Development ===
	This project involves creating an EDAM ontology of glycobiology and glycoinformatics resources for the Glyspace alliance web development. It includes a resource compilation and organization of everything related to Glyspace to create a more user friendly tool to access these resources. This process involves compiling a list of resources that are associated with the Glyspace alliance and sorting them by type, topics, tool operation, and data.		This project involves creating an EDAM ontology of glycobiology and glycoinformatics resources for the Glyspace alliance web development. It includes a resource compilation and organization of everything related to Glyspace to create a more user friendly tool to access these resources. This process involves compiling a list of resources that are associated with the Glyspace alliance and sorting them by type, topics, tool operation, and data.

			=== '''GlycositeMiner Project''' ===
			Establishing a set of rules to broadly classify glycan names into structure-based and function-based categories, and applying these rules to organize entries in the glycan dictionary. These classification rules will evolve over time, enabling the creation of more refined hierarchical categories. The ultimate goal of this rule-based glycan name categorization is to support automated literature mining, specifically for identifying glycan names in PubMed articles.

Jeetvora at 12:52, 23 July 2025

2025-07-23T12:52:15Z

← Older revision		Revision as of 12:52, 23 July 2025
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	\|10:10am		\|10:10am
	\|CFDE		\|CFDE
	\|Integrating Biocuration and Data Standardization to Generate Machine Learning-Ready Glycan Datasets		\|Integrating Biocuration and Data Standardization to Generate Machine Learning-Ready Glycan Datasets + 5 min Q/A
	\|Ana Jaramillo and Yuxin Zou (20 min)		\|Ana Jaramillo and Yuxin Zou (20 min)
	\|-		\|-
	\|10:30am		\|10:30am
	\|CFDE		\|CFDE
	\|Machine Learning Models for Linkage Prediction in Glycan Images		\|Machine Learning Models for Linkage Prediction in Glycan Images + 5 min Q/A
	\|Campbell Ross (15 min)		\|Campbell Ross (15 min)
	\|-		\|-
	\|10:45am		\|10:45am
	\|CFDE		\|CFDE
	\|A Graph-Based AI Workflow for Mining Glycan Biomarkers and Related Annotations from Publications		\|A Graph-Based AI Workflow for Mining Glycan Biomarkers and Related Annotations from Publications + 5 min Q/A
	\|Cyrus Chun Hong Au Yeung (15 min)		\|Cyrus Chun Hong Au Yeung (15 min)
	\|-		\|-
	\|11:00am		\|11:00am
	\|BiomarkerKB		\|BiomarkerKB
	\|Comprehensive Identification and LLM Based Curation of the Top 50 Clinically Relevant Disease Biomarkers		\|Comprehensive Identification and LLM Based Curation of the Top 50 Clinically Relevant Disease Biomarkers + 5 min Q/A
	\|Sohana Bahl, Isaac Kim, Sparsh Gupta (15 min)		\|Sohana Bahl, Isaac Kim, Sparsh Gupta (15 min)
	\|-		\|-
	\|11:15am		\|11:15am
	\|BiomarkerKB		\|BiomarkerKB
	\|TBA		\|TBA + 5 min Q/A
	\|Nathan Ressom, Ana Vohralikova, Mathias Belay (15 min)		\|Nathan Ressom, Ana Vohralikova, Mathias Belay (15 min)
	\|-		\|-
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	\|-		\|-
	\| colspan="4" \| ''Group 2 Moderator : Rene Ranzinger''		\| colspan="4" \| ''Group 2 Moderator : Rene Ranzinger''
			\|-
			\|1:55pm
			\| colspan="2" \|'''Introduction'''
			\|Raja Mazumder
	\|-		\|-
	\|2:00pm		\|2:00pm
	\|GlyGen		\|GlyGen
	\|GlyGen Biocuration Project		\|GlyGen Biocuration Project + 5 min Q/A
	\|Aise Arpinar, Haravinay P. Gujjulla, Nahom Abel (20 min)		\|Aise Arpinar, Haravinay P. Gujjulla, Nahom Abel (20 min)
	\|-		\|-
	\|2:20pm		\|2:20pm
	\|Predictmod Curation		\|Predictmod Curation
	\|PredictMod: PubMed Curation for Training an LLM for Recommendation		\|PredictMod: PubMed Curation for Training an LLM for Recommendation + 5 min Q/A
	\|Grace Chong, Aaron Ressom, Diya Kamalabharathy (15 min)		\|Grace Chong, Aaron Ressom, Diya Kamalabharathy (15 min)
	\|-		\|-
	\|2:35pm		\|2:35pm
	\|Glycobiology Web Development		\|Glycobiology Web Development
	\|A Resource Drill Down and Visualization for the Glyspace Alliance		\|A Resource Drill Down and Visualization for the Glyspace Alliance + 5 min Q/A
	\|Diya Kamalabharathy (5 min)		\|Diya Kamalabharathy (5 min)
	\|-		\|-
	\|2:40pm		\|2:40pm
	\|Predictmod AI-READI		\|Predictmod AI-READI
	\|Robust Classification of Glycemic Health States from Continuous Glucose		\|Robust Classification of Glycemic Health States from Continuous Glucose + 5 min Q/A
	\|Nikhil Arethiya (15 min)		\|Nikhil Arethiya (15 min)
	\|-		\|-
	\|2:55pm		\|2:55pm
	\|Argos		\|Argos
	\|Curation of Emerging Pathogen Genomes for FDA-ARGOS Database Expansion		\|Curation of Emerging Pathogen Genomes for FDA-ARGOS Database Expansion + 5 min Q/A
	\|Miao Wang (15 min)		\|Miao Wang (15 min)
	\|-		\|-

