def find_keyword_examples(filenames,
keywords,
n=10,
indorgs=None,
genders=None,
locations=None):
"""
"""
## Find Matches
mp = Pool(NUM_JOBS)
helper = partial(get_posts,
keywords=keywords,
indorgs=indorgs,
genders=genders,
locations=locations)
mp_matches = list(
tqdm(mp.imap_unordered(helper, filenames),
total=len(filenames),
leave=False,
file=sys.stdout))
mp.close()
## Sample
mp_matches = pd.DataFrame(flatten(mp_matches))
sample = []
for keyword in keywords:
mp_keyword_matches = mp_matches.loc[mp_matches["keyword"] == keyword]
mp_keyword_matches = mp_keyword_matches.drop_duplicates("text")
mp_keyword_matches = mp_keyword_matches.sample(min(
n, len(mp_keyword_matches)),
random_state=42,
replace=False)
sample.append(mp_keyword_matches)
sample = pd.concat(sample).reset_index(drop=True)
return sample
def examine_matches(matches,
match_key,
match_type,
query):
"""
"""
relevant_matches = []
for m in flatten(matches):
if match_key not in m["matches"]:
continue
if match_type not in m["matches"][match_key]:
continue
m_res = m.get("matches").get(match_key).get(match_type)
m_res_present = [(x[0], x[-1]) for x in m_res if x[0] == query]
if len(m_res_present) > 0:
m_text = m["text"]
m_text_highlighted = ""
start = 0
end = len(m_text)
for _, (term_start, term_end) in m_res_present:
m_text_highlighted += m_text[start:term_start] + "<" + m_text[term_start:term_end] + ">"
start = term_end
if start != end:
m_text_highlighted += m_text[start:end]
m_copy = deepcopy(m)
_ = m_copy.pop("matches",None)
m_copy["text"] = m_text_highlighted
relevant_matches.append(m_copy)
return relevant_matches
def tokenize_and_count(filename,
min_n=1,
max_n=1,
min_date=None,
max_date=None,
remove_retweets=True,
pretokenized=False):
"""
Args:
filename (str):
min_n (int)
max_n (int)
min_date (None or int)
max_date (None or int)
remove_retweets (bool)
pretokenized (bool)
Returns:
token_counts (Counter): Count of n-grams
"""
## Get Ngrams
ngrams = load_and_tokenize(filename,
min_n=min_n,
max_n=max_n,
min_date=min_date,
max_date=max_date,
remove_retweets=remove_retweets,
pretokenized=pretokenized,
cache_dir=None)
## Count
token_counts = Counter(flatten(ngrams))
return token_counts
def plot_marginal_influence(scores_df,
vc,
vary_cols,
metric,
aggfunc=np.mean):
"""
"""
## Get Relevant Data Aggregations
if vc not in JOINT_PARAMS.keys():
group_cols = [v for v in vary_cols if v != vc and v not in JOINT_PARAMS.keys()]
else:
group_cols = [v for v in vary_cols if v != vc and v not in flatten(JOINT_PARAMS.values())]
grouped_scores = scores_df.groupby(["domain","group"] + group_cols + [vc])[metric].agg([aggfunc, np.std])
grouped_scores_avg = scores_df.groupby(["domain","group",vc])[metric].agg(bootstrap_ci).to_frame()
for i in range(3):
grouped_scores_avg[i] = grouped_scores_avg[metric].map(lambda j: j[i])
## Generate Plot
fig, ax = plt.subplots(2, 2, sharex=True, sharey=True)
for d, domain in enumerate(["source","target"]):
for g, group in enumerate(["train","development"]):
pax = ax[d, g]
pax_data = grouped_scores.loc[domain, group].reset_index().sort_values(vc)
for opt, ind in pax_data.groupby(group_cols).groups.items():
opt_data = pax_data.loc[ind]
offset = np.random.normal(0,0.01)
pax.errorbar(np.arange(opt_data.shape[0])+offset,
opt_data[aggfunc.__name__].values,
yerr=opt_data["std"].values if not np.isnan(opt_data["std"].values).all() else None,
color="C0",
alpha=0.05,
zorder=-1)
pax.errorbar(np.arange(opt_data.shape[0]),
grouped_scores_avg.loc[domain, group][1].values,
