Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology.Comment: Minor update

Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology

Evaluation of analytical methodologies to derive vulnerability functions

The recognition of fragility functions as a fundamental tool in seismic risk assessment has led to the development of more and more complex and elaborate procedures for their computation. Although vulnerability functions have been traditionally produced using observed damage and loss data, more recent studies propose the employment of analytical methodologies as a way to overcome the frequent lack of post-earthquake data. The variation of the structural modelling approaches on the estimation of building capacity has been the target of many studies in the past, however, its influence in the resulting vulnerability model, impact in loss estimations or propagation of the uncertainty to the seismic risk calculations has so far been the object of restricted scrutiny. Hence, in this paper, an extensive study of static and dynamic procedures for estimating the nonlinear response of buildings has been carried out in order to evaluate the impact of the chosen methodology on the resulting vulnerability and risk outputs. Moreover, the computational effort and numerical stability provided by each approach were evaluated and conclusions were obtained regarding which one offers the optimal balance between accuracy and complexity

Combining local regularity estimation and total variation optimization for scale-free texture segmentation

Texture segmentation constitutes a standard image processing task, crucial to many applications. The present contribution focuses on the particular subset of scale-free textures and its originality resides in the combination of three key ingredients: First, texture characterization relies on the concept of local regularity ; Second, estimation of local regularity is based on new multiscale quantities referred to as wavelet leaders ; Third, segmentation from local regularity faces a fundamental bias variance trade-off: In nature, local regularity estimation shows high variability that impairs the detection of changes, while a posteriori smoothing of regularity estimates precludes from locating correctly changes. Instead, the present contribution proposes several variational problem formulations based on total variation and proximal resolutions that effectively circumvent this trade-off. Estimation and segmentation performance for the proposed procedures are quantified and compared on synthetic as well as on real-world textures

Supervised nonlinear spectral unmixing using a post-nonlinear mixing model for hyperspectral imagery

This paper presents a nonlinear mixing model for hyperspectral image unmixing. The proposed model assumes that the pixel reflectances are nonlinear functions of pure spectral components contaminated by an additive white Gaussian noise. These nonlinear functions are approximated using polynomial functions leading to a polynomial postnonlinear mixing model. A Bayesian algorithm and optimization methods are proposed to estimate the parameters involved in the model. The performance of the unmixing strategies is evaluated by simulations conducted on synthetic and real data

Unremarkable AI: Fitting Intelligent Decision Support into Critical, Clinical Decision-Making Processes

Clinical decision support tools (DST) promise improved healthcare outcomes by offering data-driven insights. While effective in lab settings, almost all DSTs have failed in practice. Empirical research diagnosed poor contextual fit as the cause. This paper describes the design and field evaluation of a radically new form of DST. It automatically generates slides for clinicians' decision meetings with subtly embedded machine prognostics. This design took inspiration from the notion of "Unremarkable Computing", that by augmenting the users' routines technology/AI can have significant importance for the users yet remain unobtrusive. Our field evaluation suggests clinicians are more likely to encounter and embrace such a DST. Drawing on their responses, we discuss the importance and intricacies of finding the right level of unremarkableness in DST design, and share lessons learned in prototyping critical AI systems as a situated experience

Species-level functional profiling of metagenomes and metatranscriptomes.

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types