Learning node labels with multi-category Hopfield networks

In several real-world node label prediction problems on graphs, in fields ranging from computational biology to World Wide Web analysis, nodes can be partitioned into categories different from the classes to be predicted, on the basis of their characteristics or their common properties. Such partitions may provide further information about node classification that classical machine learning algorithms do not take into account. We introduce a novel family of parametric Hopfield networks (m-category Hopfield networks) and a novel algorithm (Hopfield multi-category \u2014 HoMCat ), designed to appropriately exploit the presence of property-based partitions of nodes into multiple categories. Moreover, the proposed model adopts a cost-sensitive learning strategy to prevent the remarkable decay in performance usually observed when instance labels are unbalanced, that is, when one class of labels is highly underrepresented than the other one. We validate the proposed model on both synthetic and real-world data, in the context of multi-species function prediction, where the classes to be predicted are the Gene Ontology terms and the categories the different species in the multi-species protein network. We carried out an intensive experimental validation, which on the one hand compares HoMCat with several state-of-the-art graph-based algorithms, and on the other hand reveals that exploiting meaningful prior partitions of input data can substantially improve classification performances

Rapid Viscoelastic Deformation Slows Marine Ice Sheet Instability at Pine Island Glacier

The ice sheets of the Amundsen Sea Embayment (ASE) are vulnerable to the marine ice sheet instability (MISI), which could cause irreversible collapse and raise sea levels by over a meter. The uncertain timing and scale of this collapse depend on the complex interaction between ice, ocean, and bedrock dynamics. The mantle beneath the ASE is likely less viscous (∼1018 Pa s) than the Earth’s average mantle (∼1021 Pa s). Here we show that an effective equilibrium between Pine Island Glacier’s retreat and the response of a weak viscoelastic mantle can reduce ice mass lost by almost 30% over 150 years. Other components of solid Earth response—purely elastic deformations and geoid perturbations—provide less stability than the viscoelastic response alone. Uncertainties in mantle rheology, topography, and basal melt affect how much stability we expect, if any. Our study indicates the importance of considering viscoelastic uplift during the rapid retreat associated with MISI.Plain Language SummaryPortions of the West Antarctic Ice Sheet are vulnerable to an instability that could lead to rapid ice sheet collapse, significantly raising sea levels, but the timing and rates of collapse are highly uncertain. In response to such a large‐scale loss of overlying ice, viscoelastically deforming mantle material uplifts the surface, alleviating some drivers of unstable ice sheet retreat. While previous studies have focused on the effects mantle deformation has on continental ice dynamics over centuries to millennia, recent seismic observations suggest that the mantle beneath West Antarctica is hot and weak, potentially affecting local glacial dynamics over timescales as short as decades. To measure the importance of viscoelastic uplift in stabilizing grounding line retreat, we coupled a high‐resolution ice flow model to a viscoelastically deforming mantle. We find that rapid viscoelastic uplift can reduce the total volume of ice lost over 150 years by 30%, or 18 mm of equivalent sea level rise, making it an essential process to consider when using models to project the future evolution of marine‐based ice retreat.Key PointsWe examine the feedback between ice sheet dynamics and solid Earth viscoelastic deformation on grounding line stabilityThe viscoelastic response of a low viscosity mantle stabilizes the marine ice sheet instability over decades to centuriesViscoelastic uplift on timescales similar to grounding line migration can be a leading term in the feedback ice sheets/solid EarthPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155486/1/grl60591-sup-0001-Text_SI-S01.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155486/2/grl60591.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155486/3/grl60591_am.pd

Seismicity within a propagating ice shelf rift: The relationship between icequake locations and ice shelf structure

Iceberg calving is a dominant mass loss mechanism for Antarctic ice shelves, second only to basal melting. An important process involved in calving is the initiation and propagation of through‐penetrating fractures called rifts; however, the mechanisms controlling rift propagation remain poorly understood. To investigate the mechanics of ice shelf rifting, we analyzed seismicity associated with a propagating rift tip on the Amery Ice Shelf, using data collected during the austral summers of 2004–2007. We apply a suite of passive seismological techniques including icequake locations, back projection, and moment tensor inversion. We confirm previous results that show ice shelf rifting is characterized by periods of relative quiescence punctuated by swarms of intense seismicity of 1 to 3 h. Even during periods of quiescence, we find significant deformation around the rift tip. Moment tensors, calculated for a subset of the largest icequakes ( M w  > −2.0) located near the rift tip, show steeply dipping fault planes, horizontal or shallowly plunging stress orientations, and often have a significant volumetric component. They also reveal that much of the observed seismicity is limited to the upper 50 m of the ice shelf. This suggests a complex system of deformation that involves the propagating rift, the region behind the rift tip, and a system of rift‐transverse crevasses. Small‐scale variations in the mechanical structure of the ice shelf, especially rift‐transverse crevasses and accreted marine ice, play an important role in modulating the rate and location of seismicity associated with the propagating ice shelf rifts. Key Points Rift‐related seismicity controlled by mechanical heterogeneity Back projection reveals that seismic deformation is continuous in region Spacing of rift‐transverse crevasses controls the timing of seismic swarmsPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106935/1/jgrf20203.pd

Tight Bounds for SVM Classification Error

We find very tight bounds on the accuracy of a Support Vector Machine classification error within the Algorithmic Inference framework. The framework is specially suitable for this kind of classifier since (i) we know the number of support vectors really employed, as an ancillary output of the learning procedure, and (ii) we can appreciate confidence intervals of misclassifying probability exactly in function of the cardinality of these vectors. As a result we obtain confidence intervals that are up to an order narrower than those supplied in the literature, having a slight different meaning due to the different approach they come from, but the same operational function. We numerically check the covering of these intervals

