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The computer vision task of reconstructing 3D images, i.e., shapes, from their single 2D image slices is extremely challenging, more so in the regime of limited data. Deep learning models typically optimize geometric loss functions, which may lead to poor reconstructions as they ignore the structural properties of the shape. To tackle this, we propose a novel topological loss function based on the Euler Characteristic Transform. This loss can be used as an inductive bias to aid the optimization of any neural network toward better reconstructions in the regime of limited data. We show the effectiveness of the proposed loss function by incorporating it into SHAPR, a state-of-the-art shape reconstruction model, and test it on two benchmark datasets, viz., Red Blood Cells and Nuclei datasets. We also show a favourable property, namely injectivity and discuss the stability of the topological loss function based on the Euler Characteristic Transform., Comment: e-print

Model analogies and exchange of ideas between physics or chemistry with biology or epidemiology have often involved inter-sectoral mapping of techniques. Material mechanics has benefitted hugely from such interpolations from mathematical physics where dislocation patterning of platstically deformed metals [1,2,3] and mass transport in nanocomposite materials with high diffusivity paths such as dislocation and grain boundaries, have been traditionally analyzed using the paradigmatic Walgraef-Aifantis (W-A) double-diffusivity (D-D) model [4,5,6,7,8,9]. A long standing challenge in these studies has been the inherent nonlinear correlation between the diffusivity paths, making it extremely difficult to analyze their interdependence. Here, we present a novel method of approximating a closed form solution of the ensemble averaged density profiles and correlation statistics of coupled dynamical systems, drawing from a technique used in mathematical biology to calculate a quantity called the {\it basic reproduction number} $R_0$, which is the average number of secondary infections generated from every infected. We show that the $R_0$ formulation can be used to calculate the correlation between diffusivity paths, agreeing closely with the exact numerical solution of the D-D model. The method can be generically implemented to analyze other reaction-diffusion models., Comment: 5 two-pannelled figures, 13 pages

Clinicians make routine diagnosis by scrutinizing patients' medical signs and symptoms, a skill popularly referred to as "Clinical Eye". This skill evolves through trial-and-error and improves with time. The success of the therapeutic regime relies largely on the accuracy of interpretation of such sign-symptoms, analyzing which a clinician assesses the severity of the illness. The present study is an attempt to propose a complementary medical front by mathematically modeling the "Clinical Eye" of a VIRtual DOCtor, using Statistical and Machine Intelligence tools (SMI), to analyze Dengue epidemic infected patients (100 case studies with 11 weighted sign-symptoms). The SMI in VIRDOCD reads medical data and translates these into a vector comprising Multiple Linear Regression (MLR) coefficients to predict infection severity grades of dengue patients that clone the clinician's experience-based assessment. Risk managed through ANOVA, the dengue severity grade prediction accuracy from VIRDOCD is found higher (ca 75%) than conventional clinical practice (ca 71.4%, mean accuracy profile assessed by a team of 10 senior consultants). Free of human errors and capable of deciphering even minute differences from almost identical symptoms (to the Clinical Eye), VIRDOCD is uniquely individualized in its decision-making ability. The algorithm has been validated against Random Forest classification (RF, ca 63%), another regression-based classifier similar to MLR that can be trained through supervised learning. We find that MLR-based VIRDOCD is superior to RF in predicting the grade of Dengue morbidity. VIRDOCD can be further extended to analyze other epidemic infections, such as COVID-19., Comment: 17 pages, 5 figures, 8 tables

