Capacity of Continuous Channels with Memory via Directed Information Neural Estimator

Calculating the capacity (with or without feedback) of channels with memory and continuous alphabets is a challenging task. It requires optimizing the directed information (DI) rate over all channel input distributions. The objective is a multi-letter expression, whose analytic solution is only known for a few specific cases. When no analytic solution is present or the channel model is unknown, there is no unified framework for calculating or even approximating capacity. This work proposes a novel capacity estimation algorithm that treats the channel as a `black-box', both when feedback is or is not present. The algorithm has two main ingredients: (i) a neural distribution transformer (NDT) model that shapes a noise variable into the channel input distribution, which we are able to sample, and (ii) the DI neural estimator (DINE) that estimates the communication rate of the current NDT model. These models are trained by an alternating maximization procedure to both estimate the channel capacity and obtain an NDT for the optimal input distribution. The method is demonstrated on the moving average additive Gaussian noise channel, where it is shown that both the capacity and feedback capacity are estimated without knowledge of the channel transition kernel. The proposed estimation framework opens the door to a myriad of capacity approximation results for continuous alphabet channels that were inaccessible until now

Max-Sliced Mutual Information

Quantifying the dependence between high-dimensional random variables is central to statistical learning and inference. Two classical methods are canonical correlation analysis (CCA), which identifies maximally correlated projected versions of the original variables, and Shannon's mutual information, which is a universal dependence measure that also captures high-order dependencies. However, CCA only accounts for linear dependence, which may be insufficient for certain applications, while mutual information is often infeasible to compute/estimate in high dimensions. This work proposes a middle ground in the form of a scalable information-theoretic generalization of CCA, termed max-sliced mutual information (mSMI). mSMI equals the maximal mutual information between low-dimensional projections of the high-dimensional variables, which reduces back to CCA in the Gaussian case. It enjoys the best of both worlds: capturing intricate dependencies in the data while being amenable to fast computation and scalable estimation from samples. We show that mSMI retains favorable structural properties of Shannon's mutual information, like variational forms and identification of independence. We then study statistical estimation of mSMI, propose an efficiently computable neural estimator, and couple it with formal non-asymptotic error bounds. We present experiments that demonstrate the utility of mSMI for several tasks, encompassing independence testing, multi-view representation learning, algorithmic fairness, and generative modeling. We observe that mSMI consistently outperforms competing methods with little-to-no computational overhead.Comment: Accepted at NeurIPS 202

Extended-spectrum β-lactamase-producing enterobacteriaceae shedding in farm horses versus hospitalized horses: Prevalence and risk factors

We aimed to investigate the prevalence, molecular characteristics and risk factors of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E) shedding in horses. A prospective study included three cohorts: (i) farm horses (13 farms, n = 192); (ii) on hospital admission (n = 168) and; (iii) horses hospitalized for ≥72 h re-sampled from cohort (ii) (n = 86). Enriched rectal swabs were plated, ESBL-production was confirmed (Clinical and Laboratory Standards Institute (CLSI)) and genes were identified (polymerase chain reaction (PCR)). Identification and antibiotic susceptibility were determined (Vitek-2). Medical records and owners’ questionnaires were analyzed. Shedding rates increased from 19.6% (n = 33/168) on admission to 77.9% (n = 67/86) during hospitalization (p < 0.0001, odds ratio (OR) = 12.12). Shedding rate in farms was 20.8% (n = 40/192), significantly lower compared to hospitalized horses (p < 0.0001). The main ESBL-E species (n = 192 isolates) were E. coli (59.9%, 115/192), Enterobacter sp. (17.7%, 34/192) and Klebsiella pneumoniae (13.0%, 25/192). The main gene group was CTX-M-1 (56.8%). A significant increase in resistance rates to chloramphenicol, enrofloxacin, gentamicin, nitrofurantoin, and trimethoprim-sulpha was identified during hospitalization. Risk factors for shedding in farms included breed (Arabian, OR = 3.9), sex (stallion, OR = 3.4), and antibiotic treatment (OR = 9.8). Older age was identified as a protective factor (OR = 0.88). We demonstrated an ESBL-E reservoir in equine cohorts, with a significant ESBL-E acquisition, which increases the necessity to implement active surveillance and antibiotic stewardship programs

FABIA: factor analysis for bicluster acquisition

Motivation: Biclustering of transcriptomic data groups genes and samples simultaneously. It is emerging as a standard tool for extracting knowledge from gene expression measurements. We propose a novel generative approach for biclustering called ‘FABIA: Factor Analysis for Bicluster Acquisition’. FABIA is based on a multiplicative model, which accounts for linear dependencies between gene expression and conditions, and also captures heavy-tailed distributions as observed in real-world transcriptomic data. The generative framework allows to utilize well-founded model selection methods and to apply Bayesian techniques

Enhanced production yields of rVSV-SARS-CoV-2 vaccine using Fibra-Cel® macrocarriers

The COVID-19 pandemic has led to high global demand for vaccines to safeguard public health. To that end, our institute has developed a recombinant viral vector vaccine utilizing a modified vesicular stomatitis virus (VSV) construct, wherein the G protein of VSV is replaced with the spike protein of SARS-CoV-2 (rVSV-ΔG-spike). Previous studies have demonstrated the production of a VSV-based vaccine in Vero cells adsorbed on Cytodex 1 microcarriers or in suspension. However, the titers were limited by both the carrier surface area and shear forces. Here, we describe the development of a bioprocess for rVSV-ΔG-spike production in serum-free Vero cells using porous Fibra-Cel® macrocarriers in fixed-bed BioBLU®320 5p bioreactors, leading to high-end titers. We identified core factors that significantly improved virus production, such as the kinetics of virus production, the use of macrospargers for oxygen supply, and medium replenishment. Implementing these parameters, among others, in a series of GMP production processes improved the titer yields by at least two orders of magnitude (2e9 PFU/mL) over previously reported values. The developed process was highly effective, repeatable, and robust, creating potent and genetically stable vaccine viruses and introducing new opportunities for application in other viral vaccine platforms

Higher Levels of Postnatal Depressive Symptomatology, Post-Traumatic Growth, and Life Satisfaction among Gay Fathers through Surrogacy in Comparison to Heterosexual Fathers: A Study in Israel in Times of COVID-19

This study aimed to explore the psychological welfare, as indicated by postnatal depressive symptomatology, life satisfaction, and posttraumatic growth (growth after contending with stressful birth events), of Israeli gay fathers through surrogacy in comparison to heterosexual fathers. For that purpose, a sample of 167 Israeli fathers (M = 35.6, SD = 4.4) was recruited (68 identified as gay fathers through surrogacy and 99 as heterosexual fathers). Participants completed questionnaires assessing their postnatal depressive symptomatology, life satisfaction, and sense of posttraumatic growth after becoming fathers. Results indicated that gay fathers through surrogacy reported higher levels of life satisfaction and posttraumatic growth than heterosexual fathers. Yet, gay fathers also reported higher levels of postnatal depressive symptomatology than heterosexual fathers when life satisfaction or posttraumatic growth values were low or medium. The findings were interpreted in light of the hardships associated with cross-border surrogacy and the psychological outcomes associated with succeeding to become fathers after contending with them. The study contributes to the limited literature on postnatal depressive symptomatology and posttraumatic growth among gay fathers through surrogacy and provides clinicians and policymakers with relevant information on the psychological strengths and potential difficulties associated with cross-border surrogacy among gay fathers

Viral serine palmitoyltransferase induces metabolic switch in sphingolipid biosynthesis and is required for infection of a marine alga

Marine viruses are the most abundant biological entities in the oceans shaping community structure and nutrient cycling. The interaction between the bloom-forming alga Emiliania huxleyi and its specific large dsDNA virus (EhV) is a major factor determining the fate of carbon in the ocean, thus serving as a key host-pathogen model system. The EhV genome encodes for a set of genes involved in the de novo sphingolipid biosynthesis, not reported in any viral genome to date. We combined detailed lipidomic and biochemical analyses to characterize the functional role of this virus-encoded pathway during lytic viral infection. We identified a major metabolic shift, mediated by differential substrate specificity of virus-encoded serine palmitoyltransferase, a key enzyme of sphingolipid biosynthesis. Consequently, unique viral glycosphingolipids, composed of unusual hydroxylated C17 sphingoid bases (t17:0) were highly enriched in the infected cells, and their synthesis was found to be essential for viral assembly. These findings uncover the biochemical bases of the virus-induced metabolic rewiring of the host sphingolipid biosynthesis during the chemical "arms race" in the ocean