# Make one to use repeatedly, to re-use examples where possible:
confusion_matrix = ConfusionMatrix(
index_to_example_function=train_index_to_example)
# Train the Model
with experiment.train():
print("Logging weights as histogram (before training)...")
# Log model weights
weights = []
for name in rnn.named_parameters():
if 'weight' in name[0]:
weights.extend(name[1].detach().numpy().tolist())
experiment.log_histogram_3d(weights, step=0)
step = 0
for epoch in range(hyper_params['num_epochs']):
experiment.log_current_epoch(epoch)
correct = 0
total = 0
epoch_predictions = None
epoch_targets = None
for i, (images, labels) in enumerate(train_loader):
images = Variable(
images.view(-1, hyper_params['sequence_length'],
hyper_params['input_size']))
labels = Variable(labels)
class Logger:
def __init__(self, send_logs, tags, parameters, experiment=None):
self.stations = 5
self.send_logs = send_logs
if self.send_logs:
if experiment is None:
json_loc = glob.glob("./**/comet_token.json")[0]
with open(json_loc, "r") as f:
kwargs = json.load(f)
self.experiment = Experiment(**kwargs)
else:
self.experiment = experiment
self.sent_mb = 0
self.speed_window = deque(maxlen=100)
self.step_time = None
self.current_speed = 0
if self.send_logs:
if tags is not None:
self.experiment.add_tags(tags)
if parameters is not None:
self.experiment.log_parameters(parameters)
def begin_logging(self, episode_count, steps_per_ep, sigma, theta, step_time):
self.step_time = step_time
if self.send_logs:
self.experiment.log_parameter("Episode count", episode_count)
self.experiment.log_parameter("Steps per episode", steps_per_ep)
self.experiment.log_parameter("theta", theta)
self.experiment.log_parameter("sigma", sigma)
def log_round(self, states, reward, cumulative_reward, info, loss, observations, step):
self.experiment.log_histogram_3d(states, name="Observations", step=step)
info = [[j for j in i.split("|")] for i in info]
info = np.mean(np.array(info, dtype=np.float32), axis=0)
try:
# round_mb = np.mean([float(i.split("|")[0]) for i in info])
round_mb = info[0]
except Exception as e:
print(info)
print(reward)
raise e
self.speed_window.append(round_mb)
self.current_speed = np.mean(np.asarray(self.speed_window)/self.step_time)
self.sent_mb += round_mb
# CW = np.mean([float(i.split("|")[1]) for i in info])
CW = info[1]
# stations = np.mean([float(i.split("|")[2]) for i in info])
self.stations = info[2]
fairness = info[3]
if self.send_logs:
self.experiment.log_metric("Round reward", np.mean(reward), step=step)
self.experiment.log_metric("Per-ep reward", np.mean(cumulative_reward), step=step)
self.experiment.log_metric("Megabytes sent", self.sent_mb, step=step)
self.experiment.log_metric("Round megabytes sent", round_mb, step=step)
self.experiment.log_metric("Chosen CW", CW, step=step)
self.experiment.log_metric("Station count", self.stations, step=step)
self.experiment.log_metric("Current throughput", self.current_speed, step=step)
self.experiment.log_metric("Fairness index", fairness, step=step)
for i, obs in enumerate(observations):
self.experiment.log_metric(f"Observation {i}", obs, step=step)
self.experiment.log_metrics(loss, step=step)
def log_episode(self, cumulative_reward, speed, step):
if self.send_logs:
self.experiment.log_metric("Cumulative reward", cumulative_reward, step=step)
self.experiment.log_metric("Speed", speed, step=step)
self.sent_mb = 0
self.last_speed = speed
self.speed_window = deque(maxlen=100)
self.current_speed = 0
def end(self):
if self.send_logs:
self.experiment.end()
EPOCHS = 3
STEPS = 3
SIZE = 1000
MAX_TRIES = 20
def make_values(mu, sigma):
return [random.gauss(mu, sigma) for r in range(SIZE)]
print("Logging...")
for epoch in range(EPOCHS):
for step in range(STEPS):
e.log_histogram_3d(make_values(epoch * 10, 1 + step),
"%s/v1" % epoch,
step=step)
print("Uploading...")
e.end()
print("Testing...")
api = API(cache=False)
apie = APIExperiment(previous_experiment=e.id, api=api)
histograms_json = apie.get_asset_list("histogram_combined_3d")
count = 0
while len(histograms_json) != EPOCHS and count < MAX_TRIES:
print("Retry get assets...")
histograms_json = apie.get_asset_list("histogram_combined_3d")
count += 1
class experiment_logger:
'''
Interface for logging experiments on neptune, comet, or both.
Args: log_backend, project_name)
Other backends may also be added in the future
Currently defined methods:
add_params:
add_tags:
log_text: strings
log_metrics: numerical values
log_figure: pyplot figures
stop: end logging and close connection
'''
def __init__(self, log_backend, project_name):
'''
Parameters
----------
log_backend : STR
One of 'comet', 'neptune', 'all'
project_name : STR
one of available proyects ('yeast', 'jersey', 'wheat', 'debug', etc)
Returns
-------
None.
'''
self.proj_name = project_name
self.backend = log_backend
#Bool indicating wether neptune logging is enabled
self.neptune = log_backend=='neptune' or log_backend=='all'
#Bool indicating wether comet logging is enabled
self.comet = log_backend=='comet' or log_backend=='all'
if self.neptune:
neptune.init("dna-i/"+project_name,
api_token='eyJhcGlfYWRkcmVzcyI6Imh0dHBzOi8vdWkubmVwdHVuZS5haSIsImFwaV91cmwiOiJodHRwczovL3VpLm5lcHR1bmUuYWkiLCJhcGlfa2V5IjoiMWYzMzhjMjItYjczNC00NzZhLWFlZTYtOTI2NzE5MzUwZmNkIn0=')
print("logging experiments on neptune project "+project_name)
neptune.create_experiment()
if self.comet:
self.comet_experiment = Experiment(api_key="V0OXnWOi4KVNS4OkwLjdnxSgK",
project_name=project_name, workspace="dna-i")
print("logging experiments on comet project "+project_name)
if not (self.neptune or self.comet):
raise ValueError('Logging Backend NOT Available')
def add_params(self, params, step=None ):
'''
Adds parameters to experiment log
Parameters
----------
params : Dict
Key-Value pairs
Returns
-------
None.
