From 4f36f57bef343f25f78b153a049accc2d2f73958 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sun, 28 Jan 2018 19:11:45 -0500
Subject: [PATCH] update hyperparameters
---
.../models_class1/hyperparameters.yaml | 50 -------------------
1 file changed, 50 deletions(-)
diff --git a/downloads-generation/models_class1/hyperparameters.yaml b/downloads-generation/models_class1/hyperparameters.yaml
index 7aa63d6c..e69de29b 100644
--- a/downloads-generation/models_class1/hyperparameters.yaml
+++ b/downloads-generation/models_class1/hyperparameters.yaml
@@ -1,50 +0,0 @@
-[{
-##########################################
-# ENSEMBLE SIZE
-##########################################
-"n_models": 8,
-
-##########################################
-# OPTIMIZATION
-##########################################
-"max_epochs": 500,
-"patience": 20,
-"early_stopping": true,
-"validation_split": 0.2,
-"minibatch_size": 128,
-"loss": "custom:mse_with_inequalities",
-
-##########################################
-# RANDOM NEGATIVE PEPTIDES
-##########################################
-"random_negative_rate": 0.2,
-"random_negative_constant": 25,
-"random_negative_affinity_min": 20000.0,
-"random_negative_affinity_max": 50000.0,
-
-##########################################
-# PEPTIDE REPRESENTATION
-##########################################
-# One of "one-hot", "embedding", or "BLOSUM62".
-"peptide_amino_acid_encoding": "BLOSUM62",
-"use_embedding": false, # maintained for backward compatability
-"embedding_output_dim": 8, # only used if using embedding
-"kmer_size": 15,
-
-##########################################
-# NEURAL NETWORK ARCHITECTURE
-##########################################
-"locally_connected_layers": [
- {
- "filters": 8,
- "activation": "tanh",
- "kernel_size": 3
- }
-],
-"activation": "relu",
-"output_activation": "sigmoid",
-"layer_sizes": [16],
-"dense_layer_l1_regularization": 0.001,
-"batch_normalization": false,
-"dropout_probability": 0.0,
-}]
--
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