Vandana V. Mukherjee

23 papers A* 2Misc 3Journal 10Unranked 7
YearRankTypeTitle / Venue / Authors
2026 conf
EACL (Industry Track)
Che-Ming Chang, Prashanth Vijayaraghavan, Ashutosh Jadhav, Charles Mackin, Hsinyu Tsai, Vandana V. Mukherjee, Ehsan Degan
2026 J jnl
CoRR
Che-Ming Chang, Prashanth Vijayaraghavan, Ashutosh Jadhav, Charles Mackin, Vandana V. Mukherjee, Hsinyu Tsai, Ehsan Degan
2026 conf
EACL (Industry Track)
Prashanth Vijayaraghavan, Apoorva Nitsure, Luyao Shi, Charles Mackin, Ashutosh Jadhav, David Beymer, Ehsan Degan, Vandana V. Mukherjee
2026 J jnl
CoRR
Prashanth Vijayaraghavan, Apoorva Nitsure, Luyao Shi, Charles Mackin, Ashutosh Jadhav, David Beymer, Ehsan Degan, Vandana V. Mukherjee
2025 A* conf
ICML
Prashanth Vijayaraghavan, Luyao Shi, Ehsan Degan, Vandana V. Mukherjee, Xin Zhang
2025 J jnl
CoRR
Prashanth Vijayaraghavan, Luyao Shi, Ehsan Degan, Vandana V. Mukherjee, Xin Zhang
2025 A* conf
IJCAI
Prashanth Vijayaraghavan, Soroush Vosoughi, Lamogha Chiazor, Raya Horesh, Rogério Abreu de Paula, Ehsan Degan, Vandana V. Mukherjee
2025 J jnl
CoRR
Prashanth Vijayaraghavan, Soroush Vosoughi, Lamogha Chizor, Raya Horesh, Rogério Abreu de Paula, Ehsan Degan, Vandana V. Mukherjee
2024 conf
BIOSTEC (1)
David Beymer, Vandana V. Mukherjee, Anup Pillai, Hakan Bulu, Vanessa Burrowes, James H. Kaufman, Ed Seabolt
2022 ch.
Federated Learning
Ehsan Degan, Shafiq Abedin, David Beymer, Angshuman Deb, Nathaniel Braman, Benedikt Graf, Vandana V. Mukherjee
2022 J jnl
IEEE ACM Trans. Comput. Biol. Bioinform.
Edward E. Seabolt, Gowri Nayar, Harsha Krishnareddy, Akshay Agarwal, Kristen L. Beck, Ignacio Terrizzano, Eser Kandogan, Mark Kunitomi, Mary Roth, Vandana V. Mukherjee, James H. Kaufman
2021 conf
Computer-Aided Diagnosis
Yiting Xie, Deepta Rajan, Larissa C. Schudlo, Yusuke Takeuchi, Benedikt Graf, Adam Coy, Mohammadreza Negahdar, Vandana V. Mukherjee, David Beymer, Arun Krishnan
2021 J jnl
Patterns
Jannis Born, David Beymer, Deepta Rajan, Adam Coy, Vandana V. Mukherjee, Matteo Manica, Prasanth Prasanna, Deddeh Ballah, Michal Guindy, Dorith Shaham, Pallav L. Shah, Emmanouil Karteris, Jan L. Robertus, Maria Gabrani, Michal Rosen-Zvi
2021 J jnl
Patterns
Jannis Born, David Beymer, Deepta Rajan, Adam Coy, Vandana V. Mukherjee, Matteo Manica, Prasanth Prasanna, Deddeh Ballah, Michal Guindy, Dorith Shaham, Pallav L. Shah, Emmanouil Karteris, Jan L. Robertus, Maria Gabrani, Michal Rosen-Zvi
2021 Misc conf
AMIA
Ashutosh Jadhav, Tyler Baldwin, Joy T. Wu, Vandana V. Mukherjee, Tanveer F. Syeda-Mahmood
2020 J jnl
CoRR
Alexandros Karargyris, Satyananda Kashyap, Ismini Lourentzou, Joy T. Wu, Arjun Sharma, Matthew Tong, Shafiq Abedin, David Beymer, Vandana V. Mukherjee, Elizabeth A. Krupinski, Mehdi Moradi
2020 conf
HEALTHINF
Karina Kanjaria, Anup Pillai, Chaitanya Shivade, Marina Bendersky, Vandana V. Mukherjee, Tanveer F. Syeda-Mahmood
2020 J jnl
CoRR
Karina Kanjaria, Anup Pillai, Chaitanya Shivade, Marina Bendersky, Ashutosh Jadhav, Vandana V. Mukherjee, Tanveer F. Syeda-Mahmood
2020 conf
BioNLP
Olga Kovaleva, Chaitanya Shivade, Satyananda Kashyap, Karina Kanjaria, Joy T. Wu, Deddeh Ballah, Adam Coy, Alexandros Karargyris, Yufan Guo, David James Beymer, Anna Rumshisky, Vandana V. Mukherjee
2019 J jnl
CoRR
Edward E. Seabolt, Gowri Nayar, Harsha Krishnareddy, Akshay Agarwal, Kristen L. Beck, Ignacio Terrizzano, Eser Kandogan, Mary Roth, Vandana V. Mukherjee, James H. Kaufman
2019 conf
ViGIL@NeurIPS
Olga Kovaleva, Chaitanya Shivade, Satyananda Kashyap, Karina Kanjaria, Adam Coy, Deddeh Ballah, Yufan Guo, Joy T. Wu, Alexandros Karargyris, David Beymer, Anna Rumshisky, Vandana V. Mukherjee
2018 Misc conf
AMIA
Tyler Baldwin, Yufan Guo, Vandana V. Mukherjee, Tanveer F. Syeda-Mahmood
2018 Misc conf
AMIA
Yufan Guo, Joy T. Wu, Tyler Baldwin, David Beymer, Vandana V. Mukherjee, Tanveer F. Syeda-Mahmood
redb/extractors/extractor.py
← Index redb/extractors/extractor.py python
import hashlib
import inspect
from abc import ABCMeta, abstractmethod
from dataclasses import asdict
from functools import cached_property
from datetime import datetime, timezone
import math
from typing import Counter, List, Optional, Dict, Any, Tuple
from redb import settings
from redb.models.dataclasses import Hash
from .database_exporters import DatabaseExporter, ElasticsearchExporter, ClickHouseExporter, PrintExporter