'''
if self.neptune:
for key, value in params.items():
neptune.set_property(key, value)
if step is not None:
neptune.set_property('step', step)
if self.comet:
self.comet_experiment.log_parameters(params,step=step)
def add_tags(self, tags):
'''
Adds parameters to experiment log
Parameters
----------
params : tags
list of tags (strings)
e.g.: ['tag1', 'tag2']
Returns
-------
None.
'''
if self.neptune:
neptune.append_tag(tags)
if self.comet:
self.comet_experiment.add_tags(tags)
def log_metrics(self, name, value, epoch=None):
'''
Logging pointwise metrics
Parameters
----------
name : STR
Metric key
value : Float/Integer/(Boolean/String)
Comet also allows Boolean/string
Tuples are lallowed
epoch: (OPT) INT
Epoch - or anything used as x axis when plotting metrics
Returns
-------
None.
'''
if self.neptune:
try:
if epoch is not None:
if type(value) is tuple:
print("Logging tuple as r and p-value")
for val, n in zip(value, [" (r)", " (p-val)"]):
neptune.log_metric(name + n,epoch,y=val)
else:
neptune.log_metric(name, epoch, y=value)
else:
if type(value) is tuple:
print("Logging tuple as r and p-value")
for val, n in zip(value, [" (r)", " (p-val)"]):
neptune.log_metric(name+n, val)
else:
neptune.log_metric(name, value)
except:
print("Metric type {} not supported by neptune.".format(type(value)))
print("logging as text")
self.log_text( "{}".format(value), key=name)
if self.comet:
try:
if epoch is not None:
if type(value) is tuple:
print("Logging tuple as r and p-value")
for val, n in zip(value, [" (r)", " (p-val)"]):
self.comet_experiment.log_metric(name+n, val, step=int(epoch))
else:
self.comet_experiment.log_metric(name, value, epoch=epoch)
else:
if type(value) is tuple:
print("Logging tuple as r and p-value")
for val, n in zip(value, [" (r)", " (p-val)"]):
self.comet_experiment.log_metric(name+n, val)
else:
self.comet_experiment.log_metric(name, value)
except:
print("Metric type {} not supported by comet.".format(type(value)))
if type(value) is tuple:
print("Logging tuple as x-y pairs")
for idx, val in enumerate(value):
self.comet_experiment.log_metric(name, val, epoch=idx)
else:
print("Logging as other.")
self.comet_experiment.log_other(name, value)
def log_text(self, string, key=None, epoch=None):
'''
Logs text strings
Parameters
----------
string : STR
text to log
key: STR
log_name needed for Neptune strings
epoch: INT
epoch or any other index
Returns
-------
None.
'''
if self.neptune:
if type(string) is str:
if key is None:
print('Neptune log_name needed for logging text')
print('Using a dummy name: text')
neptune.log_text('text', string)
if epoch is None:
neptune.log_text(key, string)
else:
neptune.log_text(key, epoch, y=string)
else:
print("Wrong type: logging text must be a string")
if self.comet:
if type(string) is str:
if key is not None:
print("Commet text logging does not support keys, prepending it to text")
string = key+ ', '+string
if epoch is None:
self.comet_experiment.log_text(string)
else:
self.comet_experiment.log_text(string, step=epoch)
else:
print("Wrong type: logging text must be a string")
def log_figure(self, figure=None, figure_name=None, step=None):
'''
Logs pyplot figure
Parameters
----------
figure : pyplot figure, optional in comet mandatory in neptune.
The default is None, uses global pyplot figure.
figure_name : STR, optional in comet mandatory in neptune.
The default is None.
step : INT, optional
An index. The default is None.
Returns
-------
None.
'''
if self.neptune:
if figure is not None:
if figure_name is None:
print("Figure name must be given to neptune logger")
print("Using dummy name: figure")
figure_name = 'figure'
if step is None:
neptune.log_image(figure_name, figure)
else:
neptune.log_image(figure_name, step, y=figure)
else:
print("A figure must be passed to neptune logger")
if self.comet:
self.comet_experiment.log_figure(figure_name=figure_name, figure=figure, step=step)
def stop(self):
if self.neptune:
neptune.stop()
if self.comet:
self.comet_experiment.end()
def add_table(self, filename, tabular_data=None, headers=False):
self.comet_experiment.log_table(filename, tabular_data, headers)
def log_image(self, image=None, figure_name=None, step=None):
'''
Logs pyplot figure
Parameters
----------
figure : pyplot figure, optional in comet mandatory in neptune.
The default is None, uses global pyplot figure.
figure_name : STR, optional in comet mandatory in neptune.
The default is None.
step : INT, optional
An index. The default is None.
Returns
-------
None.
'''
self.log_image(image, name=figure_name, overwrite=False, image_format="png", image_scale=1.0, \
image_shape=None, image_colormap=None, image_minmax=None, image_channels="last", \
copy_to_tmp=True, step=step)
def log_hist3d(self, values=None, figure_name=None, step=None):
'''
Logs pyplot figure
Parameters
----------
figure : pyplot figure, optional in comet mandatory in neptune.
The default is None, uses global pyplot figure.
figure_name : STR, optional in comet mandatory in neptune.
The default is None.
step : INT, optional
An index. The default is None.
Returns
-------
None.
'''
if self.neptune:
print("not implemented")
if self.comet:
self.comet_experiment.log_histogram_3d(values, name=figure_name, step=step)
def log_table(self, name=None, data=None, headers=False):
'''
Parameters
----------
name : str
Table name
data : array, list
headers : TYPE, optional
wether to use headers
Returns
-------
None.
'''
self.comet_experiment.log_table(name+'.csv', tabular_data= data, headers = headers )
class ActiveLearning():
def __init__(self, config):
self.pipeIter = None
self.homedir = os.getcwd()
self.episode = 0
self.config = config
self.runNum = self.config.run_num
self.oracle = Oracle(self.config) # oracle needs to be initialized to initialize toy datasets
self.agent = ParameterUpdateAgent(self.config)
self.querier = Querier(self.config) # might as well initialize the querier here
self.setup()
self.getModelSize()
# Comet
if config.al.comet.project:
self.comet = Experiment(
project_name=config.al.comet.project, display_summary_level=0,
)
if config.al.comet.tags:
if isinstance(config.al.comet.tags, list):
self.comet.add_tags(config.al.comet.tags)
else:
self.comet.add_tag(config.al.comet.tags)
self.comet.set_name("run {}".format(config.run_num))
self.comet.log_parameters(vars(config))
with open(Path(self.workDir) / "comet_al.url", "w") as f:
f.write(self.comet.url + "\n")
else:
self.comet = None
# Save YAML config
with open(self.workDir + '/config.yml', 'w') as f:
yaml.dump(numpy2python(namespace2dict(self.config)), f, default_flow_style=False)
def setup(self):
'''
setup working directory
move to relevant directory
:return:
'''
if self.config.run_num == 0: # if making a new workdir
self.makeNewWorkingDirectory()
self.reset()
elif (self.config.explicit_run_enumeration == True):
self.workDir = self.config.workdir + '/run%d'%self.config.run_num # explicitly enumerate the new run directory
os.mkdir(self.workDir)
self.reset()
else:
# move to working dir
self.workDir = self.config.workdir + '/' + 'run%d' %self.config.run_num
os.chdir(self.workDir)
printRecord('Resuming run %d' % self.config.run_num)
def reset(self):
os.chdir(self.homedir)
os.mkdir(f'{self.workDir}/ckpts')
os.mkdir(f'{self.workDir}/episode{self.episode}')
os.mkdir(f'{self.workDir}/episode{self.episode}/ckpts')
os.mkdir(f'{self.workDir}/episode{self.episode}/datasets')
os.chdir(f'{self.workDir}/episode{self.episode}') # move to working dir
printRecord('Starting Fresh Run %d' %self.runNum)
self.oracle.initializeDataset() # generate toy model dataset
self.stateDict = None
self.totalLoss = None
self.testMinima = None
self.stateDictRecord = None
self.reward = None
self.terminal = None
self.model = None
self.cumulative_reward = None
self.reward_list = None
self.bottomTenLoss = None
self.action = None
self.trueMinimum = None
self.oracleRecord = None
self.bestScores = None
self.prev_iter_best = None
def makeNewWorkingDirectory(self): # make working directory
'''
make a new working directory
non-overlapping previous entries
:return:
'''
workdirs = glob.glob(self.config.workdir + '/' + 'run*') # check for prior working directories
if len(workdirs) > 0:
prev_runs = []
for i in range(len(workdirs)):
prev_runs.append(int(workdirs[i].split('run')[-1]))
prev_max = max(prev_runs)
self.workDir = self.config.workdir + '/' + 'run%d' %(prev_max + 1)
self.config.workdir = self.workDir
os.mkdir(self.workDir)
self.runNum = int(prev_max + 1)
else:
self.workDir = self.config.workdir + '/' + 'run1'
os.mkdir(self.workDir)
def runPipeline(self):
'''
run the active learning pipeline for a number of iterations
:return:
'''
self.config.dataset_size = self.config.dataset.init_length
for _ in range(self.config.al.episodes):
if self.config.dataset.type == 'toy':
self.sampleOracle() # use the oracle to pre-solve the problem for future benchmarking
self.testMinima = [] # best test loss of models, for each iteration of the pipeline
self.bestScores = [] # best optima found by the sampler, for each iteration of the pipeline
for self.pipeIter in range(self.config.al.n_iter):
printRecord(f'Starting pipeline iteration #{bcolors.FAIL}%d{bcolors.ENDC}' % int(self.pipeIter+1))
if self.pipeIter == (self.config.al.n_iter - 1):
self.terminal = 1
else:
self.terminal = 0
self.iterate() # run the pipeline
self.saveOutputs() # save pipeline outputs
# Train Policy Network - for learned AL acquisition function / policy only
# self.agent.train(BATCH_SIZE=self.config.al.q_batch_size)
#self.policy_error = self.agent.policy_error
#if self.config.al.episodes > (self.episode + 1): # if we are doing multiple al episodes
# self.reset()
# self.episode += 1
#Save Memory for Agent architecture testing
#numpy.save(f'{self.workDir}/memory.npy', self.agent.memory.memory)
#numpy.save(f'{self.workDir}/agent_error.npy', self.agent.policy_error)
def iterate(self):
'''
run one iteration of the pipeline - train model, sample sequences, select sequences, consult oracle
:return:
'''
t0 = time.time()
self.retrainModels()
printRecord('Retraining took {} seconds'.format(int(time.time()-t0)))
t0 = time.time()
self.getModelState(self.terminal) # run energy-only sampling and create model state dict
self.getDatasetReward()
printRecord('Model state calculation took {} seconds'.format(int(time.time()-t0)))
if self.terminal == 0: # skip querying if this is our final pipeline iteration
t0 = time.time()
query = self.querier.buildQuery(self.model, self.stateDict, action=self.action, comet=self.comet) # pick Samples to be scored
printRecord('Query generation took {} seconds'.format(int(time.time()-t0)))
t0 = time.time()
energies = self.oracle.score(query) # score Samples
printRecord('Oracle scoring took {} seconds'.format(int(time.time()-t0)))
printRecord('Oracle scored' + bcolors.OKBLUE + ' {} '.format(len(energies)) + bcolors.ENDC + 'queries with average score of' + bcolors.OKGREEN + ' {:.3f}'.format(np.average(energies)) + bcolors.ENDC + ' and minimum score of {:.3f}'.format(np.amin(energies)))
self.updateDataset(query, energies) # add scored Samples to dataset
if self.comet: # report query scores to comet
self.comet.log_histogram_3d(energies,name='query energies',step=self.pipeIter)
# CODE FOR LEARNED POLICY
#if self.config.al.hyperparams_learning:# and (self.pipeIter > 0):
# model_state_prev, model_state_curr = self.agent.updateModelState(self.stateDict, self.model)
# if model_state_prev is not None:
# self.agent.push_to_buffer(model_state_prev, self.action, model_state_curr, self.reward, self.terminal)
# self.action = self.agent.getAction()
#else:
# self.action = None
def getModelState(self, terminal):
'''
sample the model
report on the status of dataset
report on best scores according to models
report on model confidence
:return:
'''
# run the sampler
self.loadEstimatorEnsemble()
if terminal: # use the query-generating sampler for terminal iteration
sampleDict = self.querier.runSampling(self.model, scoreFunction = [1, 0], al_iter = self.pipeIter) # sample existing optima using standard sampler
else: # use a cheap sampler for mid-run model state calculations
sampleDict = self.querier.runSampling(self.model, scoreFunction = [1, 0], al_iter = self.pipeIter, method_overwrite = 'random') # sample existing optima cheaply with random + annealing
sampleDict = filterOutputs(sampleDict)
# we used to do clustering here, now strictly argsort direct from the sampler
sort_inds = np.argsort(sampleDict['energies']) # sort by energy
samples = sampleDict['samples'][sort_inds][:self.config.querier.model_state_size] # top-k samples from model state run
energies = sampleDict['energies'][sort_inds][:self.config.querier.model_state_size]
uncertainties = sampleDict['uncertainties'][sort_inds][:self.config.querier.model_state_size]
# get distances to relevant datasets
internalDist, datasetDist, randomDist = self.getDataDists(samples)
self.getModelStateReward(energies, uncertainties)
self.stateDict = {
'test loss': np.average(self.testMinima), # losses are evaluated on standardized data, so we do not need to re-standardize here
'test std': np.sqrt(np.var(self.testMinima)),
'all test losses': self.testMinima,
'best energies': energies, # these are already standardized #(energies - self.model.mean) / self.model.std, # standardize according to dataset statistics
'best uncertanties': uncertainties, # these are already standardized #uncertainties / self.model.std,
'best samples': samples,
'best samples internal diff': internalDist,
'best samples dataset diff': datasetDist,
'best samples random set diff': randomDist,
'clustering cutoff': self.config.al.minima_dist_cutoff, # could be a learned parameter
'n proxy models': self.config.proxy.ensemble_size,
'iter': self.pipeIter,
'budget': self.config.al.n_iter,
'model state reward': self.model_state_reward
}
printRecord('%d '%self.config.proxy.ensemble_size + f'Model ensemble training converged with average test loss of {bcolors.OKCYAN}%.5f{bcolors.ENDC}' % np.average(np.asarray(self.testMinima[-self.config.proxy.ensemble_size:])) + f' and std of {bcolors.OKCYAN}%.3f{bcolors.ENDC}'%(np.sqrt(np.var(self.testMinima[-self.config.proxy.ensemble_size:]))))
printRecord('Model state contains {} samples'.format(self.config.querier.model_state_size) +
' with minimum energy' + bcolors.OKGREEN + ' {:.2f},'.format(np.amin(energies)) + bcolors.ENDC +
' average energy' + bcolors.OKGREEN +' {:.2f},'.format(np.average(energies[:self.config.querier.model_state_size])) + bcolors.ENDC +
' and average std dev' + bcolors.OKCYAN + ' {:.2f}'.format(np.average(uncertainties[:self.config.querier.model_state_size])) + bcolors.ENDC)
printRecord("Best sample in model state is {}".format(numbers2letters(samples[np.argmin(energies)])))
printRecord('Sample average mutual distance is ' + bcolors.WARNING +'{:.2f} '.format(np.average(internalDist)) + bcolors.ENDC +
'dataset distance is ' + bcolors.WARNING + '{:.2f} '.format(np.average(datasetDist)) + bcolors.ENDC +
'and overall distance estimated at ' + bcolors.WARNING + '{:.2f}'.format(np.average(randomDist)) + bcolors.ENDC)
if self.config.al.large_model_evaluation: # we can quickly check the test error against a huge random dataset
self.largeModelEvaluation()
if self.comet:
self.comet.log_metric(name='proxy loss on best 10% of large random dataset',value = self.bottomTenLoss[0], step=self.pipeIter)
self.comet.log_metric(name='proxy loss on large random dataset', value = self.totalLoss[0], step=self.pipeIter)
if self.pipeIter == 0: # if it's the first round, initialize, else, append
self.stateDictRecord = [self.stateDict]
else:
self.stateDictRecord.append(self.stateDict)
if self.comet:
self.comet.log_histogram_3d(sampleDict['energies'], name='model state total sampling run energies', step = self.pipeIter)
self.comet.log_histogram_3d(sampleDict['uncertainties'], name='model state total sampling run std deviations', step = self.pipeIter)
self.comet.log_histogram_3d(energies[:self.config.querier.model_state_size], name='model state energies', step=self.pipeIter)
self.comet.log_histogram_3d(uncertainties[:self.config.querier.model_state_size], name='model state std deviations', step=self.pipeIter)
self.comet.log_histogram_3d(internalDist, name='model state internal distance', step=self.pipeIter)
self.comet.log_histogram_3d(datasetDist, name='model state distance from dataset', step=self.pipeIter)
self.comet.log_histogram_3d(randomDist, name='model state distance from large random sample', step=self.pipeIter)
self.comet.log_histogram_3d(self.testMinima[-1], name='proxy model test minima', step=self.pipeIter)
self.logTopK(sampleDict, prefix = "Model state ")
def getModelStateReward(self,bestEns,bestStdDevs):
'''
print the performance of the learner against a known best answer
:param bestEns:
:param bestVars:
:return:
'''
# get the best results in the standardized basis
best_ens_standardized = (bestEns - self.model.mean)/self.model.std
standardized_standard_deviations = bestStdDevs / self.model.std
adjusted_standardized_energies = best_ens_standardized + standardized_standard_deviations # consider std dev as an uncertainty envelope and take the high end
best_standardized_adjusted_energy = np.amin(adjusted_standardized_energies)
# convert to raw outputs basis
adjusted_energies = bestEns + bestStdDevs
best_adjusted_energy = np.amin(adjusted_energies) # best energy, adjusted for uncertainty
if self.pipeIter == 0:
self.model_state_reward = 0 # first iteration - can't define a reward
self.model_state_cumulative_reward = 0
self.model_state_reward_list = np.zeros(self.config.al.n_iter)
self.model_state_prev_iter_best = [best_adjusted_energy]
else: # calculate reward using current standardization
stdprev_iter_best = (self.model_state_prev_iter_best[-1] - self.model.mean)/self.model.std
self.model_state_reward = -(best_standardized_adjusted_energy - stdprev_iter_best) # reward is the delta between variance-adjusted energies in the standardized basis (smaller is better)
self.model_state_reward_list[self.pipeIter] = self.model_state_reward
self.model_state_cumulative_reward = sum(self.model_state_reward_list)
self.model_state_prev_iter_best.append(best_adjusted_energy)
printRecord('Iteration best uncertainty-adjusted result = {:.3f}, previous best = {:.3f}, reward = {:.3f}, cumulative reward = {:.3f}'.format(best_adjusted_energy, self.model_state_prev_iter_best[-2], self.model_state_reward, self.model_state_cumulative_reward))
if self.config.dataset.type == 'toy': # if it's a toy dataset, report the cumulative performance against the known minimum
stdTrueMinimum = (self.trueMinimum - self.model.mean) / self.model.std
if self.pipeIter == 0:
self.model_state_abs_score = [1 - np.abs(self.trueMinimum - best_adjusted_energy) / np.abs(self.trueMinimum)]
self.model_state_cumulative_score=0
elif self.pipeIter > 0:
# we will compute the distance from our best answer to the correct answer and integrate it over the number of samples in the dataset
xaxis = self.config.dataset_size + np.arange(0,self.pipeIter + 1) * self.config.al.queries_per_iter # how many samples in the dataset used for each
self.model_state_abs_score.append(1 - np.abs(self.trueMinimum - best_adjusted_energy) / np.abs(self.trueMinimum)) # compute proximity to correct answer in standardized basis
self.model_state_cumulative_score = np.trapz(y=np.asarray(self.model_state_abs_score), x=xaxis)
self.model_state_normed_cumulative_score = self.model_state_cumulative_score / xaxis[-1]
printRecord('Total score is {:.3f} and {:.5f} per-sample after {} samples'.format(self.model_state_abs_score[-1], self.model_state_normed_cumulative_score, xaxis[-1]))
else:
print('Error! Pipeline iteration cannot be negative')
sys.exit()
if self.comet:
self.comet.log_metric(name = "model state absolute score", value = self.model_state_abs_score[-1], step = self.pipeIter)
self.comet.log_metric(name = "model state cumulative score", value = self.model_state_cumulative_score, step = self.pipeIter)
self.comet.log_metric(name = "model state reward", value = self.model_state_reward, step = self.pipeIter)
def getDatasetReward(self):
'''
print the performance of the learner against a known best answer
:param bestEns:
:param bestVars:
:return:
'''
dataset = np.load('datasets/' + self.config.dataset.oracle + '.npy', allow_pickle=True).item()
energies = dataset['energies']
printRecord("Best sample in dataset is {}".format(numbers2letters(dataset['samples'][np.argmin(dataset['energies'])])))
best_energy = np.amin(energies)
if self.pipeIter == 0:
self.dataset_reward = 0 # first iteration - can't define a reward
self.dataset_cumulative_reward = 0
self.dataset_reward_list = np.zeros(self.config.al.n_iter)
self.dataset_prev_iter_best = [best_energy]
else: # calculate reward using current standardization
self.dataset_reward = (best_energy - self.dataset_prev_iter_best[-1]) / self.dataset_prev_iter_best[-1] # reward is the delta between variance-adjusted energies in the standardized basis (smaller is better)
self.dataset_reward_list[self.pipeIter] = self.dataset_reward
self.dataset_cumulative_reward = sum(self.dataset_reward_list)
self.dataset_prev_iter_best.append(best_energy)
printRecord('Dataset evolution metrics = {:.3f}, previous best = {:.3f}, reward = {:.3f}, cumulative reward = {:.3f}'.format(best_energy, self.dataset_prev_iter_best[-2], self.dataset_reward, self.dataset_cumulative_reward))
if self.config.dataset.type == 'toy': # if it's a toy dataset, report the cumulative performance against the known minimum
stdTrueMinimum = (self.trueMinimum - self.model.mean) / self.model.std
if self.pipeIter == 0:
self.dataset_abs_score = [1 - np.abs(self.trueMinimum - best_energy) / np.abs(self.trueMinimum)]
self.dataset_cumulative_score=0
elif self.pipeIter > 0:
# we will compute the distance from our best answer to the correct answer and integrate it over the number of samples in the dataset
xaxis = self.config.dataset_size + np.arange(0,self.pipeIter + 1) * self.config.al.queries_per_iter # how many samples in the dataset used for each
self.dataset_abs_score.append(1 - np.abs(self.trueMinimum - best_energy) / np.abs(self.trueMinimum)) # compute proximity to correct answer in standardized basis
self.dataset_cumulative_score = np.trapz(y=np.asarray(self.dataset_abs_score), x=xaxis)
self.dataset_normed_cumulative_score = self.dataset_cumulative_score / xaxis[-1]
printRecord('Dataset Total score is {:.3f} and {:.5f} per-sample after {} samples'.format(self.dataset_abs_score[-1], self.dataset_normed_cumulative_score, xaxis[-1]))
else:
print('Error! Pipeline iteration cannot be negative')
sys.exit()
if self.comet:
self.comet.log_metric(name = "dataset absolute score", value = self.dataset_abs_score[-1], step = self.pipeIter)
self.comet.log_metric(name = "dataset cumulative score", value = self.dataset_cumulative_score, step = self.pipeIter)
self.comet.log_metric(name = "dataset reward", value = self.dataset_reward, step = self.pipeIter)
def retrainModels(self):
testMins = []
for i in range(self.config.proxy.ensemble_size):
self.resetModel(i) # reset between ensemble estimators EVERY ITERATION of the pipeline
self.model.converge() # converge model
testMins.append(np.amin(self.model.err_te_hist))
if self.comet:
tr_hist = self.model.err_tr_hist
