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@@ from sentence_transformers import SentenceTransformer # Load model model = SentenceTransformer("all-roberta-large-v1") def create_faiss_index(choices): + """ + Creates a FAISS index for a list of choices using cosine similarity (inner product). + + Args: + choices (list): A list of text items to index. + + Returns: + faiss.IndexFlatIP: A FAISS index for the given embeddings. + """ embeddings = model.encode(choices, normalize_embeddings=True).astype("float32") index = faiss.IndexFlatIP(embeddings.shape[1]) # Inner product for cosine similarity index.add(embeddings) return index def get_matches_above_threshold(target, choices, index, threshold=0.7, top_k=5): + """ + Retrieves the top-k matches from a FAISS index with similarity scores above a given threshold. + + Args: + target (str): The target text to compare against the choices. + choices (list): A list of choices to match the target with. + index (faiss.IndexFlatIP): The FAISS index for fast nearest-neighbor search. + threshold (float, optional): The minimum similarity score to consider a match. Defaults to 0.7. + top_k (int, optional): The number of top matches to retrieve. Defaults to 5. + + Returns: + list: A list of tuples containing matched choice and score for each match above the threshold. + """ target_vec = model.encode([target], normalize_embeddings=True).astype("float32") similarity_scores, match_indices = index.search(target_vec, top_k) return [ @@ -35,8 +57,39 @@ def get_matches_above_threshold(target, choices, index, threshold=0.7, top_k=5): if score >= threshold ] +def crosswalk_levels(): + """ + Loads and processes crosswalk mappings for different levels (e.g., CPT, HCPCS) from CSV files, + and returns a dictionary with clean-to-description and description-to-code mappings for each level. + + Returns: + dict: A dictionary where each key is a level, and the value is a tuple containing: + - clean-to-description mapping (str -> str) + - description-to-code mapping (str -> str) + """ + # Get necessary mappings + crosswalk_dict = {} + for level in investment_values.levels: + mapping_df = pd.read_csv(f"crosswalk/mapping_csvs/proc_cd/{level}.csv", dtype=str) + level_crosswalk = CrosswalkBuilder().from_df(mapping_df, from_col="Code", to_col="Description") + clean_to_description = {get_clean_value(x) : x for x in level_crosswalk.mapping.values()} + description_to_code = level_crosswalk.create_reverse_mapping() + crosswalk_dict[level] = (clean_to_description, description_to_code) + + return crosswalk_dict def code_primary(answer_dicts, filename): + """ + Breaks down the direct code information from CONTRACT_SERVICE_CD_OR_DESC and CONTRACT_REIMBURSEMENT_METHOD fields + using an LLM prompt and adds the results to the provided answer dictionaries. + + Args: + answer_dicts (list of dict): A list of dictionaries containing service and reimbursement data. + filename (str): The name of the file being processed, used for LLM processing. + + Returns: + list of dict: The input answer dictionaries with additional primary code breakout information. These are only the codes that are explicitly written in the Service/Methodology + """ code_primary_questions = FieldSet(file_path=config.FIELD_JSON_PATH, field_type="code_primary_breakout").get_prompt_dict() code_breakout_answers = [] for answer_dict in answer_dicts: @@ -55,6 +108,12 @@ def code_primary(answer_dicts, filename): return code_breakout_answers def get_proc_crosswalk(): + """ + Loads and concatenates all CSV files in the 'proc_cd' directory, and creates a crosswalk mapping from the 'Code' to 'Description' columns. + + Returns: + CrosswalkBuilder: A CrosswalkBuilder object containing the mapping from procedure codes to descriptions. + """ all_mappings = [] mapping_dir = "crosswalk/mapping_csvs/proc_cd" for filename in os.listdir(mapping_dir): @@ -66,6 +125,15 @@ def get_proc_crosswalk(): def get_clean_value(service_description): + """ + Cleans a service description by removing stop words, replacing certain terms, and standardizing acronyms. + + Args: + service_description (str): The service description string