1. GOAL: The purpose of this activity and accompanying survey is to collect feedback about this system. The responses will be aggregated and used to inform the developers on improvements based on community needs. The data may be used in a publication reporting on this system.
2. TIMELINE AND COMMITMENT: The system review period is open from September 1 to September 30, 2021. During this period, you can explore this system at different times, with different examples. We estimate that completion of the minimal set of activities (reviewing the documentation, going over tutorial and own examples) would take 1-2 hours (but may vary with system and your own interest).
However, we do request that the survey is completed in one take (it may take approximately 30 min) after you have gone through the tutorial and your own examples.
Survey deadline: September 30.
3. WHAT IS THIS SYSTEM?
AGATHA, which stands for Automatic Graph-mining And Transformer-based
Hypothesis Generation Approach. The system was designed for finding implicit, undiscovered connections between a
variety of biomedical concepts. The system is query based, namely, it accepts a query that consists of two concepts
whose possible relation is currently unknown. AGATHA is designed as a general-purpose knowledge discovery system
with customizability in mind. Due to the current situation and community interest, we presented a model called
AGATHA-C, which is customized specifically for COVID-19-related hypothesis generation queries.
AGATHA system includes 2 main components: 1) The quantified hypothesis generation pipeline that is a complex
knowledge discovery mechanism which includes all steps from data preprocessing and fusion to deep learning predictor
model; and 2) Visualizer. The Visualizer part is where the interactivity takes place and which runs in a web-browser to
explain the findings discovered and quantified by AGATHA. This proposal is primarily focused on the interactive visualizer
part because this module is intended to be used directly by domain specialists. However, the visualizer is an intrinsic part
of the AGATHA project and it cannot be viewed or used separately.
4. ACTIVITY: Follow the instructions in the document below.
5. CONTACT US: If you have any questions or comments, please contact biocreativechallenge@gmail.com. Add in subject TRACK4 system review
