Non-significant randomized control trials can hide subgroups of good responders to experimental drugs, thus hindering subsequent development. Identifying such heterogeneous treatment effects is key for precision medicine and many post-hoc analysis methods have been developed for that purpose. While several benchmarks have been carried out to identify the strengths and weaknesses of these methods, notably for binary and continuous endpoints, similar systematic empirical evaluation of subgroup analysis for time-to-event endpoints are lacking. This work aims to fill this gap by evaluating several subgroup analysis algorithms in the context of time-to-event outcomes, by means of three different research questions: Is there heterogeneity? What are the biomarkers responsible for such heterogeneity? Who are the good responders to treatment? In this context, we propose a new synthetic and semi-synthetic data generation process that allows one to explore a wide range of heterogeneity scenarios with precise control on the level of heterogeneity. We provide an open source Python package, available on Github, containing our generation process and our comprehensive benchmark framework. We hope this package will be useful to the research community for future investigations of heterogeneity of treatment effects and subgroup analysis methods benchmarking.
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The exponential growth in scientific publications poses a severe challenge for human researchers. It forces attention to more narrow sub-fields, which makes it challenging to discover new impactful research ideas and collaborations outside one's own field. While there are ways to predict a scientific paper's future citation counts, they need the research to be finished and the paper written, usually assessing impact long after the idea was conceived. Here we show how to predict the impact of onsets of ideas that have never been published by researchers. For that, we developed a large evolving knowledge graph built from more than 21 million scientific papers. It combines a semantic network created from the content of the papers and an impact network created from the historic citations of papers. Using machine learning, we can predict the dynamic of the evolving network into the future with high accuracy, and thereby the impact of new research directions. We envision that the ability to predict the impact of new ideas will be a crucial component of future artificial muses that can inspire new impactful and interesting scientific ideas.
Measurement and comparison of distributional shift and its relation to rarity, poverty, and scarcity
The comparison of frequency distributions is a common statistical task with broad applications. However, existing measures do not explicitly quantify the magnitude and direction by which one distribution is shifted relative to another. In the present study, we define distributional shift (DS) as the concentration of frequencies towards the lowest discrete class, e.g., the left-most bin of a histogram. We measure DS via the sum of cumulative frequencies and define relative distributional shift (RDS) as the difference in DS between distributions. Using simulated random sampling, we show that RDS is highly related to measures that are widely used to compare frequency distributions. Focusing on specific applications, we show that DS and RDS provide insights into healthcare billing distributions, ecological species-abundance distributions, and economic distributions of wealth. RDS has the unique advantage of being a signed (i.e., directional) measure based on a simple difference in an intuitive property that, in turn, serves as a measure of rarity, poverty, and scarcity.
This paper presents a method for thematic agreement assessment of geospatial data products of different semantics and spatial granularities, which may be affected by spatial offsets between test and reference data. The proposed method uses a multi-scale framework allowing for a probabilistic evaluation whether thematic disagreement between datasets is induced by spatial offsets due to different nature of the datasets or not. We test our method using real-estate derived settlement locations and remote-sensing derived building footprint data.
Understanding a surgical scene is crucial for computer-assisted surgery systems to provide any intelligent assistance functionality. One way of achieving this scene understanding is via scene segmentation, where every pixel of a frame is classified and therefore identifies the visible structures and tissues. Progress on fully segmenting surgical scenes has been made using machine learning. However, such models require large amounts of annotated training data, containing examples of all relevant object classes. Such fully annotated datasets are hard to create, as every pixel in a frame needs to be annotated by medical experts and, therefore, are rarely available. In this work, we propose a method to combine multiple partially annotated datasets, which provide complementary annotations, into one model, enabling better scene segmentation and the use of multiple readily available datasets. Our method aims to combine available data with complementary labels by leveraging mutual exclusive properties to maximize information. Specifically, we propose to use positive annotations of other classes as negative samples and to exclude background pixels of binary annotations, as we cannot tell if they contain a class not annotated but predicted by the model. We evaluate our method by training a DeepLabV3 on the publicly available Dresden Surgical Anatomy Dataset, which provides multiple subsets of binary segmented anatomical structures. Our approach successfully combines 6 classes into one model, increasing the overall Dice Score by 4.4% compared to an ensemble of models trained on the classes individually. By including information on multiple classes, we were able to reduce confusion between stomach and colon by 24%. Our results demonstrate the feasibility of training a model on multiple datasets. This paves the way for future work further alleviating the need for one large, fully segmented datasets.