yerr=np.vstack([(grouped_scores_avg.loc[domain, group][1]-grouped_scores_avg.loc[domain, group][0]).values,
(grouped_scores_avg.loc[domain, group][2]-grouped_scores_avg.loc[domain, group][1]).values]),
color="black",
linewidth=2,
zorder=1,
capsize=2)
pax.set_title(f"{domain.title()} - {group.title()}")
pax.spines["right"].set_visible(False)
pax.spines["top"].set_visible(False)
if pax.get_ylim()[0] < 0:
pax.set_ylim(bottom=0)
if g == 0:
pax.set_ylabel(metric)
if d == 1:
pax.set_xlabel(f"{vc} Type")
pax.xaxis.set_major_locator(MaxNLocator(integer=True))
fig.tight_layout()
return fig, ax
def get_unique_terms(matches):
"""
"""
terms = {}
for m in flatten(matches):
for match_key, match_dict in m.get("matches").items():
if "terms" not in match_dict:
continue
if match_key not in terms:
terms[match_key] = set()
for (term, _, _) in match_dict.get("terms"):
terms[match_key].add(term)
return terms
def tokenize_user_data(self,
user_data):
"""
Tokenize user data into separate sentences
Args:
user_data (list of str): Unique posts
Returns:
sentences (list of str): Posts, tokenized into sentences and words
"""
## Sentence Tokenization
sentences = flatten(list(map(sent_tokenize, user_data)))
## Word Tokenization
sentences = list(map(TOKENIZER.tokenize, sentences))
sentences = list(filter(lambda x: len(x) > 0, sentences))
return sentences
def load_tokens(self,
filename,
n_samples=None):
"""
Load Tokens (Assume date-based filter already completed)
"""
## Load Tokens
file_data = []
with gzip.open(filename,"r") as the_file:
for line in the_file:
file_data.append(json.loads(line))
## Post-level Sampling
if n_samples is not None:
file_data = self.loader._select_documents_randomly(file_data,
n_samples)
## Flatten Sentences
sentences = flatten([i["text"] for i in file_data])
return sentences
#######################
### Reference Keywords
#######################
## Mental Health/Coronavirus Keywords
falconet_keywords = {}
falconet_keyword_dir = "./data/resources/falconet/"
for mhlist, mhfile in [("Crisis (Level 1)", "crisis_level1.keywords"),
("Crisis (Level 2)", "crisis_level2.keywords"),
("Crisis (Level 3)", "crisis_level3.keywords"),
("SMHD", "smhd.keywords"), ("CLSP", "pmi.keywords"),
("Coronavirus", "corona_virus.keywords")]:
mhkeys = list(
map(lambda i: i.strip(),
open(f"{falconet_keyword_dir}{mhfile}", "r").readlines()))
mhkeys = sorted(set(flatten([[i, i.lower()] for i in mhkeys])))
mhkeys = flatten([i, f"#{i}"] for i in mhkeys)
falconet_keywords[mhlist] = mhkeys
## Reverse Mental Health Keyword List
falconet_keywords_reverse = dict()
for mhlist, terms in falconet_keywords.items():
for t in terms:
if t not in falconet_keywords_reverse:
falconet_keywords_reverse[t] = []
falconet_keywords_reverse[t].append(mhlist)
#######################
### Helpers
#######################
return X, y
def sample_data(X, y, class_ratio=None, sample_size=None, random_seed=42):
"""
"""
## Rebalance Data
X, y = _rebalance(X, y, class_ratio, random_seed)
## Downsample Data
X, y = _downsample(X, y, sample_size, random_seed)
return X, y
## Helper Function for Converting Count Data
term_expansion = lambda x, vocab: flatten([[vocab[i]] * int(x[0, i])
for i in x.nonzero()[1]])
def generate_corpus(Xs, Xt, vocab, source=True, target=True, ys=None, yt=None):
"""
"""
corpus = tp.utils.Corpus()
missing = {"source": [], "target": []}
for i, x in tqdm(enumerate(Xs),
total=Xs.shape[0],
desc="Adding Source Documents",
file=sys.stdout):
if source:
x_flat = term_expansion(x, vocab)
else:
def find_matches(filename, level=DATE_RES, include_mentions=False):
"""
"""
## Initialize Sampler
sampler = random.Random(SAMPLE_SEED)
## Search For Matches
matches = []
timestamps = []
n = 0
n_seen = 0
with gzip.open(filename, "r") as the_file:
for post in the_file:
n += 1
if sampler.uniform(0, 1) >= SAMPLE_RATE:
continue
else:
n_seen += 1
## Load Data
post_data = json.loads(post)
## Cache Timestamp
timestamps.append(pd.to_datetime(post_data["date"]))
## Regex Version
post_regex_matches = match_post(
post_data, include_mentions=include_mentions)
## Falconet Matches
falconet_terms = post_data.get("keywords")
## Continue if None
if post_regex_matches is None and falconet_terms is None:
continue
else:
if post_regex_matches:
if SKIP_COVID and "covid" in post_regex_matches.get(
"matches"):
continue
regex_terms = [
list(row) for _, row in pd.DataFrame(
flatten([
i["terms"] for i in post_regex_matches.get(
"matches").values()
])).drop_duplicates(subset=[1, 2]).iterrows()
]
regex_terms = filter_substrings(regex_terms)
regex_terms = sorted([f[0] for f in regex_terms])
else:
regex_terms = []
if not falconet_terms:
falconet_terms = []
else:
falconet_terms = sorted(falconet_terms)
matches.append({
"tweet_id":
post_data.get("tweet_id"),
"date":
pd.to_datetime(post_data.get("date")),
"text":
post_data.get("text"),
"regex_keywords":
regex_terms,
"falconet_keywords":
falconet_terms
})
## Format Timestamps
timestamps = format_timestamps(timestamps, level)
timestamps = Counter(timestamps)
return filename, matches, n, n_seen, timestamps
"covid": {
"terms": create_regex_dict(COVID_TERMS["covid"]),
"name": "COVID-19"
}
}
## Find Procesed Files
filenames = sorted(glob(f"{DATA_DIR}*.json.gz"))
## Search For Keyword/Subreddit Matches
filenames, matches, n, n_seen, timestamps = search_files(
filenames, date_res=DATE_RES, include_mentions=False)
## Disagreement
disagreements = [
i for i in flatten(matches)
if i["regex_keywords"] != i["falconet_keywords"]
]
disagreement_rate = len(disagreements) / len(flatten(matches)) * 100
print("Disagreement Rate: {:.3f}%".format(disagreement_rate))
## Count Comparision
regex_counts = pd.Series(
Counter(flatten([i["regex_keywords"]
for i in flatten(matches)]))).to_frame("regex")
falconet_counts = pd.Series(
Counter(flatten([i["falconet_keywords"]
for i in flatten(matches)]))).to_frame("falconet")
merged_counts = pd.concat([regex_counts, falconet_counts], axis=1,
sort=True).fillna(0)
outliers = np.log((merged_counts["regex"] + 0.01) /
### Load/Parse Matches
###################
## Sample Cache File
sample_cache_file = f"{CACHE_DIR}{PLATFORM}_keyword_samples_k-{NUM_SAMPLES_PER_TERM}.json"
## Run Sampling If Necessary
if not os.path.exists(sample_cache_file):
## Load Matches
match_cache_dir = f"{CACHE_DIR}{PLATFORM}_{START_DATE}_{END_DATE}_matches/"
filenames, matches, n, n_seen, timestamps = load_keyword_search_results(match_cache_dir)
## Unique Query Terms
unique_terms = get_unique_terms(matches)
unique_terms_df = pd.DataFrame(data=sorted(set(flatten(unique_terms.values()))),
columns=["term"])
unique_terms_df["keyword_group"] = [[]] * len(unique_terms_df)
for term_group, terms in unique_terms.items():
unique_terms_df["keyword_group"] = unique_terms_df.apply(lambda row: [term_group] + row["keyword_group"] if row["term"] in terms else row["keyword_group"], axis=1)
## Get Match Sizes
match_sizes = {term:0 for term in unique_terms_df["term"]}
for match_set in matches:
for post in match_set:
for match_key, match_values in post.get("matches").items():
if "terms" not in match_values:
continue
terms_present = [t[0] for t in match_values.get("terms")]
for t in terms_present:
if t not in match_sizes:
def main():
"""
"""
######################
### Setup
######################
## Parse Command Line
args = parse_arguments()
## Load Configuration
config = Config(filepath=args.config)
## Output
if config.output_dir is not None and not os.path.exists(config.output_dir):
_ = os.makedirs(config.output_dir)
## Cache Config
if config.output_dir is not None and config.run_id is not None:
_ = os.system(
f"cp {args.config} {config.output_dir}/{config.run_id}.config.json"
)
## Set Random State
if config.random_state is not None:
np.random.seed(config.random_state)
######################
### Data Generating Process
######################
## Generate Data
X_latent, X, y, D, theta, phi = data_generating_process(
config.N,
config.sigma_0,
config.p_domain,
config.gamma,
config.V,
config.theta,
config.coef,
beta=config.beta,
random_state=config.random_state)
## Data Distribution Plot
if args.make_plots:
fig, ax = fit_latent_regression(X_latent, y, D, config.coef)
plt.show()
######################
### Fit Topic Models
######################
## Split Data into Training and Test
train_ind = list(range(int(config.N * .8)))
test_ind = list(range(int(config.N * .8), config.N))
## Generate Corpus
train_corpus = tp.utils.Corpus()
full_corpus = tp.utils.Corpus()
## Add Training Data
for n in range(X.shape[0]):
doc_n = doc_to_str(X[n])
full_corpus.add_doc(doc_n, label=[str(D[n])])
if n <= train_ind[-1]:
train_corpus.add_doc(doc_n, label=[str(D[n])])
assert len(train_corpus) == len(train_ind)
## Initialize Models (3 Topics Total)
lda = tp.LDAModel(k=3,
corpus=train_corpus,
seed=config.random_state if config.random_state
is not None else np.random.randint(1e6))
plda = tp.PLDAModel(latent_topics=1,
topics_per_label=1,
corpus=train_corpus,
seed=config.random_state if config.random_state
is not None else np.random.randint(1e6))
## Initialize Sampler
lda.train(1)
plda.train(1)
## Update Parameters based on Corpus
V_nn = lda.num_vocabs
## MCMC Storage
n_iter = max(config.n_iter_lda, config.n_iter_plda)
likelihood = np.zeros((n_iter, 2)) * np.nan
theta_lda = np.zeros((n_iter, config.N, 3)) * np.nan
theta_plda = np.zeros((n_iter, config.N, 3)) * np.nan
phi_lda = np.zeros((n_iter, 3, V_nn)) * np.nan
phi_plda = np.zeros((n_iter, 3, V_nn)) * np.nan
## Word Count
train_word_n = sum([len(d.words) for d in full_corpus[train_ind]])
test_word_n = sum([len(d.words) for d in full_corpus[test_ind]])
## Train LDA Model
for epoch in tqdm(range(config.n_iter_lda), desc="LDA Training"):
lda.train(1)
train_inf, train_ll = lda.infer(full_corpus[train_ind],
iter=config.n_sample)
test_inf, test_ll = lda.infer(full_corpus[test_ind],
iter=config.n_sample)
likelihood[epoch, 0] = train_ll.sum() / train_word_n
theta_lda[epoch] = np.vstack(
flatten([[d.get_topic_dist() for d in inf]
for inf in [train_inf, test_inf]]))
phi_lda[epoch] = np.vstack(
[lda.get_topic_word_dist(t) for t in range(lda.k)])
## Train PLDA Model
for epoch in tqdm(range(config.n_iter_plda), desc="PLDA Training"):
plda.train(1)
train_inf, train_ll = plda.infer(full_corpus[train_ind],
iter=config.n_sample)
test_inf, test_ll = plda.infer(full_corpus[test_ind],
iter=config.n_sample)
likelihood[epoch, 1] = train_ll.sum() / train_word_n
theta_plda[epoch] = np.vstack(
flatten([[d.get_topic_dist() for d in inf]
