Revisiting Robustness in Graph Machine Learning

Many works show that node-level predictions of Graph Neural Networks (GNNs) are unrobust to small, often termed adversarial, changes to the graph structure. However, because manual inspection of a graph is difficult, it is unclear if the studied perturbations always preserve a core assumption of adversarial examples: that of unchanged semantic content. To address this problem, we introduce a more principled notion of an adversarial graph, which is aware of semantic content change. Using Contextual Stochastic Block Models (CSBMs) and real-world graphs, our results uncover: $i)$ for a majority of nodes the prevalent perturbation models include a large fraction of perturbed graphs violating the unchanged semantics assumption; $ii)$ surprisingly, all assessed GNNs show over-robustness - that is robustness beyond the point of semantic change. We find this to be a complementary phenomenon to adversarial examples and show that including the label-structure of the training graph into the inference process of GNNs significantly reduces over-robustness, while having a positive effect on test accuracy and adversarial robustness. Theoretically, leveraging our new semantics-aware notion of robustness, we prove that there is no robustness-accuracy tradeoff for inductively classifying a newly added node.Comment: Published as a conference paper at ICLR 2023. Preliminary version accepted as an oral at the NeurIPS 2022 TSRML workshop and at the NeurIPS 2022 ML safety worksho

Estimates of Electronic Medical Records in U.S. Emergency Departments

Background: Policymakers advocate universal electronic medical records (EMRs) and propose incentives for “meaningful use” of EMRs. Though emergency departments (EDs) are particularly sensitive to the benefits and unintended consequences of EMR adoption, surveillance has been limited. We analyze data from a nationally representative sample of US EDs to ascertain the adoption of various EMR functionalities. Methodology/Principal: Findings We analyzed data from the National Hospital Ambulatory Medical Care Survey, after pooling data from 2005 and 2006, reporting proportions with 95% confidence intervals (95% CI). In addition to reporting adoption of various EMR functionalities, we used logistic regression to ascertain patient and hospital characteristics predicting “meaningful use,” defined as a “basic” system (managing demographic information, computerized provider order entry, and lab and imaging results). We found that 46% (95% CI 39–53%) of US EDs reported having adopted EMRs. Computerized provider order entry was present in 21% (95% CI 16–27%), and only 15% (95% CI 10–20%) had warnings for drug interactions or contraindications. The “basic” definition of “meaningful use” was met by 17% (95% CI 13–21%) of EDs. Rural EDs were substantially less likely to have a “basic” EMR system than urban EDs (odds ratio 0.19, 95% CI 0.06–0.57, p = 0.003), and Midwestern (odds ratio 0.37, 95% CI 0.16–0.84, p = 0.018) and Southern (odds ratio 0.47, 95% CI 0.26–0.84, p = 0.011) EDs were substantially less likely than Northeastern EDs to have a “basic” system. Conclusions/Significance: EMRs are becoming more prevalent in US EDs, though only a minority use EMRs in a “meaningful” way, no matter how “meaningful” is defined. Rural EDs are less likely to have an EMR than metropolitan EDs, and Midwestern and Southern EDs are less likely to have an EMR than Northeastern EDs. We discuss the nuances of how to define “meaningful use,” and the importance of considering not only adoption, but also full implementation and consequences

Estimates of Electronic Medical Records in U.S. Emergency Departments

BACKGROUND: Policymakers advocate universal electronic medical records (EMRs) and propose incentives for "meaningful use" of EMRs. Though emergency departments (EDs) are particularly sensitive to the benefits and unintended consequences of EMR adoption, surveillance has been limited. We analyze data from a nationally representative sample of US EDs to ascertain the adoption of various EMR functionalities. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed data from the National Hospital Ambulatory Medical Care Survey, after pooling data from 2005 and 2006, reporting proportions with 95% confidence intervals (95% CI). In addition to reporting adoption of various EMR functionalities, we used logistic regression to ascertain patient and hospital characteristics predicting "meaningful use," defined as a "basic" system (managing demographic information, computerized provider order entry, and lab and imaging results). We found that 46% (95% CI 39-53%) of US EDs reported having adopted EMRs. Computerized provider order entry was present in 21% (95% CI 16-27%), and only 15% (95% CI 10-20%) had warnings for drug interactions or contraindications. The "basic" definition of "meaningful use" was met by 17% (95% CI 13-21%) of EDs. Rural EDs were substantially less likely to have a "basic" EMR system than urban EDs (odds ratio 0.19, 95% CI 0.06-0.57, p = 0.003), and Midwestern (odds ratio 0.37, 95% CI 0.16-0.84, p = 0.018) and Southern (odds ratio 0.47, 95% CI 0.26-0.84, p = 0.011) EDs were substantially less likely than Northeastern EDs to have a "basic" system. CONCLUSIONS/SIGNIFICANCE: EMRs are becoming more prevalent in US EDs, though only a minority use EMRs in a "meaningful" way, no matter how "meaningful" is defined. Rural EDs are less likely to have an EMR than metropolitan EDs, and Midwestern and Southern EDs are less likely to have an EMR than Northeastern EDs. We discuss the nuances of how to define "meaningful use," and the importance of considering not only adoption, but also full implementation and consequences

Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource.