to clean. + + Returns: + str: The cleaned service description with stop words removed, specific terms replaced, and acronyms expanded. + """ stop_words = {"the", "is", "in", "and", "to", "of", "a", "an", "that", "this", "it", "for", "on", "with", "as", "was", "were", "at", "by", "but", "be"} # Experiment with not removing 'and' def remove_stop_words(text): words = text.split() @@ -83,23 +151,27 @@ def get_clean_value(service_description): return service_clean -def get_best_match(target, model, thresholds={ +def get_best_match(crosswalk_dict, target, model, thresholds={ "cpt": 0.85, "cpt_level3": 0.8, "cpt_level2": 0.75, "cpt_level1": 0.7, "hcpcs": 0.85, "hcpcs_level3": 0.8, "hcpcs_level2": 0.75, "hcpcs_level1": 0.7 }): - levels = ["cpt", "hcpcs", "cpt_level3", "cpt_level2", "hcpcs_level2", "cpt_level1", "hcpcs_level1"] + """ + Finds the best matching code from a crosswalk dictionary by comparing a target string to precomputed embeddings + using a model and similarity threshold values for different levels. - # Get necessary mappings - crosswalk_dict = {} - for level in levels: - mapping_df = pd.read_csv(f"crosswalk/mapping_csvs/proc_cd/{level}.csv", dtype=str) - level_crosswalk = CrosswalkBuilder().from_df(mapping_df, from_col="Code", to_col="Description") - clean_to_description = {get_clean_value(x) : x for x in level_crosswalk.mapping.values()} - description_to_code = level_crosswalk.create_reverse_mapping() - crosswalk_dict[level] = (clean_to_description, description_to_code) + Args: + crosswalk_dict (dict): Dictionary containing the crosswalk data for different levels. + target (str): The target string to match. + model: The model used to encode the target string into an embedding. + thresholds (dict, optional): A dictionary of similarity thresholds for each level (default values provided). + + Returns: + tuple: A tuple containing the best matching code, its description, and the similarity score. + If no match is found above the threshold, returns (None, None, 0). + """ target_vec = model.encode([target], normalize_embeddings=True).astype("float32") - for level in levels: + for level in investment_values.levels: index, _, choices = embedding_utils.load_faiss_index(index_path=os.path.join("embeddings", level, "faiss_index.bin"), embedding_path=os.path.join("embeddings", level, "embeddings.npy"), choices_path=os.path.join("embeddings", level, "choices.pkl"),) @@ -113,7 +185,7 @@ def get_best_match(target, model, thresholds={ return None, None, 0 # No valid match found -def code_indirect(answer_dicts): +def code_indirect(answer_dicts, crosswalk): """ Maps free-form service descriptions to the best-matching code and description. Caches results for efficiency and skips entries with existing codes or irrelevant text. @@ -135,7 +207,7 @@ def code_indirect(answer_dicts): if (not service # Service DNE or "covered service" in service.lower() # Is generic or isinstance(proc_code, list) # Is a list - or string_utils.is_empty(proc_code) # Is empty + or not string_utils.is_empty(proc_code) # Is not empty ): pass # pass for now - we may need to add functionality here later else: @@ -143,7 +215,7 @@ def code_indirect(answer_dicts): code = already_seen[service]['code'] description = already_seen[service]['description'] else: - code, description, score = get_best_match(service, model) + code, description, score = get_best_match(crosswalk, service, model) # print(service, " | ", description, " | ", code, " | ", score) answer_dict["CPT4_PROC_CD"] = code @@ -152,6 +224,17 @@ def code_indirect(answer_dicts): return results def get_code_description(code, code_mapping): + """ + Retrieves descriptions for a given code or list of codes using the provided code mapping. + If no description is found, attempts to resolve by modifying the code (e.g., prepending "0" or handling code patterns). + + Args: + code (str, list): A single code or a list of codes to look up. + code_mapping (Crosswalk): The mapping object containing code-to-description mappings. + + Returns: + str: A comma-separated string of descriptions for the provided codes. + """ if isinstance(code, str): if string_utils.is_empty(code): return "N/A" @@ -181,28 +264,57 @@ def get_code_description(code, code_mapping): return ",".join(code_description) -def code_description_mapping(answer_dicts): - # Get mappings +def get_mappings(): + """ + Loads and processes multiple CSV and Excel files containing code mappings for various categories + (e.g., PROC, DIAG, Grouper, Rev, Admit Type), and returns a dictionary of crosswalks for each code type. + + Returns: + dict: A dictionary containing mappings for PROC, DIAG, Grouper, Rev, and Admit Type codes. + """ + + all_mappings = {} + # PROC codes mapping_path = "crosswalk/mapping_csvs/" all_proc_mappings = pd.concat([pd.read_csv(os.path.join(mapping_path, "proc_cd", file), dtype=str) for file in os.listdir(os.path.join(mapping_path, "proc_cd")) if file.endswith(".csv")]) proc_mapping = CrosswalkBuilder().from_df(all_proc_mappings, from_col="Code", to_col="Description") + all_mappings['proc_mapping'] = proc_mapping # Diag codes all_diag_mappings = pd.concat([pd.read_csv(os.path.join(mapping_path, "diag_cd", file), dtype=str) for file in os.listdir(os.path.join(mapping_path, "diag_cd")) if file.endswith(".csv")]) diag_mapping = CrosswalkBuilder().from_df(all_diag_mappings, from_col="Code", to_col="Description") + all_mappings['diag_mapping'] = diag_mapping # Grouper codes all_grouper_mappings = pd.concat([pd.read_csv(os.path.join(mapping_path, "grouper_cd", file), dtype=str) for file in os.listdir(os.path.join(mapping_path, "grouper_cd")) if file.endswith(".csv")]) grouper_mapping = CrosswalkBuilder().from_df(all_grouper_mappings, from_col="Code", to_col="Description") grouper_version_mapping = CrosswalkBuilder().from_df(all_grouper_mappings, from_col="Code", to_col="Version") + all_mappings['grouper_mapping'] = grouper_mapping + all_mappings['grouper_version_mapping'] = grouper_version_mapping # Rev codes rev_mapping = CrosswalkBuilder().from_excel(path=os.path.join(mapping_path, "rev_cd", "rev_mapping.csv"), from_col="Code", to_col="Description") + all_mappings['rev_mapping'] = rev_mapping # Admit Type codes admit_mapping = CrosswalkBuilder().from_excel(path=os.path.join(mapping_path, "admit_type_cd", "admit_mapping.csv"), from_col="Code", to_col="Description") + all_mappings['admit_mapping'] = admit_mapping + return all_mappings + + +def code_description_mapping(answer_dicts, all_mappings): + """ + Maps code descriptions to relevant fields in the answer dictionaries using provided mappings. + + Args: + answer_dicts (list): List of dictionaries containing codes to be mapped. + all_mappings (dict): Dictionary containing the mappings for different code types. + + Returns: + list: Updated list of dictionaries with code descriptions added. + """ for answer_dict in answer_dicts: proc_code = answer_dict.get("CPT4_PROC_CD") proc_mod = answer_dict.get("CPT4_PROC_MOD") @@ -211,25 +323,36 @@ def code_description_mapping(answer_dicts): grouper_code = answer_dict.get("FACILITY_GROUPER_CD") admit_type_code = answer_dict.get("CLAIM_ADMIT_TYPE_CD") - answer_dict["CPT4_PROC_DESC"] = get_code_description(proc_code, proc_mapping) - answer_dict["CPT4_PROC_MOD_DESC"] = get_code_description(proc_mod, proc_mapping) - answer_dict["DIAG_CD_DESC"] = get_code_description(diag_code, diag_mapping) - answer_dict["REVENUE_CD_DESC"] = get_code_description(rev_code, rev_mapping) - answer_dict["FACILITY_GROUPER_DESC"] = get_code_description(grouper_code, grouper_mapping) - answer_dict["GROUPER_TYPE"] = get_code_description(grouper_code, grouper_version_mapping) - answer_dict["AUTH_ADMIT_TYPE_DESC"] = get_code_description(admit_type_code, admit_mapping) + answer_dict["CPT4_PROC_DESC"] = get_code_description(proc_code, all_mappings['proc_mapping']) + answer_dict["CPT4_PROC_MOD_DESC"] = get_code_description(proc_mod, all_mappings['proc_mapping']) + answer_dict["DIAG_CD_DESC"] = get_code_description(diag_code, all_mappings['diag_mapping']) + answer_dict["REVENUE_CD_DESC"] = get_code_description(rev_code, all_mappings['rev_mapping']) + answer_dict["FACILITY_GROUPER_DESC"] = get_code_description(grouper_code, all_mappings['grouper_mapping']) + answer_dict["GROUPER_TYPE"] = get_code_description(grouper_code, all_mappings['grouper_version_mapping']) + answer_dict["AUTH_ADMIT_TYPE_DESC"] = get_code_description(admit_type_code, all_mappings['admit_mapping']) return