Click here to read some interesting recently published papers from our community. If you have published an article in the field of in silico medicine, send it to us: we will include it in this section of the newsletter!
Annals of Biomedical Engineering: "Machine Learning for Cardiovascular Biomechanics Modeling: Challenges and Beyond"
Amirhossein Arzani et al
Recent progress in machine learning (ML), together with advanced computational power, have provided new research opportunities in cardiovascular modeling. While classifying patient outcomes and medical image segmentation with ML have already shown significant promising results, ML for the prediction of biomechanics such as blood flow or tissue dynamics is in its infancy. This perspective article discusses some of the challenges in using ML for replacing well-established physics-based models in cardiovascular biomechanics. Specifically, we discuss the large landscape of input features in 3D patient-specific modeling as well as the high-dimensional output space of field variables that vary in space and time. We argue that the end purpose of such ML models needs to be clearly defined and the tradeoff between the loss in accuracy and the gained speedup carefully interpreted in the context of translational modeling. We also discuss several exciting venues where ML could be strategically used to augment traditional physics-based modeling in cardiovascular biomechanics. In these applications, ML is not replacing physics-based modeling, but providing opportunities to solve ill-defined problems, improve measurement data quality, enable a solution to computationally expensive problems, and interpret complex spatiotemporal data by extracting hidden patterns. In summary, we suggest a strategic integration of ML in cardiovascular biomechanics modeling where the ML model is not the end goal but rather a tool to facilitate enhanced modeling.
Scientific Reports: "Convolutional mesh autoencoders for the 3-dimensional identification of FGFR-related craniosynostosis"
Eimear O’ Sullivan et al
Clinical diagnosis of craniofacial anomalies requires expert knowledge. Recent studies have shown that artificial intelligence (AI) based facial analysis can match the diagnostic capabilities of expert clinicians in syndrome identification. In general, these systems use 2D images and analyse texture and colour. They are powerful tools for photographic analysis but are not suitable for use with medical imaging modalities such as ultrasound, MRI or CT, and are unable to take shape information into consideration when making a diagnostic prediction. 3D morphable models (3DMMs), and their recently proposed successors, mesh autoencoders, analyse surface topography rather than texture enabling analysis from photography and all common medical imaging modalities and present an alternative to image-based analysis. We present a craniofacial analysis framework for syndrome identification using Convolutional Mesh Autoencoders (CMAs). The models were trained using 3D photographs of the general population (LSFM and LYHM), computed tomography data (CT) scans from healthy infants and patients with 3 genetically distinct craniofacial syndromes (Muenke, Crouzon, Apert). Machine diagnosis outperformed expert clinical diagnosis with an accuracy of 99.98%, sensitivity of 99.95% and specificity of 100%. The diagnostic precision of this technique supports its potential inclusion in clinical decision support systems. Its reliance on 3D topography characterisation make it suitable for AI assisted diagnosis in medical imaging as well as photographic analysis in the clinical setting.
Nature Communications: "Modeling the disruption of respiratory disease clinical trials by non-pharmaceutical COVID-19 interventions."
Simone Arsène at al
Respiratory disease trials are profoundly affected by non-pharmaceutical interventions (NPIs) against COVID-19 because they perturb existing regular patterns of all seasonal viral epidemics. To address trial design with such uncertainty, we developed an epidemiological model of respiratory tract infection (RTI) coupled to a mechanistic description of viral RTI episodes. We explored the impact of reduced viral transmission (mimicking NPIs) using a virtual population and in silico trials for the bacterial lysate OM-85 as prophylaxis for RTI. Ratio-based efficacy metrics are only impacted under strict lockdown whereas absolute benefit already is with intermediate NPIs (eg. mask-wearing). Consequently, despite NPI, trials may meet their relative efficacy endpoints (provided recruitment hurdles can be overcome) but are difficult to assess with respect to clinical relevance. These results advocate to report a variety of metrics for benefit assessment, to use adaptive trial design and adapted statistical analyses. They also question eligibility criteria misaligned with the actual disease burden.
Frontiers in Physiology: "Simplifying the Process of Going From Cells to Tissues Using Statistical Mechanics."
Jagir R. Hussan et al
The value of digital twins for prototyping controllers or interventions in a sandbox environment are well-established in engineering and physics. However, this is challenging for biophysics trying to seamlessly compose models of multiple spatial and temporal scale behavior into the digital twin. Two challenges stand out as constraining progress: (i) ensuring physical consistency of conservation laws across composite models and (ii) drawing useful and timely clinical and scientific information from conceptually and computationally complex models. Challenge (i) can be robustly addressed with bondgraphs. However, challenge (ii) is exacerbated using this approach. The complexity question can be looked at from multiple angles. First from the perspective of discretizations that reflect underlying biophysics (functional tissue units) and secondly by exploring maximum entropy as the principle guiding multicellular biophysics. Statistical mechanics, long applied to understanding emergent phenomena from atomic physics, coupled with the observation that cellular architecture in tissue is orchestrated by biophysical constraints on metabolism and communication, shows conceptual promise. This architecture along with cell specific properties can be used to define tissue specific network motifs associated with energetic contributions. Complexity can be addressed based on energy considerations and finding mean measures of dependent variables. A probability distribution of the tissue's network motif can be approximated with exponential random graph models. A prototype problem shows how these approaches could be implemented in practice and the type of information that could be extracted.