CF-GNNExplainer: Counterfactual Explanations for Graph Neural Networks

Given the increasing promise of graph neural networks (GNNs) in real-world applications, several methods have been developed for explaining their predictions. Existing methods for interpreting predictions from GNNs have primarily focused on generating subgraphs that are especially relevant for a particular prediction. However, such methods are not counterfactual (CF) in nature: given a prediction, we want to understand how the prediction can be changed in order to achieve an alternative outcome. In this work, we propose a method for generating CF explanations for GNNs: the minimal perturbation to the input (graph) data such that the prediction changes. Using only edge deletions, we find that our method, CF-GNNExplainer, can generate CF explanations for the majority of instances across three widely used datasets for GNN explanations, while removing less than 3 edges on average, with at least 94\% accuracy. This indicates that CF-GNNExplainer primarily removes edges that are crucial for the original predictions, resulting in minimal CF explanations.Comment: Accepted to AISTATS 202

Length and clinical effectiveness of pulmonary rehabilitation in outpatients with chronic airway obstruction

Study objective: To assess the clinical effectiveness of pulmonary rehabilitation (PR) after 10 or 20 consecutive sessions in outpatients with chronic airway obstruction (CAO). Design: Observational prospective cohort trial. Setting: Outpatient clinic of a rehabilitation center. Patients and interventions: Twenty-five outpatients (mean age, 65 +/- 9 years [+/- SD]; FEV1, 64 +/- 12% predicted) admitted to a comprehensive PR program, including exercise training. Measurements and results: The load reached on a cycloergometer (maximal achieved load [W-max]), the maximal and isoload dyspnea and leg fatigue on a Borg scale, 6-min walk distance (6MWD), and the health-related quality of life as assessed using the St. George's Respiratory Questionnaire (SGRQ) [total and components score] have been recorded as outcome measures at baseline, after 10 sessions (T10), and after 20 sessions (T20). The predefined criteria of the clinically significant improvement were as follows: + 15% W-max, + 54 m at 6MWD, - 1 point at isoload dyspnea and leg fatigue, and - 4% at SGRQ scores. There was a mean significant difference between changes at T20 and T10 for 6MWD (- 42.96 m; 95% confidence interval [0], - 57.79 to - 28.12 m; p = 0.001), total SGRQ (4.80; 95% CI, 2.29 to 7.31; p = 0.001), activity SGRQ (3.60; 95% CI, 0.48 to 6.71; p = 0.025), and symptoms SGRQ (5.96; 95% CI, 2.72 to 9.2; p = 0.001). The percentage of patients who improved was different at T20 as compared with T 10 for W-max (68% and 48%, respectively; p = 0.025), 6MWD (76% and 20%, p = 0.001), and total SGRQ (64% and 36%, p = 0.008). Conclusions: A 10-session course of PR provides only limited clinically significant changes of outcome measures when compared with a 20-session course in outpatients with CAO of mild-to-moderate severity

Giant magnetic enhancement in Fe/Pd films and its influence on the magnetic interlayer coupling

The magnetic properties of thin Pd fcc(001) films with embedded monolayers of Fe are investigated by means of first principles density functional theory. The induced spin polarization in Pd is calculated and analyzed in terms of quantum interference within the Fe/Pd/Fe bilayer system. An investigation of the magnetic enhancement effects on the spin polarization is carried out and its consequences for the magnetic interlayer coupling are discussed. In contrast to {\it e.g.} the Co/Cu fcc(001) system we find a large effect on the magnetic interlayer coupling due to magnetic enhancement in the spacer material. In the case of a single embedded Fe monolayer we find aninduced Pd magnetization decaying with distance $n$ from the magnetic layer as ~$n^{-\alpha}$ with $\alpha \approx 2.4$. For the bilayer system we find a giant magnetic enhancement (GME) that oscillates strongly due to interference effects. This results in a strongly modified magnetic interlayer coupling, both in phase and magnitude, which may not be described in the pure Ruderman-Kittel-Kasuya-Yoshida (RKKY) picture. No anti-ferromagnetic coupling was found and by comparison with magnetically constrained calculations we show that the overall ferromagnetic coupling can be understood from the strong polarization of the Pd spacer

New insights into the magmatic-hydrothermal system and volatile budget of Lastarria volcano, Chile: Integrated results from the 2014 IAVCEI CCVG 12th Volcanic Gas Workshop.