answer_dicts -def get_code_breakout(answer_dicts: list[dict], filename: str): +def get_code_breakout(answer_dicts: list[dict], filename: str, all_dataset: dict): + """ + Extracts and maps codes from contract data, including primary, indirect, and description mappings. + + Args: + answer_dicts (list[dict]): List of dictionaries containing contract-related answers. + filename (str): The name of the file being processed. + all_dataset (dict): Dictionary containing crosswalk and mappings for code translation. + + Returns: + dict: A dictionary with primary, indirect/derived, and mapped code descriptions. + """ # Code Primary (Pull codes directly from CONTRACT_SERVICE_CD_OR_DESC and CONTRACT_REIMBURSEMENT_METHOD) code_primary_answers = code_primary(answer_dicts, filename) # Only used for Implicit. Code Indirect (Derive codes indirectly from CONTRACT_SERVICE_CD_OR_DESC and CONTRACT_REIMBURSEMENT_METHOD) - code_indirect_answers = code_indirect(code_primary_answers) + code_indirect_answers = code_indirect(code_primary_answers, all_dataset['codes_crosswalk']) # Code Descriptions (Pull standardized descriptions from codes) - code_description_answers = code_description_mapping(code_indirect_answers) + code_description_answers = code_description_mapping(code_indirect_answers, all_dataset['codes_mappings']) return code_description_answers \ No newline at end of file diff --git a/fieldExtraction/src/investment/file_processing.py b/fieldExtraction/src/investment/file_processing.py index eba6700..6577297 100644 --- a/fieldExtraction/src/investment/file_processing.py +++ b/fieldExtraction/src/investment/file_processing.py @@ -20,7 +20,8 @@ from datetime import datetime def datetime_str(): return datetime.now().strftime("[%Y-%m-%d %H:%M:%S]") -def process_file(file_object, run_timestamp): + +def process_file(file_object, all_dataset, run_timestamp): filename, contract_text = file_object print(f"{datetime_str()} Processing {filename}...") @@ -38,7 +39,7 @@ def process_file(file_object, run_timestamp): ################## ONE TO N ################## if string_utils.contains_reimbursement(contract_text): - one_to_n_results = run_one_to_n_prompts(filename, text_dict, exhibit_pages, exhibit_chunk_mapping) # Return df + one_to_n_results = run_one_to_n_prompts(filename, text_dict, exhibit_pages, exhibit_chunk_mapping, all_dataset) # Return df one_to_n_results['CONTRACT_FILE_NAME'] = filename contract_results = pd.merge(one_to_one_results, one_to_n_results, how='outer', on='CONTRACT_FILE_NAME') else: @@ -90,7 +91,7 @@ def run_one_to_one_prompts(filename, contract_text, text_dict, top_sheet_dict): return final_df -def run_one_to_n_prompts(filename, text_dict, exhibit_pages, exhibit_chunk_mapping): +def run_one_to_n_prompts(filename, text_dict, exhibit_pages, exhibit_chunk_mapping, all_dataset): ################## RUN PROMPTS ################## one_to_n_results = [] @@ -111,7 +112,7 @@ def run_one_to_n_prompts(filename, text_dict, exhibit_pages, exhibit_chunk_mappi exhibit_level_answers['EXHIBIT_PAGE'] = exhibit_page ################## GET REIMBURSEMENT-LEVEL ANSWERS (INCLUDING DYNAMIC) ################## - reimbursement_level_answers = reimbursement_level(exhibit_chunk, filename, reimbursement_level_fields) # Return list of dictionaries + reimbursement_level_answers = reimbursement_level(exhibit_chunk, filename, reimbursement_level_fields, all_dataset) # Return list of dictionaries ################## COMBINE ANSWERS ################## full_answer_dict = combine_one_to_n_answers(exhibit_level_answers, reimbursement_level_answers, tin_npi_answers) @@ -121,3 +122,6 @@ def run_one_to_n_prompts(filename, text_dict, exhibit_pages, exhibit_chunk_mappi ################## CONVERT TO DF ################## one_to_n_df = pd.DataFrame(one_to_n_results) return one_to_n_df + + + diff --git a/fieldExtraction/src/investment/main.py b/fieldExtraction/src/investment/main.py index 9d6af8d..3a8961f 100644 --- a/fieldExtraction/src/investment/main.py +++ b/fieldExtraction/src/investment/main.py @@ -30,11 +30,14 @@ def main(testing=False, test_params = {}): input_dict = {k: v for k, v in input_dict.items() if k in test_params['input_files']} print(f"Total Input Files : {len(input_dict)}") + + # load all crosswalk files and mappings + all_dataset = io_utils.load_all_dataset() # Process files with run_timestamp all_results = [] with concurrent.futures.ThreadPoolExecutor(max_workers=max_workers) as executor: - results = executor.map(lambda item: file_processing.process_file(item, run_timestamp), input_dict.items()) + results = executor.map(lambda item: file_processing.process_file(item, all_dataset, run_timestamp), input_dict.items()) all_results.extend(results) FINAL_RESULT_DF = pd.concat(all_results) diff --git a/fieldExtraction/src/investment/one_to_n_funcs.py b/fieldExtraction/src/investment/one_to_n_funcs.py index 8460e95..8f2d079 100644 --- a/fieldExtraction/src/investment/one_to_n_funcs.py +++ b/fieldExtraction/src/investment/one_to_n_funcs.py @@ -263,9 +263,9 @@ def get_service_breakout(answer_dicts, filename): filename ) ) - already_seen[service_methodology] = service_breakout_answer + already_seen[service_methodology] = service_breakout_dict else: - service_breakout_answer = already_seen[service_methodology] + service_breakout_dict = already_seen[service_methodology] service_breakout_answers.append({**answer_dict, **service_breakout_dict}) @@ -330,7 +330,7 @@ def combine_one_to_n_answers(exhibit_level_answers: dict, reimbursement_level_an return combined_answers -def reimbursement_level(exhibit_text, filename, reimbursement_level_fields): +def reimbursement_level(exhibit_text, filename, reimbursement_level_fields, all_dataset): """ Processes reimbursement-level fields. Currently, runs REIMBURSEMENT_LEVEL_PRIMARY prompt only. Future secondary prompts will go in this function @@ -349,6 +349,6 @@ def reimbursement_level(exhibit_text, filename, reimbursement_level_fields): # Later, we will only run methodology breakout for those without certain carveout indicators. We will run carveout-specific breakouts for the others methodology_breakout_answers = get_methodology_breakout(carveout_answers, filename) service_breakout_answers = get_service_breakout(methodology_breakout_answers, filename) - code_breakout_answers = code_funcs.get_code_breakout(service_breakout_answers, filename) + code_breakout_answers = code_funcs.get_code_breakout(service_breakout_answers, filename, all_dataset) return code_breakout_answers diff --git a/fieldExtraction/src/utils/io_utils.py b/fieldExtraction/src/utils/io_utils.py index 67f4c77..0918bde 100644 --- a/fieldExtraction/src/utils/io_utils.py +++ b/fieldExtraction/src/utils/io_utils.py @@ -7,6 +7,7 @@ from pyxlsb import open_workbook import src.tracking.tracking_utils as tracking_utils from src import config +from src.investment.code_funcs import crosswalk_levels, get_mappings def read_local(file_path): # io_utils.py @@ -258,4 +259,15 @@ def write_s3(df, filename, run_timestamp, output_type): if output_type == "final": print(f"Saved batch output file: {output_path}") elif output_type == "individual": - print(f"Saved individual output file: {output_path}") \ No newline at end of file + print(f"Saved individual output file: {output_path}") + + +def load_all_dataset(): + """_summary_: loads all csv files required for processing contracts including crosswalk files + and mappings (embeddings, past results may be added later) + """ + all_dataset = {} + all_dataset['codes_crosswalk'] = crosswalk_levels() + all_dataset['codes_mappings'] = get_mappings() + + return all_dataset \ No newline at end of file diff --git a/fieldExtraction/src/utils/string_utils.py b/fieldExtraction/src/utils/string_utils.py index 830e008..acaa521 100644 --- a/fieldExtraction/src/utils/string_utils.py +++ b/fieldExtraction/src/utils/string_utils.py @@ -289,6 +289,9 @@ def is_empty(value): Returns: bool: True if the value is empty or invalid, False otherwise. """ + if isinstance(value, list): # Handle list inputs + return not value or all(is_empty(v) for v in value) + if pd.isna(value): return True else: