We Are Not Your Real Parents: Telling Causal from Confounded using MDL

Given data over variables $(X_1,...,X_m, Y)$ we consider the problem of finding out whether $X$ jointly causes $Y$ or whether they are all confounded by an unobserved latent variable $Z$. To do so, we take an information-theoretic approach based on Kolmogorov complexity. In a nutshell, we follow the postulate that first encoding the true cause, and then the effects given that cause, results in a shorter description than any other encoding of the observed variables. The ideal score is not computable, and hence we have to approximate it. We propose to do so using the Minimum Description Length (MDL) principle. We compare the MDL scores under the models where $X$ causes $Y$ and where there exists a latent variables $Z$ confounding both $X$ and $Y$ and show our scores are consistent. To find potential confounders we propose using latent factor modeling, in particular, probabilistic PCA (PPCA). Empirical evaluation on both synthetic and real-world data shows that our method, CoCa, performs very well -- even when the true generating process of the data is far from the assumptions made by the models we use. Moreover, it is robust as its accuracy goes hand in hand with its confidence

{VoG}: {Summarizing} and Understanding Large Graphs

How can we succinctly describe a million-node graph with a few simple sentences? How can we measure the "importance" of a set of discovered subgraphs in a large graph? These are exactly the problems we focus on. Our main ideas are to construct a "vocabulary" of subgraph-types that often occur in real graphs (e.g., stars, cliques, chains), and from a set of subgraphs, find the most succinct description of a graph in terms of this vocabulary. We measure success in a well-founded way by means of the Minimum Description Length (MDL) principle: a subgraph is included in the summary if it decreases the total description length of the graph. Our contributions are three-fold: (a) formulation: we provide a principled encoding scheme to choose vocabulary subgraphs; (b) algorithm: we develop \method, an efficient method to minimize the description cost, and (c) applicability: we report experimental results on multi-million-edge real graphs, including Flickr and the Notre Dame web graph

Neuroimmune guidance cues in vascular (patho)physiology

The vascular system delivers oxygen and nutrients through the entire body. In addition, it enables distribution of hormones and immune cells. A proper functioning vascular system is important in preventing cardiovascular disease (CVD). In recent years, several risk factors, e.g. smoking and obesity, have been described. Also genetic variants have been shown to influence vascular function and thereby the risk on developing CVD.In this thesis the role of Neuroimmune Guidance Cues (NGCs) in the development of atherosclerosis, one of the main causes of CVD is investigated. The development of atherosclerosis is characterized by the deposition of fatty acids and immune cells in the vessel wall. With several experiments we have shown that NGCs play an important role in the vessel wall and regulate atherosclerosis-related processes. We show that PLXNA4 regulates endothelial permeability, while the Eph receptor B2 regulates migration of monocytes through the vessel. In addition, we have shown that genetic variants in Eph receptor B4, EphrinB2 and Netrin-1 can modulate atherosclerosis-related processes and thereby could influence the development of CVD.The results shown here give us new insights in the function of the vascular system and provide novel targets to treat and/or prevent CVD.LUMC / Geneeskund

Label-Descriptive Patterns and their Application to Characterizing Classification Errors

State-of-the-art deep learning methods achieve human-like performance on many tasks, but make errors nevertheless. Characterizing these errors in easily interpretable terms gives insight into whether a model is prone to making systematic errors, but also gives a way to act and improve the model. In this paper we propose a method that allows us to do so for arbitrary classifiers by mining a small set of patterns that together succinctly describe the input data that is partitioned according to correctness of prediction. We show this is an instance of the more general label description problem, which we formulate in terms of the Minimum Description Length principle. To discover good pattern sets we propose the efficient and hyperparameter-free Premise algorithm, which through an extensive set of experiments we show on both synthetic and real-world data performs very well in practice; unlike existing solutions it ably recovers ground truth patterns, even on highly imbalanced data over many unique items, or where patterns are only weakly associated to labels. Through two real-world case studies we confirm that Premise gives clear and actionable insight into the systematic errors made by modern NLP classifiers