te_hist = self.model.err_te_hist
epochs = len(te_hist)
for i in range(epochs):
self.comet.log_metric('proxy train loss iter {}'.format(self.pipeIter), step=i, value=tr_hist[i])
self.comet.log_metric('proxy test loss iter {}'.format(self.pipeIter), step=i, value=te_hist[i])
self.testMinima.append(testMins)
def loadEstimatorEnsemble(self):
'''
load all the trained models at their best checkpoints
and initialize them in an ensemble model where they can all be queried at once
:return:
'''
ensemble = []
for i in range(self.config.proxy.ensemble_size):
self.resetModel(i)
self.model.load(i)
ensemble.append(self.model.model)
del self.model
self.model = modelNet(self.config,0)
self.model.loadEnsemble(ensemble)
self.model.getMinF()
#print('Loaded {} estimators'.format(int(self.config.proxy.ensemble_size)))
def resetModel(self,ensembleIndex, returnModel = False):
'''
load a new instance of the model with reset parameters
:return:
'''
try: # if we have a model already, delete it
del self.model
except:
pass
self.model = modelNet(self.config,ensembleIndex)
#printRecord(f'{bcolors.HEADER} New model: {bcolors.ENDC}', getModelName(ensembleIndex))
if returnModel:
return self.model
def getModelSize(self):
self.model = modelNet(self.config, 0)
nParams = get_n_params(self.model.model)
printRecord('Proxy model has {} parameters'.format(int(nParams)))
del(self.model)
def largeModelEvaluation(self):
'''
if we are using a toy oracle, we should be able to easily get the test loss on a huge sample of the dataset
:return:
'''
self.loadEstimatorEnsemble()
numSamples = min(int(1e3), self.config.dataset.dict_size ** self.config.dataset.max_length // 100) # either 1e5, or 1% of the sample space, whichever is smaller
randomData = self.oracle.initializeDataset(save=False, returnData=True, customSize=numSamples) # get large random dataset
randomSamples = randomData['samples']
randomScores = randomData['energies']
sortInds = np.argsort(randomScores) # sort randoms
randomSamples = randomSamples[sortInds]
randomScores = randomScores[sortInds]
modelScores, modelStd = [[],[]]
sampleLoader = data.DataLoader(randomSamples, batch_size = self.config.proxy.mbsize, shuffle=False, num_workers = 0, pin_memory=False)
for i, testData in enumerate(sampleLoader):
score, std_dev = self.model.evaluate(testData.float(), output='Both')
modelScores.extend(score)
modelStd.extend(std_dev)
bestTenInd = numSamples // 10
totalLoss = F.mse_loss((torch.Tensor(modelScores).float() - self.model.mean) / self.model.std, (torch.Tensor(randomScores).float() - self.model.mean) / self.model.std) # full dataset loss (standardized basis)
bottomTenLoss = F.mse_loss((torch.Tensor(modelScores[:bestTenInd]).float() - self.model.mean) / self.model.std, (torch.Tensor(randomScores[:bestTenInd]).float() - self.model.mean) / self.model.std) # bottom 10% loss (standardized basis)
if self.pipeIter == 0: # if it's the first round, initialize, else, append
self.totalLoss = [totalLoss]
self.bottomTenLoss = [bottomTenLoss]
else:
self.totalLoss.append(totalLoss)
self.bottomTenLoss.append(bottomTenLoss)
printRecord("Model has overall loss of" + bcolors.OKCYAN + ' {:.5f}, '.format(totalLoss) + bcolors.ENDC + 'best 10% loss of' + bcolors.OKCYAN + ' {:.5f} '.format(bottomTenLoss) + bcolors.ENDC + 'on {} toy dataset samples'.format(numSamples))
def runPureSampler(self):
ti = time.time()
self.model = None
self.pipeIter = 0
if self.config.al.sample_method == 'mcmc':
gammas = np.logspace(self.config.mcmc.stun_min_gamma, self.config.mcmc.stun_max_gamma, self.config.mcmc.num_samplers)
mcmcSampler = Sampler(self.config, self.config.seeds.sampler, [1,0], gammas)
sampleDict = mcmcSampler.sample(self.model, useOracle=True) # do a genuine search
elif self.config.al.sample_method == 'random':
samples = generateRandomSamples(self.config.al.num_random_samples,
[self.config.dataset.min_length,self.config.dataset.max_length],
self.config.dataset.dict_size,
variableLength = self.config.dataset.variable_length,
seed = self.config.seeds.sampler)
outputs = {
'samples': samples,
'energies': self.oracle.score(samples),
'scores': np.zeros(len(samples)),
'uncertainties': np.zeros(len(samples))
}
sampleDict = self.querier.doAnnealing([1,0], model, outputs, useOracle=True)
elif self.config.al.sample_method == 'gflownet':
gflownet = GFlowNetAgent(self.config, comet = self.comet, proxy=None, al_iter=0, data_path=None)
t0 = time.time()
gflownet.train()
printRecord('Training GFlowNet took {} seconds'.format(int(time.time()-t0)))
t0 = time.time()
sampleDict, times = gflownet.sample(
self.config.gflownet.n_samples, self.config.dataset.max_length,
self.config.dataset.min_length, self.config.dataset.dict_size,
self.config.gflownet.min_word_len,
self.config.gflownet.max_word_len, self.oracle.score, get_uncertainties=False
)
printRecord('Sampling {} samples from GFlowNet took {} seconds'.format(self.config.gflownet.n_samples, int(time.time()-t0)))
sampleDict['uncertainties'] = np.zeros(len(sampleDict['energies']))
sampleDict = filterOutputs(sampleDict)
if self.config.gflownet.annealing:
sampleDict = self.querier.doAnnealing([1, 0], model, sampleDict, useOracle=True)
sampleDict = filterOutputs(sampleDict) # remove duplicates
# take only the top XX samples, for memory purposes
maxLen = 10000
if len(sampleDict['samples']) > maxLen:
bestInds = np.argsort(sampleDict['energies'])[:maxLen]
for key in sampleDict.keys():
sampleDict[key] = sampleDict[key][bestInds]
self.logTopK(sampleDict, prefix = "Pure sampling")
# run clustering as a form of diversity analysis
# more clusters means more diverse
# this way won't penalize one (e.g., MCMC) for badly oversampling one area
# only penalize it for not sampling *enough distinct areas*
clusters, clusterScores, clusterVars = doAgglomerativeClustering(
sampleDict['samples'], sampleDict['scores'],
sampleDict['uncertainties'], self.config.dataset.dict_size,
cutoff=self.config.al.minima_dist_cutoff)
clusterDict = {
