Merge pull request #3354 from sussillo/master

Fix simple errors in synthetic examples in lfads.

research/lfads/README.md

@@ -7,7 +7,7 @@ This code implements the model from the paper "[LFADS - Latent Factor Analysis v
 
 The code is written in Python 2.7.6. You will also need:
 
-* **TensorFlow** version 1.2.1 ([install](https://www.tensorflow.org/install/)) -
+* **TensorFlow** version 1.5 ([install](https://www.tensorflow.org/install/)) -
 * **NumPy, SciPy, Matplotlib** ([install SciPy stack](https://www.scipy.org/install.html), contains all of them)
 * **h5py** ([install](https://pypi.python.org/pypi/h5py))
 
@@ -98,7 +98,18 @@ $ python run_lfads.py --kind=train \
 --output_filename_stem="" \
 --ic_prior_var_max=0.1 \
 --prior_ar_atau=10.0 \
---do_train_io_only=false
+--do_train_io_only=false \
+--do_train_encoder_only=false
+
+# Run LFADS on chaotic rnn data with no input pulses (g = 1.5) with Gaussian noise
+$ python run_lfads.py --kind=train \
+--data_dir=/tmp/rnn_synth_data_v1.0/ \
+--data_filename_stem=gaussian_chaotic_rnn_no_inputs \
+--lfads_save_dir=/tmp/lfads_chaotic_rnn_inputs_g2p5 \
+--co_dim=1 \
+--factors_dim=20 \
+--output_dist=gaussian
+
 
 # Run LFADS on chaotic rnn data with input pulses (g = 2.5)
 $ python run_lfads.py --kind=train \

research/lfads/synth_data/generate_itb_data.py

@@ -39,7 +39,7 @@ flags.DEFINE_integer("C", 800, "Number of conditions")
 flags.DEFINE_integer("N", 50, "Number of units for the RNN")
 flags.DEFINE_float("train_percentage", 4.0/5.0,
                    "Percentage of train vs validation trials")
-flags.DEFINE_integer("nspikifications", 5,
+flags.DEFINE_integer("nreplications", 5,
                      "Number of spikifications of the same underlying rates.")
 flags.DEFINE_float("tau", 0.025, "Time constant of RNN")
 flags.DEFINE_float("dt", 0.010, "Time bin")
@@ -90,8 +90,8 @@ u_rng = np.random.RandomState(seed=FLAGS.synth_data_seed+1)
 T = FLAGS.T
 C = FLAGS.C
 N = FLAGS.N  # must be same N as in trained model (provided example is N = 50)
-nspikifications = FLAGS.nspikifications
-E = nspikifications * C  # total number of trials
+nreplications = FLAGS.nreplications
+E = nreplications * C  # total number of trials
 train_percentage = FLAGS.train_percentage
 ntimesteps = int(T / FLAGS.dt)
 batch_size = 1  # gives one example per ntrial
@@ -144,7 +144,7 @@ with tf.Session() as sess:
     outputs_t_bxn = np.squeeze(np.asarray(outputs_t_bxn))
     r_sxt = np.dot(P_nxn, states_nxt)
 
-    for s in xrange(nspikifications):
+    for s in xrange(nreplications):
       data_e.append(r_sxt)
       u_e.append(u_1xt)
       outs_e.append(outputs_t_bxn)
@@ -154,7 +154,7 @@ with tf.Session() as sess:
 spiking_data_e = spikify_data(truth_data_e, rng, dt=FLAGS.dt,
                               max_firing_rate=FLAGS.max_firing_rate)
 train_inds, valid_inds = get_train_n_valid_inds(E, train_percentage,
-                                                nspikifications)
+                                                nreplications)
 
 data_train_truth, data_valid_truth = split_list_by_inds(truth_data_e,
                                                         train_inds,
@@ -188,7 +188,7 @@ data = { 'train_truth': data_train_truth,
          'train_data' : data_train_spiking,
          'valid_data' : data_valid_spiking,
          'train_percentage' : train_percentage,
-         'nspikifications' : nspikifications,
+         'nreplications' : nreplications,
          'dt' : FLAGS.dt,
          'u_std' : FLAGS.u_std,
          'max_firing_rate': FLAGS.max_firing_rate,

research/lfads/synth_data/generate_labeled_rnn_data.py

@@ -40,7 +40,7 @@ flags.DEFINE_integer("C", 400, "Number of conditions")
 flags.DEFINE_integer("N", 50, "Number of units for the RNN")
 flags.DEFINE_float("train_percentage", 4.0/5.0,
                    "Percentage of train vs validation trials")
-flags.DEFINE_integer("nspikifications", 10,
+flags.DEFINE_integer("nreplications", 10,
                      "Number of spikifications of the same underlying rates.")
 flags.DEFINE_float("g", 1.5, "Complexity of dynamics")
 flags.DEFINE_float("x0_std", 1.0,
@@ -56,8 +56,8 @@ rnn_rngs = [np.random.RandomState(seed=FLAGS.synth_data_seed+1),
 T = FLAGS.T
 C = FLAGS.C
 N = FLAGS.N
-nspikifications = FLAGS.nspikifications
-E = nspikifications * C
+nreplications = FLAGS.nreplications
+E = nreplications * C
 train_percentage = FLAGS.train_percentage
 ntimesteps = int(T / FLAGS.dt)
 
