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Josh Fass maxentile

  • Relay Therapeutics
  • Cambridge, MA
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@dominicrufa
dominicrufa / realnvp_toy_flow.ipynb
Created August 23, 2021 21:31
realnvp integrator in n dims without equivariance
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@jthorton
jthorton / Running_QCEngine.ipynb
Created November 19, 2020 16:01
Running QCEngine from OFFTK
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@j-wags
j-wags / slots.md
Created October 16, 2020 22:48
On slots

What are slots?

  • For the System object: A way to map between applied parameters in a System and the underlying graph molecule(s)
  • For ParameterHandlers: A way to look at a Topology and determine
    • how many parameters should be assigned
    • whether one SMIRKS parameter should clobber another, or both parameters should coexist
  • In formal math: An customizable language (algebra?) for describing how to take a graph where each node has a unique index and:
    • enumerate desired graph substructures
    • define an equivalence operator for graph substructures
@wutobias
wutobias / DiverseQCA.ipynb
Last active September 30, 2020 23:35
Example for making a diverse subset selection from QC molecules with common substructures
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@gngdb
gngdb / example_usage.py
Last active May 18, 2022 05:32
Wrap PyTorch functions for scipy's optimize.minimize: https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.minimize.html (I also made a repo to do this https://github.com/gngdb/pytorch-minimize, although I had forgotten about this gist at the time)
import torch
import torch.nn as nn
import torch.optim as optim
import torch.nn.functional as F
import numpy as np
from scipy import optimize
from obj import PyTorchObjective
@johnhw
johnhw / umap_sparse.py
Last active January 6, 2024 16:09
1 million prime UMAP layout
### JHW 2018
import numpy as np
import umap
# This code from the excellent module at:
# https://stackoverflow.com/questions/4643647/fast-prime-factorization-module
import random