Jacopo Lenkowicz

pMineR: An Innovative R Library for Performing Process Mining in Medicine

Process Mining is an emerging discipline investigating tasks related with the automated identification of process models, given real-world data (Process Discovery). The analysis of such models can provide useful insights to domain experts. In addition, models of processes can be used to test if a given process complies (Conformance Checking) with specifications. For these capabilities, Process Mining is gaining importance and attention in healthcare.

Assessing the conformity to clinical guidelines in oncology: An example for the multidisciplinary management of locally advanced colorectal cancer treatment

Purpose The purpose of this paper is to describe a methodology to deal with conformance checking through the implementation of computer-interpretable-clinical guidelines (CIGs), and present an application of the methodology to real-world data and a clinical pathway for radiotherapy-related oncological treatment. Design/methodology/approach This methodology is implemented by a software able to use the hospital electronic health record data to assess the adherence of the actual executed clinical processes to a clinical pathway, monitoring at the same time management-related efficiency and performance parameters, and ideally, suggesting ways to improve them. Findings Three use cases are presented, in which the results of conformance checking are used to compare different branches of the executed guidelines with respect to the adherence to ideal process, temporal distribution of state-to-state transitions, and overall treatment efficacy, in order to extract data-driven evidence that could be of interest for the hospital management. Originality/value This approach has the result of applying management-oriented data mining technique on sequential data, typical of process mining, to the result of a conformity check between the preliminary knowledge defined by clinicians and the real-world data, typical of CIGs.

Preliminary Data Analysis in Healthcare Multicentric Data Mining: a Privacy-preserving Distributed Approach

The new era of cognitive health care systems offers a large amount of patient data that can be used to develop prediction models and clinical decision support systems. In this frame, the multi-institutional approach is strongly encouraged in order to reach more numerous samples for data mining and more reliable statistics. For these purposes, shared ontologies need to be developed for data management to ensure database semantic coherence in accordance with the various centers’ ethical and legal policies. Therefore, we propose a privacy-preserving distributed approach as a preliminary data analysis tool to identify possible compliance issues and heterogeneity from the agreed multi-institutional research protocol before training a clinical prediction model. This kind of preliminary analysis appeared fast and reliable and its results corresponded to those obtained using the traditional centralized approach. A real time interactive dashboard has also been presented to show analysis results and make the workflow swifter and easier.

Generating and Comparing Knowledge Graphs of Medical Processes Using pMineR

Process mining focuses on extracting knowledge, under the form of models, from data generated and stored in information systems. The analysis of generated models can provide useful insights to domain experts. In addition, models of processes can be used to test if a considered process complies with some given specifications. For these reasons, process mining is gaining significant importance in the healthcare domain, where the complexity and flexibility of processes makes extremely hard to evaluate and assess how patients have been treated. In this paper we describe how pMineR, an R library designed and developed for performing process mining in the medical domain, is currently exploited in Hospitals for supporting domain experts in the analysis of the extracted knowledge models. In its current release, pMineR can encode extracted processes under the form of directed graphs, which are easy to interpret and understand by experts of the domain. It also provides graphical comparison between different processes, allows to model the adherence to a given clinical guidelines and to estimate performance and the workload of the available resources in healthcare.

ENT COBRA ONTOLOGY: the covariates classification system proposed by the Head & Neck and Skin GEC-ESTRO Working Group for interdisciplinary standardized data collection in head and neck patient cohorts treated with interventional radiotherapy (brachytherapy)

Purpose Clinical data collecting is expensive in terms of time and human resources. Data can be collected in different ways; therefore, performing multicentric research based on previously stored data is often difficult. The primary objective of the ENT COBRA (COnsortium for BRachytherapy data Analysis) ontology is to define a specific terminological system to standardized data collection for head and neck (H&N) cancer patients treated with interventional radiotherapy. Material and methods ENT-COBRA is a consortium for standardized data collection for H&N patients treated with interventional radiotherapy. It is linked to H&N and Skin GEC-ESTRO Working Group and includes 11 centers from 6 countries. Its ontology was firstly defined by a multicentric working group, then evaluated by the consortium followed by a multi-professional technical commission involving a mathematician, an engineer, a physician with experience in data storage, a programmer, and a software expert. Results Two hundred and forty variables were defined on 13 input forms. There are 3 levels, each offering a specific type of analysis: 1. Registry level (epidemiology analysis); 2. Procedures level (standard oncology analysis); 3. Research level (radiomics analysis). The ontology was approved by the consortium and technical commission; an ad-hoc software architecture (“broker”) remaps the data present in already existing storage systems of the various centers according to the shared terminology system. The first data sharing was successfully performed using COBRA software and the ENT COBRA Ontology, automatically collecting data directly from 3 different hospital databases (Lübeck, Navarra, and Rome) in November 2017. Conclusions The COBRA Ontology is a good response to the multi-dimensional criticalities of data collection, retrieval, and usability. It allows to create a software for large multicentric databases with implementation of specific remapping functions wherever necessary. This approach is well-received by all involved parties, primarily because it does not change a single center’s storing technologies, procedures, and habits.

Phase I and II trial on infusional 5-fluorouracil and gefitinib in combination with preoperative radiotherapy in rectal cancer: 10-years median follow-up

Highlights • We report the long-term results of addiction of gefitinib to preoperative chemoradiotherapy in locally advanced rectal cancer.• We wanted to see if the hight rate of pCR, already shown in previous studies, influenced survival outcomes.• The first promising results have not been confirmed by a significant improvement in outcomes.

Towards a modular decision support system for radiomics: A case study on rectal cancer

Following the personalized medicine paradigm, there is a growing interest in medical agents capable of predicting the effect of therapies on patients, by exploiting the amount of data that is now available for each patient. In disciplines like oncology, where images and scans are available, the exploitation of medical images can provide an additional source of potentially useful information. The study and analysis of features extracted by medical images, exploited for predictive purposes, is termed radiomics. A number of tools are available for supporting some of the steps of the radiomics process, but there is a lack of approaches which are able to deal with all the steps of the process. In this paper, we introduce a medical agent-based decision support system capable of handling the whole radiomics process. The proposed system is tested on two independent data sets of patients treated for rectal cancer. Experimental results indicate that the system is able to generate highly performant centre-specific predictive model, and show the issues related to differences in data sets collected by different centres, and how such issues can affect the performance of the generated predictive models.