Influence of age, reproductive cycling status, and menstruation on the vaginal microbiome in baboons (Papio anubis)

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111197/1/ajp22378.pd

Preliminary Investigation of Cardiovascular–Renal Disorders in Dogs with Chronic Mitral Valve Disease

Background: Veterinary literature lacks data about cardiovascular\u2013renal disorders (CvRD) and cardiorenal-anemia syndrome (CRAS) in dogs. Hypothesis: A direct correlation exists between ACVIM class and IRIS stage; chronic kidney disease (CKD) complicates chronic mitral valve disease (CMVD) more often than does anemia in dogs. Animals: One hundred and fifty-eight client-owned dogs with CMVD. Methods: Signalment, physical examination findings, electrocardiography, thoracic radiographs, echocardiography, and blood analysis were retrospectively evaluated to assess the prevalence of CKD and anemia in dogs with CMVD and to investigate the relationships among ACVIM class, IRIS stage, and survival. Results: The prevalence of CKD and anemia in dogs with CMVD was significantly higher than in the general population of dogs. Dogs being treated for heart failure had a significantly higher prevalence of CKD than did dogs that had not received treatment. A statistically significant direct correlation was found between ACVIM class and IRIS stage. Severe heart disease, severe renal disease or both, furosemide administration, and advanced age at diagnosis of heart disease were associated with shorter survival time. Survival time of dogs affected by CvRD was statistically shorter than survival time of dogs affected by CMVD alone. Conclusion and Clinical Relevance: Chronic mitral valve disease is associated with increased prevalence of CKD and anemia in dogs. Treatment for medical management of heart failure may play a role in inducing CKD. Class of heart disease and IRIS stage were directly correlated. Cardiovascular\u2013renal disorders decrease survival time compared to the only presence of CMVD alone, whereas anemia does not play a central role in worsening heart function

Strategies to build a positive and inclusive Antarctic field work environment

Support from National Science Foundation (NSF: Grants 1738913, 1738896, 1738942, 1738992, 1738896, 1738934) and Natural Environment Research Council (NERC: Grants NE/S006788/1, NE/S006605/1, NE/S00677X/1). This research was supported in part by the NOAA cooperative agreement NA17OAR4320101. Logistics provided by NSF-U.S. Antarctic Program and NERC-British Antarctic Survey. ITGC Contribution No. ITGC-084.To increase inclusivity, diversity, equity and accessibility in Antarctic science, we must build more positive and inclusive Antarctic field work environments. The International Thwaites Glacier Collaboration (ITGC) has engaged in efforts to contribute to that goal through a variety of activities since 2018, including creating an open-access 'Field and Ship Best Practices' guide, engaging in pre-field season team dynamics meetings, and surveying post-field season reflections and experiences. We report specific actions taken by ITGC and their outcomes. We found that strong and supported early career researchers brought new and important perspectives regarding strategies for transforming culture. We discovered that engaged and involved senior leadership was also critical for expanding participation and securing funding to support efforts. Pre-field discussions involving all field team members were particularly helpful for setting expectations, improving sense of belonging, describing field work best practices, and co-creating a positive work culture.Publisher PDFPeer reviewe

Microbiological profiles of sputum and gastric juice aspirates in Cystic Fibrosis patients.

Gastro-Oesophageal Reflux (GOR) is a key problem in Cystic Fibrosis (CF), but the relationship between lung and gastric microbiomes is not well understood. We hypothesised that CF gastric and lung microbiomes are related. Gastric and sputum cultures were obtained from fifteen CF patients receiving percutaneous endoscopic gastrostomy feeding. Non-CF gastric juice data was obtained through endoscopy from 14 patients without lung disease. Bacterial and fungal isolates were identified by culture. Molecular bacterial profiling used next generation sequencing (NGS) of the 16S rRNA gene. Cultures grew bacteria and/or fungi in all CF gastric juice and sputa and in 9/14 non-CF gastric juices. Pseudomonas aeruginosa(Pa) was present in CF sputum in 11 patients, 4 had identical Pa strains in the stomach. NGS data from non-CF gastric juice samples were significantly more diverse compared to CF samples. NGS showed CF gastric juice had markedly lower abundance of normal gut bacteria; Bacteroides and Faecalibacterium, but increased Pseudomonas compared with non-CF. Multivariate partial least squares discriminant analysis demonstrated similar bacterial profiles of CF sputum and gastric juice samples, which were distinct from non-CF gastric juice. We provide novel evidence suggesting the existence of an aerodigestive microbiome in CF, which may have clinical relevance

Bacteria isolated from lung modulate asthma susceptibility in mice

Asthma is a chronic, non-curable, multifactorial disease with increasing incidence in industrial countries. This study evaluates the direct contribution of lung microbial components in allergic asthma in mice. Germ-Free and Specific-Pathogen-Free mice display similar susceptibilities to House Dust Mice-induced allergic asthma, indicating that the absence of bacteria confers no protection or increased risk to aeroallergens. In early life, allergic asthma changes the pattern of lung microbiota, and lung bacteria reciprocally modulate aeroallergen responsiveness. Primo-colonizing cultivable strains were screened for their immunoregulatory properties following their isolation from neonatal lungs. Intranasal inoculation of lung bacteria influenced the outcome of allergic asthma development: the strain CNCM I 4970 exacerbated some asthma features whereas the pro-Th1 strain CNCM I 4969 had protective effects. Thus, we confirm that appropriate bacterial lung stimuli during early life are critical for susceptibility to allergic asthma in young adults