A Machine Learning Approach for Mortality Prediction in COVID-19 Pneumonia: Development and Evaluation of the Piacenza Score.

BACKGROUND: Several models have been developed to predict mortality in patients with COVID-19 pneumonia, but only a few have demonstrated enough discriminatory capacity. Machine learning algorithms represent a novel approach for the data-driven prediction of clinical outcomes with advantages over statistical modeling. OBJECTIVE: We aimed to develop a machine learning-based score-the Piacenza score-for 30-day mortality prediction in patients with COVID-19 pneumonia. METHODS: The study comprised 852 patients with COVID-19 pneumonia, admitted to the Guglielmo da Saliceto Hospital in Italy from February to November 2020. Patients' medical history, demographics, and clinical data were collected using an electronic health record. The overall patient data set was randomly split into derivation and test cohorts. The score was obtained through the naïve Bayes classifier and externally validated on 86 patients admitted to Centro Cardiologico Monzino (Italy) in February 2020. Using a forward-search algorithm, 6 features were identified: age, mean corpuscular hemoglobin concentration, PaO2/FiO2 ratio, temperature, previous stroke, and gender. The Brier index was used to evaluate the ability of the machine learning model to stratify and predict the observed outcomes. A user-friendly website was designed and developed to enable fast and easy use of the tool by physicians. Regarding the customization properties of the Piacenza score, we added a tailored version of the algorithm to the website, which enables an optimized computation of the mortality risk score for a patient when some of the variables used by the Piacenza score are not available. In this case, the naïve Bayes classifier is retrained over the same derivation cohort but using a different set of patient characteristics. We also compared the Piacenza score with the 4C score and with a naïve Bayes algorithm with 14 features chosen a priori. RESULTS: The Piacenza score exhibited an area under the receiver operating characteristic curve (AUC) of 0.78 (95% CI 0.74-0.84, Brier score=0.19) in the internal validation cohort and 0.79 (95% CI 0.68-0.89, Brier score=0.16) in the external validation cohort, showing a comparable accuracy with respect to the 4C score and to the naïve Bayes model with a priori chosen features; this achieved an AUC of 0.78 (95% CI 0.73-0.83, Brier score=0.26) and 0.80 (95% CI 0.75-0.86, Brier score=0.17), respectively. CONCLUSIONS: Our findings demonstrated that a customizable machine learning-based score with a purely data-driven selection of features is feasible and effective for the prediction of mortality among patients with COVID-19 pneumonia.

Predicting multiple taste sensations with a multiobjective machine learning method.

Taste perception plays a pivotal role in guiding nutrient intake and aiding in the avoidance of potentially harmful substances through five basic tastes - sweet, bitter, umami, salty, and sour. Taste perception originates from molecular interactions in the oral cavity between taste receptors and chemical tastants. Hence, the recognition of taste receptors and the subsequent perception of taste heavily rely on the physicochemical properties of food ingredients. In recent years, several advances have been made towards the development of machine learning-based algorithms to classify chemical compounds' tastes using their molecular structures. Despite the great efforts, there remains significant room for improvement in developing multi-class models to predict the entire spectrum of basic tastes. Here, we present a multi-class predictor aimed at distinguishing bitter, sweet, and umami, from other taste sensations. The development of a multi-class taste predictor paves the way for a comprehensive understanding of the chemical attributes associated with each fundamental taste. It also opens the potential for integration into the evolving realm of multi-sensory perception, which encompasses visual, tactile, and olfactory sensations to holistically characterize flavour perception. This concept holds promise for introducing innovative methodologies in the rational design of foods, including pre-determining specific tastes and engineering complementary diets to augment traditional pharmacological treatments.

Informed classification of sweeteners/bitterants compounds via explainable machine learning.

Perception of taste is an emergent phenomenon arising from complex molecular interactions between chemical compounds and specific taste receptors. Among all the taste perceptions, the dichotomy of sweet and bitter tastes has been the subject of several machine learning studies for classification purposes. While previous studies have provided accurate sweeteners/bitterants classifiers, there is ample scope to enhance these models by enriching the understanding of the molecular basis of bitter-sweet tastes. Towards these goals, our study focuses on the development and testing of several machine learning strategies coupled with the novel SHapley Additive exPlanations (SHAP) for a rational sweetness/bitterness classification. This allows the identification of the chemical descriptors of interest by allowing a more informed approach toward the rational design and screening of sweeteners/bitterants. To support future research in this field, we make all datasets and machine learning models publicly available and present an easy-to-use code for bitter-sweet taste prediction.