'energies': np.asarray([np.amin(cluster_scores) for cluster_scores in clusterScores]),
'samples': np.asarray([cluster[0] for cluster in clusters]) # this one doesn't matter
}
top_cluster_energies = self.logTopK(clusterDict, prefix = "Pure sampling - clusters", returnScores=True)
# identify the clusters within XX% of the known global minimum
global_minimum = min(np.amin(sampleDict['energies']), self.getTrueMinimum(sampleDict))
found_minimum = np.amin(sampleDict['energies'])
bottom_ranges = [10, 25, 50] # percent difference from known minimum
abs_cluster_numbers = []
rel_cluster_numbers = []
for bottom_range in bottom_ranges:
global_minimum_cutoff = global_minimum - bottom_range * global_minimum / 100
found_minimum_cutoff = found_minimum - bottom_range * found_minimum / 100
n_low_clusters1 = np.sum(clusterDict['energies'] < global_minimum_cutoff)
n_low_clusters2 = np.sum(clusterDict['energies'] < found_minimum_cutoff)
abs_cluster_numbers.append(n_low_clusters1)
rel_cluster_numbers.append(n_low_clusters2)
if self.comet:
self.comet.log_metric("Number of clusters {} % from known minimum with {} cutoff".format(bottom_range, self.config.al.minima_dist_cutoff),
n_low_clusters1)
self.comet.log_metric("Number of clusters {} % from found minimum with {} cutoff".format(bottom_range, self.config.al.minima_dist_cutoff),
n_low_clusters2)
if self.comet:
self.comet.log_histogram_3d(sampleDict['energies'], name="pure sampling energies", step=0)
self.comet.log_metric("Best energy", np.amin(sampleDict['energies']))
self.comet.log_metric("Proposed true minimum", self.trueMinimum)
self.comet.log_metric("Best sample", numbers2letters(sampleDict['samples'][np.argmin(sampleDict["energies"])]))
print("Key metrics:")
print("Best found sample was {}".format(numbers2letters(sampleDict['samples'][np.argmin(sampleDict['energies'])])))
print("Top K Cluster Energies {:.3f} {:.3f} {:.3f}".format(top_cluster_energies[0], top_cluster_energies[1], top_cluster_energies[2]))
print("Top K Absolute # Clusters {} {} {}".format(abs_cluster_numbers[0], abs_cluster_numbers[1], abs_cluster_numbers[2]))
print("Top K Relative # Clusters {} {} {}".format(rel_cluster_numbers[0], rel_cluster_numbers[1], rel_cluster_numbers[2]))
print("Proposed True Global Minimum is {}".format(global_minimum))
print("Pure sampling took a total of {} seconds".format(int(time.time()-ti)))
return sampleDict
def sampleOracle(self):
'''
for toy models
do global optimization directly on the oracle to find the true minimum
:return:
'''
printRecord("Asking toy oracle for the true minimum")
self.model = 'abc'
gammas = np.logspace(self.config.mcmc.stun_min_gamma,self.config.mcmc.stun_max_gamma,self.config.mcmc.num_samplers)
mcmcSampler = Sampler(self.config, 0, [1,0], gammas)
if (self.config.dataset.oracle == 'linear') or ('nupack' in self.config.dataset.oracle):
sampleDict = mcmcSampler.sample(self.model, useOracle=True, nIters = 100) # do a tiny number of iters - the minimum is known
else:
sampleDict = mcmcSampler.sample(self.model, useOracle=True) # do a genuine search
bestMin = self.getTrueMinimum(sampleDict)
printRecord(f"Sampling Complete! Lowest Energy Found = {bcolors.FAIL}%.3f{bcolors.ENDC}" % bestMin + " from %d" % self.config.mcmc.num_samplers + " sampling runs.")
printRecord("Best sample found is {}".format(numbers2letters(sampleDict['samples'][np.argmin(sampleDict['energies'])])))
self.oracleRecord = sampleDict
self.trueMinimum = bestMin
if self.comet:
self.comet.log_histogram_3d(sampleDict['energies'], name="energies_true",step=0)
def getTrueMinimum(self, sampleDict):
if self.config.dataset.oracle == 'wmodel': # w model minimum is always zero - even if we don't find it
bestMin = 0
else:
bestMin = np.amin(sampleDict['energies'])
if 'nupack' in self.config.dataset.oracle: # compute minimum energy for this length - for reweighting purposes
goodSamples = np.ones((4, self.config.dataset.max_length)) * 4 # GCGC CGCG GGGCCC CCCGGG
goodSamples[0,0:-1:2] = 3
goodSamples[1,1:-1:2] = 3
goodSamples[2,:self.config.dataset.max_length//2] = 3
goodSamples[3,self.config.dataset.max_length//2:] = 3
min_nupack_ens = self.oracle.score(goodSamples)
# append suggestions for known likely solutions
if self.config.dataset.oracle == "linear":
goodSamples = np.zeros((4,self.config.dataset.max_length)) # all of one class usually best
goodSamples[0] = goodSamples[1] + 1
goodSamples[1] = goodSamples[1] + 2
goodSamples[2] = goodSamples[2] + 3
goodSamples[3] = goodSamples[3] + 4
ens = self.oracle.score(goodSamples)
if np.amin(ens) < bestMin:
bestMin = np.amin(ens)
printRecord("Pre-loaded minimum was better than one found by sampler")
elif (self.config.dataset.oracle == "nupack energy"):
if np.amin(min_nupack_ens) < bestMin:
bestMin = np.amin(min_nupack_ens)
printRecord("Pre-loaded minimum was better than one found by sampler")
elif self.config.dataset.oracle == "nupack pairs":
goodSamples = np.ones((4, self.config.dataset.max_length)) * 4 # GCGC CGCG GGGCCC CCCGGG
goodSamples[0,0:-1:2] = 3
goodSamples[1,1:-1:2] = 3
goodSamples[2,:self.config.dataset.max_length//2] = 3
goodSamples[3,self.config.dataset.max_length//2:] = 3
ens = self.oracle.score(goodSamples)
if np.amin(ens) < bestMin:
bestMin = np.amin(ens)
printRecord("Pre-loaded minimum was better than one found by sampler")
elif self.config.dataset.oracle == "nupack pins":
max_pins = self.config.dataset.max_length // 12 # a conservative estimate - 12 bases per stable hairpin
if max_pins < bestMin:
bestMin = max_pins
printRecord("Pre-run guess was better than one found by sampler")
elif self.config.dataset.oracle == "nupack open loop":
biggest_loop = self.config.dataset.max_length - 8 # a conservative estimate - 8 bases for the stem (10 would be more conservative) and the rest are open
if biggest_loop < bestMin:
bestMin = biggest_loop
printRecord("Pre-run guess was better than one found by sampler")
elif self.config.dataset.oracle == 'nupack motif':
