Conveners
Lightning Talks: Morning Session
- Nick Carriero (FI SCC)
Lightning Talks: Morning Session
- Doug Renfrew
Lightning Talks: Afternoon Session
- Julia Koehler-Leman
Lightning Talks: Morning Session
- Andrea Giovannucci
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Kathleen Chen10/24/18, 11:00 AM
To enable the application of deep learning in biology, we developed Selene, a PyTorch-based library for fast and easy development, training, and application of deep learning model architectures to sequence-level (e.g. DNA, RNA) datasets. In this presentation, I will discuss how we designed Selene to support sequence-based deep learning across a broad range of biological questions and made the...
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Nils Wentzell10/24/18, 11:15 AM
Scientific algorithms for the solution of the correlated many-body problem and beyond are rapidly growing in complexity. This development shows also in their respective numerical implementations, leading to growing number of library dependencies, toolchain dependencies as well as inter-dependencies with other scientific applications. This often makes a proper setup on workstations, but in...
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Wen Yan10/24/18, 11:30 AM
Running FFTs, possibly with different sizes and types, from multiple threads is becoming necessary to improve both the program flexibility and execution efficiency, with an increasing number of CPU cores on a typical SMP machine. However, the native interface in FFTW and Intel MKL does not fully support this use scenario due to thread safety issues. To address this issue, SafeFFT is designed...
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Rodrigo Luger10/25/18, 11:15 AM
I will discuss the ongoing development of the open-source STARRY code for computation of fast light curves for stellar and exoplanet science. I will focus mainly on computational aspects, including (1) obtaining model derivatives via autodifferentiation for use in gradient-based inference schemes such as Hamiltonian Monte Carlo, (2) developing simultaneous C++, Julia, and Python interfaces to...
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Andrea Giovannucci, Eftychios Pnevmatikakis10/25/18, 11:30 AM
CaImAn is an open-source software framework for the analysis of brain imaging data. We will share our experience interacting with the CaImAn user-base, mostly composed of neuroscience researchers. Properly managing the interaction with users is essential to the success of scientific software, because of the received feedback, the potential contributions to the code-base, and the community...
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James Jun10/25/18, 11:45 AM
Software engineering focus:
Robust performance under physical drift over time
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Validation using simulated and biophysical ground-truth datasets
Realtime performance up to 1000 channels using parallel computing hardware (GPU, CPU) -
Giuseppe Carleo10/25/18, 4:15 PM
I will discuss the open-source project NetKet (https://www.netket.org/), and the challenges in designing a software flexible enough for research purposes while keeping the pace of large-scale machine learning software developed by industry. I will also discuss the strategies that we have put in place to stimulate external collaborations to the project.
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Dylan Simon, Shy Genel10/25/18, 4:30 PM
As envisioned by the galaxy formation group, our goal is to provide tools to discover, share, and access cosmological and other astrophysical simulations through web-based platforms, enabling efficient analysis of large datasets by distributed users. Currently in the planning and prototyping phase, this will ultimately involve creating ways to query object catalogs, access portions of raw...
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Hao Shi10/26/18, 11:15 AM
I will present a quantum Monte Carlo software for the strongly-correlated many-electron systems. The software focuses on ab initio simulations for realistic materials and quantum chemistry systems. I will also talk about massively parallel design in the software.
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Jeremy Magland10/26/18, 11:30 AM
Spike sorting is an crucial component of most neurophysiology pipelines that precedes downstream analysis of neural firing data. With a dozen or so spike sorting software packages in the mix, there is little to no consensus on which algorithm is most suitable, depending on the experimental setup. This is due to a number of factors including lack of realistic ground truth recordings, no clear...
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David Stein10/26/18, 11:45 AM
The solution of certain elliptic partial differential equations (Laplace, Stokes, Helmholtz, etc.) provides one of the primary building blocks necessary for the study of a wide range of physical problems. For simple domains, the solution of these equations is trivial. On complex domains, this is not the case, and many researchers have depended on methods that are slow, inaccurate, or both....
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Dylan Simon, Shy Genel
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James Jun
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