@@ -77,8 +77,8 @@ condition_labels = []
 condition_number = 0
 for c in range(C):
   x0 = FLAGS.x0_std * rng.randn(N, 1)
-  x0s.append(np.tile(x0, nspikifications))
-  for ns in range(nspikifications):
+  x0s.append(np.tile(x0, nreplications))
+  for ns in range(nreplications):
     condition_labels.append(condition_number)
   condition_number += 1
 x0s = np.concatenate(x0s, axis=1)
@@ -107,7 +107,7 @@ for trial in xrange(E):
 
 # split into train and validation sets
 train_inds, valid_inds = get_train_n_valid_inds(E, train_percentage,
-                                                nspikifications)
+                                                nreplications)
 
 rates_train, rates_valid = split_list_by_inds(rates, train_inds, valid_inds)
 spikes_train, spikes_valid = split_list_by_inds(spikes, train_inds, valid_inds)
@@ -129,7 +129,7 @@ data = {'train_truth': rates_train,
         'train_ext_input' : np.array(ext_input_train),
         'valid_ext_input': np.array(ext_input_valid),
         'train_percentage' : train_percentage,
-        'nspikifications' : nspikifications,
+        'nreplications' : nreplications,
         'dt' : FLAGS.dt,
         'P_sxn' : P_nxn,
         'condition_labels_train' : condition_labels_train,

research/lfads/synth_data/run_generate_synth_data.sh

@@ -19,22 +19,22 @@
 SYNTH_PATH=/tmp/rnn_synth_data_v1.0/
 
  echo "Generating chaotic rnn data with no input pulses (g=1.5) with spiking noise"
- python generate_chaotic_rnn_data.py --save_dir=$SYNTH_PATH --datafile_name=chaotic_rnn_no_inputs --synth_data_seed=5 --T=1.0 --C=400 --N=50 --S=50 --train_percentage=0.8 --nspikifications=10 --g=1.5 --x0_std=1.0 --tau=0.025 --dt=0.01 --input_magnitude=0.0 --max_firing_rate=30.0 --noise_type='poisson'
+ python generate_chaotic_rnn_data.py --save_dir=$SYNTH_PATH --datafile_name=chaotic_rnn_no_inputs --synth_data_seed=5 --T=1.0 --C=400 --N=50 --S=50 --train_percentage=0.8 --nreplications=10 --g=1.5 --x0_std=1.0 --tau=0.025 --dt=0.01 --input_magnitude=0.0 --max_firing_rate=30.0 --noise_type='poisson'
 
 echo "Generating chaotic rnn data with no input pulses (g=1.5) with Gaussian noise"
-python generate_chaotic_rnn_data.py --save_dir=$SYNTH_PATH --datafile_name=chaotic_rnn_no_inputs_gaussian --synth_data_seed=5 --T=1.0 --C=400 --N=50 --S=50 --train_percentage=0.8 --nspikifications=10 --g=1.5 --x0_std=1.0 --tau=0.025 --dt=0.01 --input_magnitude=0.0 --max_firing_rate=30.0 --noise_type='gaussian'
+python generate_chaotic_rnn_data.py --save_dir=$SYNTH_PATH --datafile_name=gaussian_chaotic_rnn_no_inputs --synth_data_seed=5 --T=1.0 --C=400 --N=50 --S=50 --train_percentage=0.8 --nreplications=10 --g=1.5 --x0_std=1.0 --tau=0.025 --dt=0.01 --input_magnitude=0.0 --max_firing_rate=30.0 --noise_type='gaussian'
 
  echo "Generating chaotic rnn data with input pulses (g=1.5)"
- python generate_chaotic_rnn_data.py --save_dir=$SYNTH_PATH --datafile_name=chaotic_rnn_inputs_g1p5 --synth_data_seed=5 --T=1.0 --C=400 --N=50 --S=50 --train_percentage=0.8 --nspikifications=10 --g=1.5 --x0_std=1.0 --tau=0.025 --dt=0.01 --input_magnitude=20.0 --max_firing_rate=30.0 --noise_type='poisson'
+ python generate_chaotic_rnn_data.py --save_dir=$SYNTH_PATH --datafile_name=chaotic_rnn_inputs_g1p5 --synth_data_seed=5 --T=1.0 --C=400 --N=50 --S=50 --train_percentage=0.8 --nreplications=10 --g=1.5 --x0_std=1.0 --tau=0.025 --dt=0.01 --input_magnitude=20.0 --max_firing_rate=30.0 --noise_type='poisson'
 
  echo "Generating chaotic rnn data with input pulses (g=2.5)"
- python generate_chaotic_rnn_data.py --save_dir=$SYNTH_PATH --datafile_name=chaotic_rnn_inputs_g2p5 --synth_data_seed=5 --T=1.0 --C=400 --N=50 --S=50 --train_percentage=0.8 --nspikifications=10 --g=2.5 --x0_std=1.0 --tau=0.025 --dt=0.01 --input_magnitude=20.0 --max_firing_rate=30.0 --noise_type='poisson'
+ python generate_chaotic_rnn_data.py --save_dir=$SYNTH_PATH --datafile_name=chaotic_rnn_inputs_g2p5 --synth_data_seed=5 --T=1.0 --C=400 --N=50 --S=50 --train_percentage=0.8 --nreplications=10 --g=2.5 --x0_std=1.0 --tau=0.025 --dt=0.01 --input_magnitude=20.0 --max_firing_rate=30.0 --noise_type='poisson'
 
  echo "Generate the multi-session RNN data (no multi-session synth example in paper)"
- python generate_chaotic_rnn_data.py --save_dir=$SYNTH_PATH --datafile_name=chaotic_rnn_multisession --synth_data_seed=5 --T=1.0 --C=150 --N=100 --S=20 --npcs=10 --train_percentage=0.8 --nspikifications=40 --g=1.5 --x0_std=1.0 --tau=0.025 --dt=0.01 --input_magnitude=0.0 --max_firing_rate=30.0 --noise_type='poisson'
+ python generate_chaotic_rnn_data.py --save_dir=$SYNTH_PATH --datafile_name=chaotic_rnn_multisession --synth_data_seed=5 --T=1.0 --C=150 --N=100 --S=20 --npcs=10 --train_percentage=0.8 --nreplications=40 --g=1.5 --x0_std=1.0 --tau=0.025 --dt=0.01 --input_magnitude=0.0 --max_firing_rate=30.0 --noise_type='poisson'
 
  echo "Generating Integration-to-bound RNN data"
- python generate_itb_data.py --save_dir=$SYNTH_PATH --datafile_name=itb_rnn --u_std=0.25 --checkpoint_path=SAMPLE_CHECKPOINT --synth_data_seed=5 --T=1.0 --C=800 --N=50 --train_percentage=0.8 --nspikifications=5 --tau=0.025 --dt=0.01 --max_firing_rate=30.0
+ python generate_itb_data.py --save_dir=$SYNTH_PATH --datafile_name=itb_rnn --u_std=0.25 --checkpoint_path=SAMPLE_CHECKPOINT --synth_data_seed=5 --T=1.0 --C=800 --N=50 --train_percentage=0.8 --nreplications=5 --tau=0.025 --dt=0.01 --max_firing_rate=30.0
 
  echo "Generating chaotic rnn data with external input labels (no external input labels example in paper)"
- python generate_labeled_rnn_data.py --save_dir=$SYNTH_PATH --datafile_name=chaotic_rnns_labeled --synth_data_seed=5 --T=1.0 --C=400 --N=50  --train_percentage=0.8 --nspikifications=10 --g=1.5 --x0_std=1.0 --tau=0.025 --dt=0.01 --max_firing_rate=30.0
+ python generate_labeled_rnn_data.py --save_dir=$SYNTH_PATH --datafile_name=chaotic_rnns_labeled --synth_data_seed=5 --T=1.0 --C=400 --N=50  --train_percentage=0.8 --nreplications=10 --g=1.5 --x0_std=1.0 --tau=0.025 --dt=0.01 --max_firing_rate=30.0

research/lfads/synth_data/synthetic_data_utils.py

@@ -176,13 +176,13 @@ def gaussify_data(data_e, rng, dt=1.0, max_firing_rate=100):
 
 
 
-def get_train_n_valid_inds(num_trials, train_fraction, nspikifications):
+def get_train_n_valid_inds(num_trials, train_fraction, nreplications):
   """Split the numbers between 0 and num_trials-1 into two portions for
   training and validation, based on the train fraction.
   Args:
     num_trials: the number of trials
     train_fraction: (e.g. .80)
-    nspikifications: the number of spiking trials per initial condition
+    nreplications: the number of spiking trials per initial condition
   Returns:
     a 2-tuple of two lists: the training indices and validation indices
     """
@@ -192,7 +192,7 @@ def get_train_n_valid_inds(num_trials, train_fraction, nspikifications):
     # This line divides up the trials so that within one initial condition,
     # the randomness of spikifying the condition is shared among both
     # training and validation data splits.
-    if (i % nspikifications)+1 > train_fraction * nspikifications:
+    if (i % nreplications)+1 > train_fraction * nreplications:
       valid_inds.append(i)
     else:
       train_inds.append(i)