Covid-19 is raging a devastating trail with the highest mortality-to-infected ratio ever for a pandemic. Lack of vaccine and therapeutic has rendered social exclusion through lockdown as the singular mode of containment. Harnessing the predictive powers of Machine Learning within a 6 dimensional infection kinetic model, depicting interactive evolution of 6 infection stages - healthy susceptible ($H$), predisposed comorbid susceptible ($P$), infected ($I$), recovered ($R$), herd immunized ($V$) and mortality ($D$) - the model, PHIRVD, provides the first accurate mortality prediction of 18 countries at varying stages of strategic lockdown, up to 30 days beyond last data training. PHIRVD establishes mortality-to-infection ratio as the correct pandemic descriptor, substituting reproduction number, and highlights the importance of early and prolonged but strategic lockdown to contain secondary relapse. Significance Statement: 1. Accurate prediction of the day-by-day mortality profiles of 18 countries, 30 days beyond the last data of data training. 2. Precise quantification of the impact of early-vs-later lockdown impositions. 3. Accurate prediction of secondary relapse timelines/ 4. Establishment of mortality-to-infected ratio as the correct pandemic descriptor substituting the popular choice of reproduction number, a proven failure in predicting future infection kinetics and secondary surge. The outcomes have potential to redefine healthy policy landscape, particularly in light of secondary relapse and possible future SARS-COV/Ebola group incursion., Comment: 13 pages main text (8figures, 2 tables), 20 pages of appendices (21 figures, 5 tables)

Linguistic analysis of protein sequences is an underexploited technique. Here, we capitalize on the concept of the lipogram to characterize sequences at the proteome levels. A lipogram is a literary composition which omits one or more letters. A protein lipogram likewise omits one or more types of amino acid. In this article, we establish a usable terminology for the decomposition of a sequence collection in terms of the lipogram. Next, we characterize Uniref50 using a lipogram decomposition. At the global level, protein lipograms exhibit power-law properties. A clear correlation with metabolic cost is seen. Finally, we use the lipogram construction to differentiate proteomes between the four branches of the tree-of-life: archaea, bacteria, eukaryotes and viruses. We conclude from this pilot study that the lipogram demonstrates considerable potential as an additional tool for sequence analysis and proteome classification., Comment: 8 pages, 2 columns, 5 figures

Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative success of modern-day sequence alignment algorithms, so-called alignment-free approaches offer a complementary means of determining and expressing similarity, with potential benefits in certain key applications, such as regression analysis of protein structure-function studies, where alignment-base similarity has performed poorly. Here, we offer a fresh, statistical physics-based perspective focusing on the question of alignment-free comparison, in the process adapting results from 'first passage probability distribution' to summarize statistics of ensemble averaged amino acid propensity values. In this article, we introduce and elaborate this approach., Comment: 6 pages, 3 figures; published in Bioinformatics Journal, vol 31(15), pages 2469-2474; doi: 10.1093/bioinformatics/btv167

Recent epidemiological evidences indicate that arsenic exposure increases risk of atherosclerosis, cardiovascular diseases and microangiopathies in addition to the serious global health concern related to its carcinogenic effects. In experiments on animals, acute and chronic exposure to arsenic directly correlates cardiac tachyarrhythmia, and atherogenesis in a concentration and duration dependent manner. Moreover, the other effects of long-term arsenic exposure include induction of non-insulin dependent diabetes by mechanisms yet to be understood. On the other hand, there are controversial issues, gaps in knowledge, and future research priorities of accelerated incidences of CVD and mortalities in patients with HIV who are under long-term anti-retroviral therapy (ART). Although, both HIV infection itself and various components of ART initiate significant pathological alterations in the myocardium and the vasculature, simultaneous environmental exposure to arsenic which is more convincingly being recognized as a facilitator of HIV viral cycling in the infected immune cells, may contribute an additional layer of adversity in these patients. In this mini-review which have been fortified with our own preliminary data, we will discuss some of the key current understating of chronic arsenic exposure, and its possible impact on the accelerated HIV/ART induced CVD. The review will conclude with notes on recent developments in mathematical modeling in this field that probabilistically forecast incidence prevalence as functions of aging and life style parameters, most of which vary with time themselves; this interdisciplinary approach provides a complementary kernel to conventional biology., Comment: 15 pages, 4 figures; accepted in Bengal Heart Journal