This Jupyter Notebook (edome_2d_plot.ipynb) reads an input file (edo.in) with parameters employed to calculate Walsh metrics (Walsh et al., 2021). It evaluates the predictive performance of features and scoring functions against a defined target variable (e.g., pKi) (de Azevedo et al., 2024). The input file (edo.in) should be in the content directory during a Colab session. It is also necessary to upload a CSV file with columns for all features and the target variable. This code outputs a CSV file for statistical analysis and a plot for all features defined in the input file (edo.in). EDOME relies on Scikit-Learn to calculate most of the metrics used to evaluate predictive performance (Pedregosa et al., 2011).
Schematic flowchart for EDOME. It reads binding affinity data from a CSV file with features and scoring functions and calculates metrics and generates a 2D plot. EDOME reads edo.in to define plot parameters. It determines the predictive performance of scoring functions using metrics defined elsewhere (Walsh et 2021; de Azevedo et al., 2024).
References
de Azevedo WF Jr, Quiroga R, Villarreal MA, da Silveira NJF, Bitencourt-Ferreira G, da Silva AD, Veit-Acosta M, Oliveira PR, Tutone M, Biziukova N, Poroikov V, Tarasova O, Baud S. SAnDReS 2.0: Development of machine-learning models to explore the scoring function space. J Comput Chem. 2024;45(27):2333-2346. DOI
Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, Verplas J, Passos A, Cournapeau D, Brucher M, Perrot M, Duchesnay E. Scikitlearn: Machine Learning in Python. J Mach Learn Res., 2011; 12:2825–2830. DOI
Walsh I, Fishman D, Garcia-Gasulla D, Titma T, Pollastri G; ELIXIR Machine Learning Focus Group; Harrow J, Psomopoulos FE, Tosatto SCE. DOME: recommendations for supervised machine learning validation in biology. Nat Methods. 2021; 18(10): 1122-1127. DOI
My scientific interests are interdisciplinary, with three main emphases: computational structural biology, artificial intelligence, and complex systems. In my studies, I developed several free software programs to explore the concept of Scoring Function Space.
As a result of my research, I published over 200 scientific works about protein structures, computer models of complex systems, and simulations of protein systems. These publications have generated over 12,000 citations on Google Scholar (h-index of 63) and more than 10,000 citations and an h-index of 58 in Scopus.
Due to the impact of my work, I have been ranked among the most influential researchers in the world (Fields: Biophysics, Biochemistry & Molecular Biology, and Biomedical Research) according to a database created by Journal Plos Biology (see news here). The application of the same set of metrics recognized the influence of my work from 2021 to 2025 (Baas et al., 2021; Ioannidis, 2022; Ioannidis, 2023; Ioannidis, 2024; Ioannidis, 2025). Not bad for a poor guy who was a shoe seller at a store in São Paulo and had the opportunity to study at the University of São Paulo with a scholarship for food and housing. I was 23 when I initiated my undergraduate studies and was the first in my family to have access to higher education.
Regarding scientific impact (Peterson, 2005), Hirsch said that for a physicist, an h-index of 45 or higher could mean membership in the National Academy of Sciences of the USA. So far, there have been no invitations. No hard feelings because I am in good company. Carl Sagan was never allowed into the National Academy of Sciences. According to an analysis of citations performed on Nov. 9, 2024 (The Conversation), his work accumulates more than 1,000 citations per year on Google Scholar. Indeed, his current citation rate exceeds that of many members of the National Academy of Sciences.
I will continue working in science with low-budget and interdisciplinary projects, combating denialism with science and technology. The fight against denialism is a continuing work, and scientists should not forget their role in a complex society where social media has given the right to speak to legions of imbeciles.
“Social media gives the right to speak to legions of imbeciles who previously only spoke at the bar after a glass of wine, without damaging the community. They were immediately silenced, but now they have the same right to speak as a Nobel Prize winner. It’s the invasion of imbeciles.”
Umberto Eco. Source: Quote Investigator
"Let the light of science end the darkness of denialism." My quote (DOI:10.2174/092986732838211207154549).