Cluster Analysis of Categorical Variables of Parkinson’s Disease Patients

Parkinson’s disease (PD) is a chronic disease. No treatment stops its progression, and it presents symptoms in multiple areas. One way to understand the PD population is to investigate the clustering of patients by demographic and clinical similarities. Previous PD cluster studies included scores from clinical surveys, which provide a numerical but ordinal, non-linear value. In addition, these studies did not include categorical variables, as the clustering method utilized was not applicable to categorical variables. It was discovered that the numerical values of patient age and disease duration were similar among past cluster results, pointing to the need to exclude these values. This paper proposes a novel and automatic discovery method to cluster PD patients by incorporating categorical variables. No estimate of the number of clusters is required as input, whereas the previous cluster methods require a guess from the end user in order for the method to be initiated. Using a patient dataset from the Parkinson’s Progression Markers Initiative (PPMI) website to demonstrate the new clustering technique, our results showed that this method provided an accurate separation of the patients. In addition, this method provides an explainable process and an easy way to interpret clusters and describe patient subtypes.

Evolutionary computational platform for the automatic discovery of nanocarriers for cancer treatment

We present the EVONANO platform for the evolution of nanomedicines with application to anti-cancer treatments. Our work aims to decrease both the time and cost required to develop nanoparticle designs. EVONANO includes a simulator to grow tumours, extract representative scenarios, and simulate nanoparticle transport through these scenarios in order to predict nanoparticle distribution. The nanoparticle designs are optimised using machine learning to efficiently find the most effective anti-cancer treatments. We demonstrate EVONANO with two examples optimising the properties of nanoparticles and treatment to selectively kill cancer cells over a range of tumour environments. Our platform shows how in silico models that capture both tumour and tissue-scale dynamics can be combined with machine learning to optimise nanomedicine.

EVOLUTIONARY GAUSSIAN PROCESSES

Emulation plays an important role in engineering design. However, most emulators such as Gaussian processes (GPs) are exclusively developed for interpolation/regression and their performance significantly deteriorates in extrapolation. To address this shortcoming, we introduce evolutionary Gaussian processes (EGPs) that aim to increase the extrapolation capabilities of GPs. An EGP differs from a GP in that its training involves automatic discovery of some free-form symbolic bases that explain the data reasonably well. In our approach, this automatic discovery is achieved via evolutionary programming (EP) which is integrated with GP modeling via maximum likelihood estimation, bootstrap sampling, and singular value decomposition. As we demonstrate via examples that include a host of analytical functions as well as an engineering problem on materials modeling, EGP can improve the performance of ordinary GPs in terms of not only extrapolation, but also interpolation/regression and numerical stability.

Automatic discovery of photoisomerization mechanisms with nanosecond machine learning photodynamics simulations

Photochemical reactions are widely used by academia and industry to construct complex molecular architectures via mechanisms that are often inaccessible by other means.