BACKGROUND: Physcomitrella patens, a haploid dominant plant, is fast becoming a useful molecular genetics and bioinformatics tool due to its key phylogenetic position as a bryophyte in the post-genomic era. Genome sequences from select reference species were compared bioinformatically to Physcomitrella patens using reciprocal blasts with the InParanoid software package. A reference protein interaction database assembled using MySQL by compiling BioGrid, BIND, DIP, and Intact databases was queried for moss orthologs existing for both interacting partners. This method has been used to successfully predict interactions for a number of angiosperm plants. RESULTS: The first predicted protein-protein interactome for a bryophyte based on the interolog method contains 67,740 unique interactions from 5,695 different Physcomitrella patens proteins. Most conserved interactions among proteins were those associated with metabolic processes. Over-represented Gene Ontology categories are reported here. CONCLUSION: Addition of moss, a plant representative 200 million years diverged from angiosperms to interactomic research greatly expands the possibility of conducting comparative analyses giving tremendous insight into network evolution of land plants. This work helps demonstrate the utility of guilt-by-association models for predicting protein interactions, providing provisional roadmaps that can be explored using experimental approaches. Included with this dataset is a method for characterizing subnetworks and investigating specific processes, such as the Calvin-Benson-Bassham cycle

Gene therapy targeting SARM1 blocks pathological axon degeneration in mice

Axonal degeneration (AxD) following nerve injury, chemotherapy, and in several neurological disorders is an active process driven by SARM1, an injury-activated NADase. Axons of SARM1-null mice exhibit greatly delayed AxD after transection and in models of neurological disease, suggesting that inhibiting SARM1 is a promising strategy to reduce pathological AxD. Unfortunately, no drugs exist to target SARM1. We, therefore, developed SARM1 dominant-negatives that potently block AxD in cellular models of axotomy and neuropathy. To assess efficacy in vivo, we used adeno-associated virus-mediated expression of the most potent SARM1 dominant-negative and nerve transection as a model of severe AxD. While axons of vehicle-treated mice degenerate rapidly, axons of mice expressing SARM1 dominant-negative can remain intact for \u3e10 d after transection, similar to the protection observed in SARM1-null mice. We thus developed a novel in vivo gene therapeutic to block pathological axon degeneration by inhibiting SARM1, an approach that may be applied clinically to treat manifold neurodegenerative diseases characterized by axon loss

Transformers Meet Directed Graphs

Transformers were originally proposed as a sequence-to-sequence model for text but have become vital for a wide range of modalities, including images, audio, video, and undirected graphs. However, transformers for directed graphs are a surprisingly underexplored topic, despite their applicability to ubiquitous domains, including source code and logic circuits. In this work, we propose two direction- and structure-aware positional encodings for directed graphs: (1) the eigenvectors of the Magnetic Laplacian - a direction-aware generalization of the combinatorial Laplacian; (2) directional random walk encodings. Empirically, we show that the extra directionality information is useful in various downstream tasks, including correctness testing of sorting networks and source code understanding. Together with a data-flow-centric graph construction, our model outperforms the prior state of the art on the Open Graph Benchmark Code2 relatively by 14.7%.Comment: 29 page

Measuring Quality: The Impact of Minimally Invasive Surgery and Operative Time on Surgical Site Infections

Objective: To evaluate the relationship between operative approach, operative time, and SSI rate.Methods: Inpatient database review identified patients undergoing 5 common procedures from 1/2010-12/2011. Patients were stratified into laparoscopic or open approaches. The main outcome measure was the relationship between operative time and SSI by approach.Results: 226,006 patients were evaluated- 28.2% open and 71.8% laparoscopic. Mean overall operative time was significantly shorter laparoscopically (p<0.001). Laparoscopy was associated with significantly lower costs and shorter length of stay (LOS) overall and for each procedure(p<0.0001). Multivariate analysis found SSI increased directly with operative time: for every 30-minute increase, SSI risk increased by 12%. Operative approach was an independent risk factor for SSI: open surgery increased SSI risk by 78%. A direct relationship between open procedures, operative time, and SSI risk was found.Conclusions: Laparoscopy has overall shorter operative time and improved outcomes in SSI rate, LOS, and total costs for common surgical procedures. As operative time and approach were independent risk factors for SSI, the use of laparoscopy and operative time are valuable quality measures

Population Gradients in Local Group Dwarf Spheroidals

We present a systematic and homogeneous analysis of population gradients for the Local Group dwarf spheroidals (dSphs) Carina, Sculptor, Sextans, Tucana, Andromeda I-III, V, and VI. For all of the Milky Way companions studied here we find significant population gradients. The same is true for the remote dSph Tucana located at the outskirts of the LG. Among the M 31 dSph companions only Andromeda I and VI show obvious gradients. In all cases where a HB morphology gradient is visible, the red HB stars are more centrally concentrated. The occurence of a HB morphological gradient shows a correlation with a morphology gradient in the red giant branch. It seems likely that metallicity is the driver of the gradients in Sextans, Sculptor, Tucana, and Andromeda VI, while age is an important factor in Carina. We find no evidence that the vicinity of a nearby massive spiral galaxy influences the formation of the population gradients.Comment: accepted for publication in AJ; 25 pages; 11 images in jpeg and png forma

Familienangehörige spielerisch zusammenführen – Systemkonzept

Immer mehr ältere Menschen leben von ihren Angehörigen getrennt und können über Kommunikationsmedien wie Telefon und Skype nur eingeschränkt gemeinsame Erlebnisse erzeugen. In diesem Paper wird die technische Umsetzung eines Konzeptes vorgestellt, das es Familienmitgliedern ermöglicht über das Internet gemeinsam „Mensch-ärgere-dich-nicht“ zu spielen. Durch Videotelefonie und eine besondere Anordnung der Hardware werden die Spieler trotz räumlicher Trennung virtuell an einen Tisch gebracht und dadurch ein gemeinsames Erlebnis erzeugt. Die Clientanwendung wird dabei als plattformunabhängiger Webservice und die Videotelefonie mittels verschiedener Standards und Server realisiert