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PROTS-RF: A Robust Model for Predicting Mutation-Induced Protein Stability Changes

The ability to improve protein thermostability via protein engineering is of great scientific interest and also has significant practical value. In this report we present PROTS-RF, a robust model based on the Random Forest algorithm capable of predicting thermostability changes induced by not only single-, but also double- or multiple-point mutations. The model is built using 41 features including evolutionary information, secondary structure, solvent accessibility and a set of fragment-based features. It achieves accuracies of 0.799,0.782, 0.787, and areas under receiver operating characteristic (ROC) curves of 0.873, 0.868 and 0.862 for single-, double- and multiple- point mutation datasets, respectively. Contrary to previous suggestions, our results clearly demonstrate that a robust predictive model trained for predicting single point mutation induced thermostability changes can be capable of predicting double and multiple point mutations. It also shows high levels of robustness in the tests using hypothetical reverse mutations. We demonstrate that testing datasets created based on physical principles can be highly useful for testing the robustness of predictive models

Fairness of ChatGPT

Understanding and addressing unfairness in LLMs are crucial for responsible AI deployment. However, there is a limited availability of quantitative analyses and in-depth studies regarding fairness evaluations in LLMs, especially when applying LLMs to high-stakes fields. This work aims to fill this gap by providing a systematic evaluation of the effectiveness and fairness of LLMs using ChatGPT as a study case. We focus on assessing ChatGPT's performance in high-takes fields including education, criminology, finance and healthcare. To make thorough evaluation, we consider both group fairness and individual fairness and we also observe the disparities in ChatGPT's outputs under a set of biased or unbiased prompts. This work contributes to a deeper understanding of LLMs' fairness performance, facilitates bias mitigation and fosters the development of responsible artificial intelligence systems

Synthesis, Crystal Structure, and Physical Properties of the Perovskite Iridates

Perovskite iridates have emerged as a new paradigm for studying the strongly correlated electron physics with strong spin-orbit coupling. The “113” alkaline-earth iridates AIrO3 (A = Ca, Sr, Ba) display a rich variety of crystallographic and electronic states and are now attracting growing research interest. This chapter aims to provide an overview for these “113” iridates, including the materials’ synthesis, crystal structure, major physical properties, and other interesting results such as the effects of pressure and chemical substitutions, as well as theoretical perspectives

A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants

<p>Abstract</p> <p>Background</p> <p>The ability to design thermostable proteins is theoretically important and practically useful. Robust and accurate algorithms, however, remain elusive. One critical problem is the lack of reliable methods to estimate the relative thermostability of possible mutants.</p> <p>Results</p> <p>We report a novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting the relative thermostability of protein mutants. The scoring function was developed based on an elaborate analysis of a set of features calculated or predicted from 540 pairs of hyperthermophilic and mesophilic protein ortholog sequences. It was constructed by a linear combination of ten important features identified by a feature ranking procedure based on the random forest classification algorithm. The weights of these features in the scoring function were fitted by a hill-climbing algorithm. This scoring function has shown an excellent ability to discriminate hyperthermophilic from mesophilic sequences. The prediction accuracies reached 98.9% and 97.3% in discriminating orthologous pairs in training and the holdout testing datasets, respectively. Moreover, the scoring function can distinguish non-homologous sequences with an accuracy of 88.4%. Additional blind tests using two datasets of experimentally investigated mutations demonstrated that the scoring function can be used to predict the relative thermostability of proteins and their mutants at very high accuracies (92.9% and 94.4%). We also developed an amino acid substitution preference matrix between mesophilic and hyperthermophilic proteins, which may be useful in designing more thermostable proteins.</p> <p>Conclusions</p> <p>We have presented a novel scoring function which can distinguish not only HP/MP ortholog pairs, but also non-homologous pairs at high accuracies. Most importantly, it can be used to accurately predict the relative stability of proteins and their mutants, as demonstrated in two blind tests. In addition, the residue substitution preference matrix assembled in this study may reflect the thermal adaptation induced substitution biases. A web server implementing the scoring function and the dataset used in this study are freely available at <url>http://www.abl.ku.edu/thermorank/</url>.</p