Flatware

Session

Lightning Talks

Oct 24, 2018, 11:00 AM

2nd floor GDFA (160 5th Ave.)

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

40. Selene: A framework for training sequence level deep learning networks

Kathleen Chen

10/24/18, 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...

48. Containerization in Modern Scientific Applications

Nils Wentzell

10/24/18, 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...

42. SafeFFT: A thread safe interface to FFTW and MKL

Wen Yan

10/24/18, 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...

45. STARRY: Light curve modeling suite

Rodrigo Luger

10/25/18, 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...

46. CaImAn: Large scale brain imaging data analysis for the 99%

Andrea Giovannucci, Eftychios Pnevmatikakis

10/25/18, 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...

44. IronClust: Real-time, drift-resistant spike-sorting based on density-based clustering

James Jun

10/25/18, 11:45 AM

Software engineering focus:

Robust performance under physical drift over time
Validation using simulated and biophysical ground-truth datasets
Realtime performance up to 1000 channels using parallel computing hardware (GPU, CPU)

41. NetKet: challenges and desiderata in designing machine learning software for quantum physics

Giuseppe Carleo

10/25/18, 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.

43. CCA Simulation Repository: common frameworks for sharing, distributing, and processing astrophysical simulation data

Dylan Simon, Shy Genel

10/25/18, 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...

50. Auxiliary Field Quantum Monte Carlo software

Hao Shi

10/26/18, 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.

51. A spike sorting meta package and website for algorithm comparison

Jeremy Magland

10/26/18, 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...

53. A flexible and fast package for boundary integral equations in two dimensions

David Stein

10/26/18, 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....

6. Lightning Talk: CCA

Dylan Simon, Shy Genel

7. Lightning Talk: CCM?

James Jun

47. TBD

49. TBD