Recent geophysical evidence for large-scale regional crustal inflation and localized crustal magma intrusion has made Lastarria volcano (northern Chile) the target of numerous geological, geophysical, and geochemical studies. The chemical composition of volcanic gases sampled during discrete campaigns from Lastarria volcano indicated a well-developed hydrothermal system from direct fumarole samples in A.D. 2006, 2008, and 2009, and shallow magma degassing using measurements from in situ plume sampling techniques in 2012. It is unclear if the differences in measured gas compositions and resulting interpretations were due to artifacts of the different sampling methods employed, short-term excursions from baseline due to localized changes in stress, or a systematic change in Lastarria's magmatic-hydrothermal system between 2009 and 2012. Integrated results from a two-day volcanic gas sampling and measurement campaign during the 2014 International Association of Volcanology and Chemistry of the Earth's Interior (IAVCEI) Commission on the Chemistry of Volcanic Gases (CCVG) 12th Gas Workshop are used here to compare and evaluate current gas sampling and measurement techniques, refine the existing subsurface models for Lastarria volcano, and provide new constraints on its magmatic-hydrothermal system and total degassing budget. While compositional differences among sampling methods are present, distinct compositional changes are observed, which if representative of longterm trends, indicate a change in Lastarria's overall magmatic-hydrothermal system. The composition of volcanic gases measured in 2014 contained high proportions of relatively magma- and water-soluble gases consistent with degassing of shallow magma, and in agreement with the 2012 gas composition. When compared with gas compositions measured in 2006-2009, higher relative H2O/CO2 ratios combined with lower relative CO2/St and H2O/St and stable HCl/St ratios (where St is total S [SO2 + H2S]) are observed in 2012 and 2014. These compositional changes suggest variations in the magmatic-hydrothermal system between 2009 and 2012, with possible scenarios to explain these trends including: (1) decompression-induced degassing due to magma ascent within the shallow crust; (2) crystallization-induced degassing of a stalled magma body; (3) depletion of the hydrothermal system due to heating, changes in local stress, and/or minimal precipitation; and/or (4) acidification of the hydrothermal system. These scenarios are evaluated and compared against the geophysical observations of continuous shallow inflation at ~8 km depth between 1997 and 2016, and near-surface ( < 1 km) inflation between 2000 and 2008, to further refine the existing subsurface models. Higher relative H2O/CO2 observed in 2012 and 2014 is not consistent with the depletion or acidification of a hydrothermal system, while all other observations are consistent with the four proposed models. Based on these observations, we find that scenarios 1 or 2 are the most likely to explain the geochemical and geophysical observations, and propose that targeted shallow interferometric synthetic-aperture radar (InSAR) studies could help discriminate between these two scenarios. Lastly, we use an average SO2 flux of 604 \ub1 296 t/d measured on 22 November 2014, along with the average gas composition and diffuse soil CO2 flux measurements, to estimate a total volatile flux from Lastarria volcano in 2014 of ~12,400 t/d, which is similar to previous estimates from 2012

3-D Ultrastructure of O. tauri: Electron Cryotomography of an Entire Eukaryotic Cell

The hallmark of eukaryotic cells is their segregation of key biological functions into discrete, membrane-bound organelles. Creating accurate models of their ultrastructural complexity has been difficult in part because of the limited resolution of light microscopy and the artifact-prone nature of conventional electron microscopy. Here we explored the potential of the emerging technology electron cryotomography to produce three-dimensional images of an entire eukaryotic cell in a near-native state. Ostreococcus tauri was chosen as the specimen because as a unicellular picoplankton with just one copy of each organelle, it is the smallest known eukaryote and was therefore likely to yield the highest resolution images. Whole cells were imaged at various stages of the cell cycle, yielding 3-D reconstructions of complete chloroplasts, mitochondria, endoplasmic reticula, Golgi bodies, peroxisomes, microtubules, and putative ribosome distributions in-situ. Surprisingly, the nucleus was seen to open long before mitosis, and while one microtubule (or two in some predivisional cells) was consistently present, no mitotic spindle was ever observed, prompting speculation that a single microtubule might be sufficient to segregate multiple chromosomes

Cryo-electron tomography of cells: connecting structure and function

Cryo-electron tomography (cryo-ET) allows the visualization of cellular structures under close-to-life conditions and at molecular resolution. While it is inherently a static approach, yielding structural information about supramolecular organization at a certain time point, it can nevertheless provide insights into function of the structures imaged, in particular, when supplemented by other approaches. Here, we review the use of experimental methods that supplement cryo-ET imaging of whole cells. These include genetic and pharmacological manipulations, as well as correlative light microscopy and cryo-ET. While these methods have mostly been used to detect and identify structures visualized in cryo-ET or to assist the search for a feature of interest, we expect that in the future they will play a more important role in the functional interpretation of cryo-tomograms