181,278 research outputs found
Integrating Machine Learning and Multiscale Modeling: Perspectives, Challenges, and Opportunities in the Biological, Biomedical, and Behavioral Sciences
Fueled by breakthrough technology developments, the biological, biomedical,
and behavioral sciences are now collecting more data than ever before. There is
a critical need for time- and cost-efficient strategies to analyze and
interpret these data to advance human health. The recent rise of machine
learning as a powerful technique to integrate multimodality, multifidelity
data, and reveal correlations between intertwined phenomena presents a special
opportunity in this regard. However, classical machine learning techniques
often ignore the fundamental laws of physics and result in ill-posed problems
or non-physical solutions. Multiscale modeling is a successful strategy to
integrate multiscale, multiphysics data and uncover mechanisms that explain the
emergence of function. However, multiscale modeling alone often fails to
efficiently combine large data sets from different sources and different levels
of resolution. We show how machine learning and multiscale modeling can
complement each other to create robust predictive models that integrate the
underlying physics to manage ill-posed problems and explore massive design
spaces. We critically review the current literature, highlight applications and
opportunities, address open questions, and discuss potential challenges and
limitations in four overarching topical areas: ordinary differential equations,
partial differential equations, data-driven approaches, and theory-driven
approaches. Towards these goals, we leverage expertise in applied mathematics,
computer science, computational biology, biophysics, biomechanics, engineering
mechanics, experimentation, and medicine. Our multidisciplinary perspective
suggests that integrating machine learning and multiscale modeling can provide
new insights into disease mechanisms, help identify new targets and treatment
strategies, and inform decision making for the benefit of human health
Classification in biological networks with hypergraphlet kernels
Abstract
Motivation
Biological and cellular systems are often modeled as graphs in which vertices represent objects of interest (genes, proteins and drugs) and edges represent relational ties between these objects (binds-to, interacts-with and regulates). This approach has been highly successful owing to the theory, methodology and software that support analysis and learning on graphs. Graphs, however, suffer from information loss when modeling physical systems due to their inability to accurately represent multiobject relationships. Hypergraphs, a generalization of graphs, provide a framework to mitigate information loss and unify disparate graph-based methodologies.
Results
We present a hypergraph-based approach for modeling biological systems and formulate vertex classification, edge classification and link prediction problems on (hyper)graphs as instances of vertex classification on (extended, dual) hypergraphs. We then introduce a novel kernel method on vertex- and edge-labeled (colored) hypergraphs for analysis and learning. The method is based on exact and inexact (via hypergraph edit distances) enumeration of hypergraphlets; i.e. small hypergraphs rooted at a vertex of interest. We empirically evaluate this method on fifteen biological networks and show its potential use in a positive-unlabeled setting to estimate the interactome sizes in various species.This work was partially supported by the National Science Foundation (NSF) [DBI-1458477], National Institutes of Health (NIH) [R01 MH105524], the Indiana University Precision Health Initiative, the European Research Council (ERC) [Consolidator Grant 770827], UCL Computer Science, the Slovenian Research Agency project [J1-8155], the Serbian Ministry of Education and Science Project [III44006] and the Prostate Project.Peer ReviewedPostprint (author's final draft
Negative Results in Computer Vision: A Perspective
A negative result is when the outcome of an experiment or a model is not what
is expected or when a hypothesis does not hold. Despite being often overlooked
in the scientific community, negative results are results and they carry value.
While this topic has been extensively discussed in other fields such as social
sciences and biosciences, less attention has been paid to it in the computer
vision community. The unique characteristics of computer vision, particularly
its experimental aspect, call for a special treatment of this matter. In this
paper, I will address what makes negative results important, how they should be
disseminated and incentivized, and what lessons can be learned from cognitive
vision research in this regard. Further, I will discuss issues such as computer
vision and human vision interaction, experimental design and statistical
hypothesis testing, explanatory versus predictive modeling, performance
evaluation, model comparison, as well as computer vision research culture
The view from elsewhere: perspectives on ALife Modeling
Many artificial life researchers stress the interdisciplinary character of the field. Against such a backdrop, this report reviews and discusses artificial life, as it is depicted in, and as it interfaces with, adjacent disciplines (in particular, philosophy, biology, and linguistics), and in the light of a specific historical example of interdisciplinary research (namely cybernetics) with which artificial life shares many features. This report grew out of a workshop held at the Sixth European Conference on Artificial Life in Prague and features individual contributions from the workshop's eight speakers, plus a section designed to reflect the debates that took place during the workshop's discussion sessions. The major theme that emerged during these sessions was the identity and status of artificial life as a scientific endeavor
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