Lorikrammer at 17:45, 22 July 2025

2025-07-22T17:45:41Z

← Older revision		Revision as of 17:45, 22 July 2025
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	\|-		\|-
	\|2:20pm		\|2:20pm
			\|Predictmod Curation
			\|PredictMod: PubMed Curation for Training an LLM for Recommendation
			\|Grace Chong, Aaron Ressom, Diya Kamalabharathy (15 min)
			\|-
			\|2:35pm
	\|Glycobiology Web Development		\|Glycobiology Web Development
	\|A Resource Drill Down and Visualization for the Glyspace Alliance		\|A Resource Drill Down and Visualization for the Glyspace Alliance
	\|Diya Kamalabharathy (5 min)		\|Diya Kamalabharathy (5 min)
	\|-
	~~\|2:25pm~~
	~~\|Predictmod Curation~~
	~~\|PredictMod: PubMed Curation for Training an LLM for Recommendation~~
	~~\|Grace Chong, Aaron Ressom, Diya Kamalabharathy (15 min)~~
	\|-		\|-
	\|2:40pm		\|2:40pm

Lorikrammer: /* Project Description */

2025-07-21T15:40:01Z

Project Description

← Older revision		Revision as of 15:40, 21 July 2025
Line 113:		Line 113:

	=== BiomarkerKB Biocuration Project ===		=== BiomarkerKB Biocuration Project ===
	The Biomarker Biocuration project focuses on biomarker curation from abstracts and publications in the BiomarkerKB data model. A key challenge in curating biomarkers is the vast amount of data that is present over various publications. Manual curation requires reading, inferring, and understanding key elements of biomarker data and being able to map it to the defined biomarker data model. LLM methodologies will help immensely in being able to recognize biomarker and condition data and being able to map information found into the data model while also automatically mapping other contextual and standardized data to the model to allow data to be AI ~~andmachine leanring~~ ready.		The Biomarker Biocuration project focuses on biomarker curation from abstracts and publications in the BiomarkerKB data model. A key challenge in curating biomarkers is the vast amount of data that is present over various publications. Manual curation requires reading, inferring, and understanding key elements of biomarker data and being able to map it to the defined biomarker data model. LLM methodologies will help immensely in being able to recognize biomarker and condition data and being able to map information found into the data model while also automatically mapping other contextual and standardized data to the model to allow data to be AI and machine learning ready.

	=== ArgosDB Curation Project ===		=== ArgosDB Curation Project ===
	This project focuses on evaluating and curating high-quality genomes of emerging and clinically relevant pathogens, with an emphasis on fungal species. Using public genomic repositories and FDA-ARGOS inclusion criteria, I identify candidate organisms for database expansion to support diagnostic assay development and public health surveillance.		This project focuses on evaluating and curating high-quality genomes of emerging and clinically relevant pathogens, with an emphasis on fungal species. Using public genomic repositories and FDA-ARGOS inclusion criteria, I identify candidate organisms for database expansion to support diagnostic assay development and public health surveillance.

			=== PredictMod Curation Project ===
			Identifying relevant and useful publicly-available datasets for machine learning is currently a resource-intensive task. This curation project aims to develop a corpus for training an AI model to recommend PMIDs with publicly-available datasets useful for intervention outcome prediction models. The corpus will include an annotation spreadsheet + annotated PDFs for PubMed articles relevant to prostate, lung, breast, and liver cancer, and focus on indicators such as condition, intervention, and response.

			=== PredictMod AI-READI Project ===
			This project creates a data-driven pipeline that uses continuous glucose monitoring (CGM) data to distinguish truly healthy individuals from those with underlying glycemic dysregulation, even if they're mislabeled. Using the AI-READI dataset funded by the NIH Bridge2AI program, the pipeline combines unsupervised clustering, handcrafted feature engineering, and LSTM-based deep learning to identify metabolic health states and extract insights into glycemic variability, with potential real-time applications in personalized health monitoring.

			=== Glycobiology Web Development ===
			This project involves creating an EDAM ontology of glycobiology and glycoinformatics resources for the Glyspace alliance web development. It includes a resource compilation and organization of everything related to Glyspace to create a more user friendly tool to access these resources. This process involves compiling a list of resources that are associated with the Glyspace alliance and sorting them by type, topics, tool operation, and data.

Daniallmasood: /* Agenda */

2025-07-21T15:14:32Z

Agenda

← Older revision		Revision as of 15:14, 21 July 2025
Line 47:		Line 47:
	\|11:00am		\|11:00am
	\|BiomarkerKB		\|BiomarkerKB
	\|~~TBA~~		\|Comprehensive Identification and LLM Based Curation of the Top 50 Clinically Relevant Disease Biomarkers
	\|Sohana Bahl, Isaac Kim, Sparsh Gupta (15 min)		\|Sohana Bahl, Isaac Kim, Sparsh Gupta (15 min)
	\|-		\|-