Grasping learning, optimization, and knowledge transfer in the robotics field.

Service robotics is a fast-developing sector, requiring embedded intelligence into robotic platforms to interact with the humans and the surrounding environment. One of the main challenges in the field is robust and versatile manipulation in everyday life activities. An appealing opportunity is to exploit compliant end-effectors to address the manipulation of deformable objects. However, the intrinsic compliance of such grippers results in increased difficulties in grasping control. Within the described context, this work addresses the problem of optimizing the grasping of deformable objects making use of a compliant, under-actuated, sensorless robotic hand. The main aim of the paper is, therefore, finding the best position and joint configuration for the mentioned robotic hand to grasp an unforeseen deformable object based on collected RGB image and partial point cloud. Due to the complex grasping dynamics, learning-from-simulations approaches (e.g., Reinforcement Learning) are not effective in the faced context. Thus, trial-and-error-based methodologies have to be exploited. In order to save resources, a samples-efficient approach has to be employed. Indeed, a Bayesian approach to address the optimization of the grasping strategy is proposed, enhancing it with transfer learning capabilities to exploit the acquired knowledge to grasp (partially) new objects. A PAL Robotics TIAGo (a mobile manipulator with a 7-degrees-of-freedom arm and an anthropomorphic underactuated compliant hand) has been used as a test platform, executing a pouring task while manipulating plastic (i.e., deformable) bottles. The sampling efficiency of the data-driven learning is shown, compared to an evenly spaced grid sampling of the input space. In addition, the generalization capability of the optimized model is tested (exploiting transfer learning) on a set of plastic bottles and other liquid containers, achieving a success rate of the 88%.

Fragmented blind docking: a novel protein-ligand binding prediction protocol.

In the present paper we propose a novel blind docking protocol based on Autodock-Vina. The developed docking protocol can provide binding site identification and binding pose prediction at the same time, by a systematical exploration of the protein volume performed with several preliminary docking calculations. In our opinion, this protocol can be successfully applied during the first steps of the virtual screening pipeline, because it provides binding site identification and binding pose prediction at the same time without visual evaluation of the binding site. After the binding pose prediction, MM/GBSA re-scoring rescoring procedures has been applied to improve the accuracy of the protein-ligand bound state. The FRAD protocol has been tested on 116 protein-ligand complexes of the Heat Shock Protein 90 - alpha, on 176 of Human Immunodeficiency virus protease 1, and on more than 100 protein-ligand system taken from the PDBbind dataset. Overall, the FRAD approach combined to MM/GBSA re-scoring can be considered as a powerful tool to increase the accuracy and efficiency with respect to other standard docking approaches when the ligand-binding site is unknown.Communicated by Ramaswamy H. Sarma.

Toward a general and interpretable umami taste predictor using a multi-objective machine learning approach.

The umami taste is one of the five basic taste modalities normally linked to the protein content in food. The implementation of fast and cost-effective tools for the prediction of the umami taste of a molecule remains extremely interesting to understand the molecular basis of this taste and to effectively rationalise the production and consumption of specific foods and ingredients. However, the only examples of umami predictors available in the literature rely on the amino acid sequence of the analysed peptides, limiting the applicability of the models. In the present study, we developed a novel ML-based algorithm, named VirtuousUmami, able to predict the umami taste of a query compound starting from its SMILES representation, thus opening up the possibility of potentially using such a model on any database through a standard and more general molecular description. Herein, we have tested our model on five databases related to foods or natural compounds. The proposed tool will pave the way toward the rationalisation of the molecular features underlying the umami taste and toward the design of specific peptide-inspired compounds with specific taste properties.

A survey on computational taste predictors.

Taste is a sensory modality crucial for nutrition and survival, since it allows the discrimination between healthy foods and toxic substances thanks to five tastes, i.e., sweet, bitter, umami, salty, and sour, associated with distinct nutritional or physiological needs. Today, taste prediction plays a key role in several fields, e.g., medical, industrial, or pharmaceutical, but the complexity of the taste perception process, its multidisciplinary nature, and the high number of potentially relevant players and features at the basis of the taste sensation make taste prediction a very complex task. In this context, the emerging capabilities of machine learning have provided fruitful insights in this field of research, allowing to consider and integrate a very large number of variables and identifying hidden correlations underlying the perception of a particular taste. This review aims at summarizing the latest advances in taste prediction, analyzing available food-related databases and taste prediction tools developed in recent years. Supplementary Information: The online version contains supplementary material available at 10.1007/s00217-022-04044-5.