for inf in [train_inf, test_inf]]))
phi_plda[epoch] = np.vstack(
[plda.get_topic_word_dist(t) for t in range(plda.k)])
## Plot Likelihood
if args.make_plots:
plt.figure(figsize=(10, 5.8))
plt.plot(likelihood[:, 0], label="LDA")
plt.plot(likelihood[:, 1], label="PLDA")
plt.xlabel("Training Epoch", fontweight="bold")
plt.ylabel("Log Likelihood Per Word", fontweight="bold")
plt.legend(loc="lower right")
plt.tight_layout()
plt.show()
## Plot Traces for Phi
if args.make_plots:
fig, axes = plt.subplots(phi_lda.shape[1], 2, figsize=(10, 5.8))
for m, (mphi,
mdl) in enumerate(zip([phi_lda, phi_plda], ["LDA", "PLDA"])):
ax = axes[:, m]
for k in range(mphi.shape[1]):
ax[k].plot(mphi[:, k, :])
ax[k].set_ylabel("Parameter Value", fontweight="bold")
ax[k].spines["top"].set_visible(False)
ax[k].spines["right"].set_visible(False)
ax[k].set_xlabel("Training Epoch", fontweight="bold")
ax[0].set_title(f"{mdl} $\\phi$ Trace", fontweight="bold")
fig.tight_layout()
plt.show()
## Plot Sample Traces for Theta
if args.make_plots:
fig, ax = plt.subplots(5, 2, sharex=False, figsize=(10, 5.8))
for d, doc in enumerate(
sorted(np.random.choice(config.N, 5, replace=False))):
ax[d, 0].plot(theta_lda[:, doc, :])
ax[d, 1].plot(theta_plda[:, doc, :])
for i in range(2):
ax[d, i].spines["right"].set_visible(False)
ax[d, i].spines["top"].set_visible(False)
ax[d, i].set_title(f"Document {doc}",
loc="left",
fontstyle="italic")
ax[d, i].set_ylabel("$\\theta$")
for m, mdl in enumerate(["LDA", "PLDA"]):
ax[-1, m].set_xlabel(f"{mdl} Training Epoch", fontweight="bold")
fig.tight_layout()
plt.show()
## Get Final Representations
X_latent_lda = np.vstack([
d.get_topic_dist() for d in lda.infer(
full_corpus, iter=config.n_sample, together=False)[0]
])
X_latent_plda = np.vstack([
d.get_topic_dist() for d in plda.infer(
full_corpus, iter=config.n_sample, together=False)[0]
])
## Isolate Latent Variables and Normalize
X_latent_plda = X_latent_plda[:, -plda.latent_topics:]
## Fit Classifiers
source_train_ind = sorted(set(train_ind) & set(np.where(D == 0)[0]))
lr_lda = LogisticRegression()
lr_lda.fit(X_latent_lda[source_train_ind], y[source_train_ind])
lr_plda = LogisticRegression()
lr_plda.fit(X_latent_plda[source_train_ind], y[source_train_ind])
## Make Test Predictions
y_test_lda = lr_lda.predict_proba(X_latent_lda)[:, 1]
y_test_plda = lr_plda.predict_proba(X_latent_plda)[:, 1]
## Score Predictions
scores = score_model(y, y_test_lda, y_test_plda, D, test_ind, True)
if config.output_dir is not None and config.run_id is not None:
with open(f"{config.output_dir}/{config.run_id}.scores.json",
"w") as the_file:
json.dump(scores, the_file)
ax[i, d].set_xlabel(f"Feature {i}", fontweight="bold")
ax[i, 0].set_ylabel("Outcome", fontweight="bold")
for a in ax:
for b in a:
b.spines["right"].set_visible(False)
b.spines["top"].set_visible(False)
b.axvline(0, color="black", alpha=0.5, linestyle="--")
for i, t in enumerate(["Source Domain", "Target Domain"]):
ax[0, i].set_title(t, fontweight="bold")
ax[0, 0].legend(loc="lower right")
fig.tight_layout()
return fig, ax
## Helper Function
doc_to_str = lambda x: flatten([[str(i)] * int(j) for i, j in enumerate(x)])
## Scoring
def score_model(y, y_test_lda, y_test_plda, D, test_ind, verbose=True):
"""
"""
## Score Cache
scores = {"LDA": {}, "PLDA": {}}
## Printing
if verbose:
print("~~~~~~ Test Set Performance ~~~~~~")
## Cycle through Domain Groups
for d, domain in enumerate(["Source", "Target", "Overall"]):
## Domain Indices