Bilateral multiple coronary artery fistulae with angina pectoris and syncope

AbstractCoronary artery fistulae (CAF) are rare cardiac anomalies. They frequently arise from the right coronary artery (RCA) with fistulae originating from the left anterior descending artery (LAD) or from multiple arteries being less common. They do not usually cause symptoms and are incidentally diagnosed on routine cardiac imaging. We report a 70years old male patient presenting with chest pain and syncope during physical activity. Diagnostic coronary angiography revealed bilateral multiple CAF originating from both the LAD and RCA. As high blood flow output was recognized in these large vascular anomalies contributing to ‘steal phenomenon’ surgical intervention was planned. This manuscript aimed to present the case and review the current literature for the management and treatment of these coronary anomalies

Ephs and ephrins in adult endothelial biology

Eph receptors and their ephrin ligands are important guidance molecules during neurological and vascular development. In recent years, it has become clear that the Eph protein family remains functional in adult physiology. A subset of Ephs and ephrins is highly expressed by endothelial cells. As endothelial cells form the first barrier between the blood and surrounding tissues, maintenance of a healthy endothelium is crucial for tissue homeostasis. This review gives an overview of the current insights of the role of ephrin ligands and receptors in endothelial function and leukocyte recruitment in the (patho)physiology of adult vascular biology.Nephrolog

Tropical peatland biogeochemistry along an ecological transect: the enigmatic fate of organic matter

This is the final version. Available from the European Association of Geoscientists & Engineers via the DOI in this record. Peatlands play a pivotal role in the global carbon cycle. Despite only covering 3% of the world’s surface, peatlands hold 500–700 Gt of carbon (Page & Baird, 2016). These dense carbon stocks are sensitive to direct and/or indirect human intervention and can quickly turn from carbon sink to carbon source when perturbed. Additionally, peat deposits are crucial for our understanding of terrestrial environmental change by recording environmental parameters such as temperature and biogeochemical cycling through geological time (Naafs et al., 2019). Constraining the magnitude and rate of change during past periods of climatic change in the terrestrial realm is essential for accurately predicting the effects of anthropogenic global warming. Most peatland studies have focussed on reconstructing environmental parameters such as water table depth, temperature, vegetation, and pH, because those are readily available through quick observation or meteorological data. However, changes in the nature of the organic matter (OM) is often harder to characterize but is imperative to the tight balance between accumulation and degradation of peat. Especially in tropical peatlands, the nature of OM is largely understudied. Tropical peats are more carbon-dense compared to boreal peatlands, have a more active methane cycle, and can have a wider range of vegetation, which makes understanding their biogeochemistry vitally important. We investigated the biogeochemistry of a tropical peat along an ecological transect consisting of 5 sites: mangrove, mixed tropical forest, hardwood tropical forest, stunted forest with sawgrass and ombrotrophic (i.e., rain-fed) sawgrass bog. From each site, a 1–2 meter core was collected and analysed by pyrolysis-GC/MS, GC/MS (of apolar and polar fractions), 16S rRNA genomic profiling and, UPLC-QToF-MS. Our unique dataset allows for a direct comparison of the biogeochemistry of tropical peats under different vegetation and nutrient concentrations, but constant temperature

EPH receptor B2 stimulates human monocyte adhesion and migration independently of its EphrinB ligands

The molecular basis of atherosclerosis is not fully understood and mice studies have shown that Ephrins and EPH receptors play a role in the atherosclerotic process. We set out to assess the role for monocytic EPHB2 and its Ephrin ligands in human atherosclerosis and show a role for EPHB2 in monocyte functions independently of its EphrinB ligands. Immunohistochemical staining of human aortic sections at different stages of atherosclerosis showed that EPHB2 and its ligand EphrinB are expressed in atherosclerotic plaques and that expression proportionally increases with plaque severity. Functionally, stimulation with EPHB2 did not affect endothelial barrier function, nor did stimulation with EphrinB1 or EphrinB2 affect monocyte-endothelial interactions. In contrast, reduced expression of EPHB2 in monocytes resulted in decreased monocyte adhesion to endothelial cells and a decrease in monocyte transmigration, mediated by an altered morphology and a decreased ability to phosphorylate FAK. Our results suggest that EPHB2 expression in monocytes results in monocyte accumulation by virtue of an increase of transendothelial migration, which can subsequently contribute to atherosclerotic plaque progression.Nephrolog