An Empirical Investigation of Pre-Trained Deep Learning Model Reuse in the Scientific Process
Organizations: Computer Science Department, Loyola University Chicago, Chicago, IL, USA · Electrical and Computer Engineering Department, Purdue University, West Lafayette, IN, USA
Abstract
Deep learning has achieved recognition for its impact within natural sciences, yet the prohibitive financial and technical cost of training models from scratch inhibit adoption. Following software engineering community guidance, natural scientists are reusing pre-trained deep learning models (PTMs) to amortize these costs. While prior works recommend PTM reuse patterns, we present the first empirical study of PTM reuse patterns in the natural sciences, quantifying the utilization and impact of PTM reuse within the scientific process across 17,718 peer reviewed, open access papers. Our results show that "Biochemistry, Genetics and Molecular Biology" has outpaced other natural scientific fields in PTM reuse, "adaptation" reuse is the most prevalent PTM reuse pattern identified across all natural science fields, and the "testing" stage of the scientific process has been most impacted by PTM integration.
Figures & tables
| Reuse Pattern | Definition | Examples |
| Conceptual | Replicate or reengineer PTMs described in academic literature. | [ 19 , 20 , 21 ] |
| Adaptation | Modify existing PTMs to address different tasks. | [ 22 , 23 , 24 ] |
| Deployment | Engineer existing PTMs for use in different computational frameworks. | [ 25 , 26 , 27 ] |
| OpenAlex Topic Field | Examples | Prop. |
| Biochemistry, Genetics and Molecular Biology | [ 61 , 62 , 63 ] | 36.91% |
| Environmental Science | [ 64 , 65 , 66 ] | 19.31% |
| Neuroscience | [ 67 , 68 , 69 ] | 18.59% |
| Agricultural and Biological Sciences | [ 70 , 71 , 72 ] | 12.18% |
| Earth and Planetary Sciences | [ 73 , 74 , 75 ] | 4.09% |
| Immunology and Microbiology | [ 76 , 77 , 78 ] | 3.48% |
Appendix figures & tables1 asset
Supplementary material from the paper’s appendix.
Appendix
| Paper Title | OpenAlex Topic 1 | OpenAlex Topic 2 | OpenAlex Topic 3 | Filtered |
|---|---|---|---|---|
| Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning [ 21 ] | Biochemistry, Genetics and Molecular Biology | Biochemistry, Genetics and Molecular Biology | Biochemistry, Genetics and Molecular Biology | True |
| The genome of the migratory nematode, Radopholus similis , reveals signatures of close association to the sedentary cyst nematodes [ 27 ] | Agricultural and Biological Sciences | Agricultural and Biological Sciences | Agricultural and Biological Sciences | True |
| Generalizing biological surround suppression based on center surround similarity via deep neural network models [ 20 ] | Neuroscience | Neuroscience | Neuroscience | True |
| Integration of smart sensors and phytoremediation for real-time pollution monitoring and ecological restoration in agricultural waste management [ 66 ] | Environmental Science | Environmental Science | Environmental Science | True |
| A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection [ 98 ] | Chemistry | Chemistry | Biochemistry, Genetics and Molecular Biology | True |
| Progress and prospects for research on Martian topographic features and typical landform identification [ 99 ] | Physics and Astronomy | Physics and Astronomy | Physics and Astronomy | True |
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