Publications (10)
Cascade Neural Ensemble for Identifying Scientifically Sound Articles
Ashwin Karthik Ambalavanan, Murthy Devarakonda
Background: A significant barrier to conducting systematic reviews and meta-analysis is efficiently finding scientifically sound relevant articles. Typically, less than 1% of artic…
Training Models to Extract Treatment Plans from Clinical Notes Using Contents of Sections with Headings
Ananya Poddar, Bharath Dandala, Murthy Devarakonda
Objective: Using natural language processing (NLP) to find sentences that state treatment plans in a clinical note, would automate plan extraction and would further enable their us…
Customizing Knowledge Graph Embedding to Improve Clinical Study Recommendation
Xiong Liu, Iya Khalil, Murthy Devarakonda
Inferring knowledge from clinical trials using knowledge graph embedding is an emerging area. However, customizing graph embeddings for different use cases remains a significant ch…
sc-OTGM: Single-Cell Perturbation Modeling by Solving Optimal Mass Transport on the Manifold of Gaussian Mixtures
Andac Demir, Elizaveta Solovyeva, James Boylan +6
Influenced by breakthroughs in LLMs, single-cell foundation models are emerging. While these models show successful performance in cell type clustering, phenotype classification, a…
COVID-19: Comparative Analysis of Methods for Identifying Articles Related to Therapeutics and Vaccines without Using Labeled Data
Mihir Parmar, Ashwin Karthik Ambalavanan, Hong Guan +3
Here we proposed an approach to analyze text classification methods based on the presence or absence of task-specific terms (and their synonyms) in the text. We applied this approa…
Knowledge Guided Named Entity Recognition for BioMedical Text
Pratyay Banerjee, Kuntal Kumar Pal, Murthy Devarakonda +1
In this work, we formulate the NER task as a multi-answer knowledge guided QA task (KGQA) which helps to predict entities only by assigning B, I and O tags without associating enti…
Robustly Pre-trained Neural Model for Direct Temporal Relation Extraction
Hong Guan, Jianfu Li, Hua Xu +1
Background: Identifying relationships between clinical events and temporal expressions is a key challenge in meaningfully analyzing clinical text for use in advanced AI application…
A Scalable AI Approach for Clinical Trial Cohort Optimization
Xiong Liu, Cheng Shi, Uday Deore +4
FDA has been promoting enrollment practices that could enhance the diversity of clinical trial populations, through broadening eligibility criteria. However, how to broaden eligibi…
Clinical Trial Information Extraction with BERT
Xiong Liu, Greg L. Hersch, Iya Khalil +1
Natural language processing (NLP) of clinical trial documents can be useful in new trial design. Here we identify entity types relevant to clinical trial design and propose a frame…
Developing and Using Special-Purpose Lexicons for Cohort Selection from Clinical Notes
Samarth Rawal, Ashok Prakash, Soumya Adhya +4
Background and Significance: Selecting cohorts for a clinical trial typically requires costly and time-consuming manual chart reviews resulting in poor participation. To help autom…