bestMin = -1 # 100% agreement is the best possible
return bestMin
def saveOutputs(self):
'''
save config and outputs in a dict
:return:
'''
outputDict = {}
outputDict['config'] = Namespace(**dict(vars(self.config)))
if "comet" in outputDict['config']:
del outputDict['config'].comet
outputDict['state dict record'] = self.stateDictRecord
outputDict['model state rewards'] = self.model_state_reward_list
outputDict['dataset rewards'] = self.dataset_reward_list
if self.config.al.large_model_evaluation:
outputDict['big dataset loss'] = self.totalLoss
outputDict['bottom 10% loss'] = self.bottomTenLoss
if self.config.dataset.type == 'toy':
outputDict['oracle outputs'] = self.oracleRecord
if self.pipeIter > 1:
outputDict['model state score record'] = self.model_state_abs_score
outputDict['model state cumulative score'] = self.model_state_cumulative_score,
outputDict['model state per sample cumulative score'] = self.model_state_normed_cumulative_score
outputDict['dataset score record'] = self.dataset_abs_score
outputDict['dataset cumulative score'] = self.dataset_cumulative_score,
outputDict['dataset per sample cumulative score'] = self.dataset_normed_cumulative_score
np.save('outputsDict', outputDict)
def updateDataset(self, oracleSequences, oracleScores):
'''
loads dataset, appends new datapoints from oracle, and saves dataset
:param params: model parameters
:param oracleSequences: sequences which were sent to oracle
:param oracleScores: scores of sequences sent to oracle
:return: n/a
'''
dataset = np.load('datasets/' + self.config.dataset.oracle + '.npy', allow_pickle=True).item()
dataset['samples'] = np.concatenate((dataset['samples'], oracleSequences))
dataset['energies'] = np.concatenate((dataset['energies'], oracleScores))
self.logTopK(dataset, prefix = "Dataset") # log statistics on top K samples from the dataset
self.config.dataset_size = len(dataset['samples'])
printRecord(f"Added{bcolors.OKBLUE}{bcolors.BOLD} %d{bcolors.ENDC}" % int(len(oracleSequences)) + " to the dataset, total dataset size is" + bcolors.OKBLUE + " {}".format(int(len(dataset['samples']))) + bcolors.ENDC)
printRecord(bcolors.UNDERLINE + "=====================================================================" + bcolors.ENDC)
np.save('datasets/' + self.config.dataset.oracle, dataset)
np.save('datasets/' + self.config.dataset.oracle + '_iter_{}'.format(self.pipeIter),dataset)
if self.comet:
self.comet.log_histogram_3d(dataset['energies'], name='dataset energies', step=self.pipeIter)
dataset2 = dataset.copy()
dataset2['samples'] = numbers2letters(dataset['samples'])
self.comet.log_table(filename = 'dataset_at_iter_{}.csv'.format(self.pipeIter), tabular_data=pd.DataFrame.from_dict(dataset2))
def logTopK(self, dataset, prefix, returnScores = False):
if self.comet:
self.comet.log_histogram_3d(dataset['energies'], name=prefix + ' energies', step=self.pipeIter)
idx_sorted = np.argsort(dataset["energies"])
top_scores = []
for k in [1, 10, 100]:
topk_scores = dataset["energies"][idx_sorted[:k]]
topk_samples = dataset["samples"][idx_sorted[:k]]
top_scores.append(np.average(topk_scores))
dist = binaryDistance(topk_samples, pairwise=False, extractInds=len(topk_samples))
self.comet.log_metric(prefix + f" mean top-{k} energies", np.mean(topk_scores), step=self.pipeIter)
self.comet.log_metric(prefix + f" std top-{k} energies", np.std(topk_scores), step=self.pipeIter)
self.comet.log_metric(prefix + f" mean dist top-{k}", np.mean(dist), step=self.pipeIter)
if returnScores:
return np.asarray(top_scores)
def getScalingFactor(self):
'''
since regression is not normalized, we identify a scaling factor against which we normalize our results
:return:
'''
truncationFactor = 0.1 # cut off x% of the furthest outliers
dataset = np.load('datasets/' + self.config.dataset.oracle + '.npy', allow_pickle=True).item()
energies = dataset['energies']
d1 = [np.sum(np.abs(energies[i] - energies)) for i in range(len(energies))]
scores = energies[np.argsort(d1)] # sort according to mutual distance
margin = int(len(scores) * truncationFactor)
scores = scores[:-margin] # cut 'margin' of furthest points
self.scalingFactor = np.ptp(scores)
def addRandomSamples(self, samples, energies, uncertainties, minClusterSamples, minClusterEns, minClusterVars):
rands = np.random.randint(0, len(samples), size=self.config.querier.model_state_size - len(minClusterSamples))
randomSamples = samples[rands]
randomEnergies = energies[rands]
randomUncertainties = uncertainties[rands]
minClusterSamples = np.concatenate((minClusterSamples, randomSamples))
minClusterEns = np.concatenate((minClusterEns, randomEnergies))
minClusterVars = np.concatenate((minClusterVars, randomUncertainties))
printRecord('Padded model state with {} random samples from sampler run'.format(len(rands)))
return minClusterSamples, minClusterEns, minClusterVars
def getDataDists(self, samples):
'''
compute average binary distances between a set of samples and
1 - itself
2 - the training dataset
3 - a large random sample
:param samples:
:return:
'''
# training dataset
dataset = np.load('datasets/' + self.config.dataset.oracle + '.npy', allow_pickle=True).item()
dataset = dataset['samples']
# large, random sample
numSamples = min(int(1e3), self.config.dataset.dict_size ** self.config.dataset.max_length // 100) # either 1eX, or 1% of the sample space, whichever is smaller
randomData = self.oracle.initializeDataset(save=False, returnData=True, customSize=numSamples) # get large random dataset
randomSamples = randomData['samples']
internalDist = binaryDistance(samples, self.config.dataset.dict_size, pairwise=False,extractInds=len(samples))
datasetDist = binaryDistance(np.concatenate((samples, dataset)), self.config.dataset.dict_size, pairwise=False, extractInds = len(samples))
randomDist = binaryDistance(np.concatenate((samples,randomSamples)), self.config.dataset.dict_size, pairwise=False, extractInds=len(samples))
return internalDist, datasetDist, randomDist