Radon is a carcinogenic, radioactive gas that can accumulate indoors. Therefore, accurate knowledge of indoor radon concentration is crucial for assessing radon-related health effects or identifying radon-prone areas. Indoor radon concentration at the national scale is usually estimated on the basis of extensive measurement campaigns. However, characteristics of the sample often differ from the characteristics of the population due to the large number of relevant factors that control the indoor radon concentration such as the availability of geogenic radon or floor level. Furthermore, the sample size usually does not allow estimation with high spatial resolution. We propose a model-based approach that allows a more realistic estimation of indoor radon distribution with a higher spatial resolution than a purely data-based approach. A two-stage modelling approach was applied: 1) a quantile regression forest using environmental and building data as predictors was applied to estimate the probability distribution function of indoor radon for each floor level of each residential building in Germany; (2) a probabilistic Monte Carlo sampling technique enabled the combination and population weighting of floor-level predictions. In this way, the uncertainty of the individual predictions is effectively propagated into the estimate of variability at the aggregated level. The results show an approximate lognormal distribution with an arithmetic mean of 63 Bq/m3, a geometric mean of 41 Bq/m3 and a 95 %ile of 180 Bq/m3. The exceedance probability for 100 Bq/m3 and 300 Bq/m3 are 12.5 % (10.5 million people) and 2.2 % (1.9 million people), respectively.
Many phenomena in real world social networks are interpreted as spread of influence between activated and non-activated network elements. These phenomena are formulated by combinatorial graphs, where vertices represent the elements and edges represent social ties between elements. A main problem is to study important subsets of elements (target sets or dynamic monopolies) such that their activation spreads to the entire network. In edge-weighted networks the influence between two adjacent vertices depends on the weight of their edge. In models with incentives, the main problem is to minimize total amount of incentives (called optimal target vectors) which can be offered to vertices such that some vertices are activated and their activation spreads to the whole network. Algorithmic study of target sets and vectors is a hot research field. We prove an inapproximability result for optimal target sets in edge weighted networks even for complete graphs. Some other hardness and polynomial time results are presented for optimal target vectors and degenerate threshold assignments in edge-weighted networks.
In an error estimation of finite element solutions to the Poisson equation, we usually impose the shape regularity assumption on the meshes to be used. In this paper, we show that even if the shape regularity condition is violated, the standard error estimation can be obtained if "bad" elements (elements that violate the shape regularity or maximum angle condition) are covered virtually by "good" simplices. A numerical experiment confirms the theoretical result.
Tactile sensing in mobile robots remains under-explored, mainly due to challenges related to sensor integration and the complexities of distributed sensing. In this work, we present a tactile sensing architecture for mobile robots based on wheel-mounted acoustic waveguides. Our sensor architecture enables tactile sensing along the entire circumference of a wheel with a single active component: an off-the-shelf acoustic rangefinder. We present findings showing that our sensor, mounted on the wheel of a mobile robot, is capable of discriminating between different terrains, detecting and classifying obstacles with different geometries, and performing collision detection via contact localization. We also present a comparison between our sensor and sensors traditionally used in mobile robots, and point to the potential for sensor fusion approaches that leverage the unique capabilities of our tactile sensing architecture. Our findings demonstrate that autonomous mobile robots can further leverage our sensor architecture for diverse mapping tasks requiring knowledge of terrain material, surface topology, and underlying structure.
In large-scale, data-driven applications, parameters are often only known approximately due to noise and limited data samples. In this paper, we focus on high-dimensional optimization problems with linear constraints under uncertain conditions. To find high quality solutions for which the violation of the true constraints is limited, we develop a linear shrinkage method that blends random matrix theory and robust optimization principles. It aims to minimize the Frobenius distance between the estimated and the true parameter matrix, especially when dealing with a large and comparable number of constraints and variables. This data-driven method excels in simulations, showing superior noise resilience and more stable performance in both obtaining high quality solutions and adhering to the true constraints compared to traditional robust optimization. Our findings highlight the effectiveness of our method in improving the robustness and reliability of optimization in high-dimensional, data-driven scenarios.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
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