class Extractor(metaclass=ABCMeta):
    def __init__(
        self,
        filepath: str,
        log: Any,
        exporters: Optional[List[DatabaseExporter]] = None,
        index_prefix: Optional[str] = None,
        source: Optional[str] = None,
        elastic_index: Optional[str] = None,
        known_benign: bool = False,
        known_malicious: bool = False,
        precomputed_hashes: Optional[Dict[str, str]] = None,
    ):
        self.log = log
        self.log.debug(f"Creating {self.__class__.__name__}")
        self.filepath = filepath
        self.source = source
        self.exporters = exporters or []
        self.index_prefix = index_prefix if index_prefix else settings.ELASTIC_BINARIES_COLLECTION
        self.elastic_index = self.index_prefix + (elastic_index if elastic_index else "")
        self.known_benign = known_benign
        self.known_malicious = known_malicious

        # Use precomputed hashes if provided (e.g., from machofile, pefile)
        # Otherwise compute them from binary
        if precomputed_hashes:
            self.md5 = precomputed_hashes.get('md5') or precomputed_hashes.get('MD5')
            self.sha1 = precomputed_hashes.get('sha1') or precomputed_hashes.get('SHA1')
            self.sha256 = precomputed_hashes.get('sha256') or precomputed_hashes.get('SHA256')
        else:
            self.md5 = hashlib.md5(self.binary).hexdigest()
            self.sha1 = hashlib.sha1(self.binary).hexdigest()
            self.sha256 = hashlib.sha256(self.binary).hexdigest()
        self.hash = Hash(self.md5, self.sha1, self.sha256)

    @cached_property
    def binary(self):
        with open(self.filepath, "rb") as f:
            data = f.read()
        return data

    @property
    @abstractmethod
    def tag(self):
        pass

    @abstractmethod
    def extract(self):
        """
        this method defines the extracted data
        """

    @staticmethod
    def process_binary_string(s):
        # Remove \x00 padding
        s = s.rstrip(b"\x00")

        # Check if there are any non-printable characters
        has_non_printable = any(byte < 32 or byte > 126 for byte in s)

        if not has_non_printable:
            # If all characters are printable, decode the string
            return s.decode()
        else:
            # If there are non-printable characters, represent them as \xDD
            return "".join(
                [
                    f"\\x{byte:02x}" if byte < 32 or byte > 126 else chr(byte)
                    for byte in s
                ]
            )

    @staticmethod
    def remove_non_utf8(binary_string):
        decoded = b""
        for i in range(len(binary_string)):
            try:
                # Try to decode each byte
                char = binary_string[i : i + 1].decode("utf-8")
                decoded += char.encode("utf-8")
            except UnicodeDecodeError:
                # Skip this byte if it can't be decoded
                continue
        return decoded

    def calculate_entropy(self, data):
        """Calculate the entropy of a chunk of data.
        Based on pefile.SectionStructure.entropy_H.
        """
        # self.log.debug(inspect.currentframe().f_code.co_name)
        if not data:
            return 0.0

        if type(data) == str:
            counts = Counter(data)
            frequencies = ((i / len(data)) for i in counts.values())
            return - sum(f * math.log(f, 2) for f in frequencies)
        else:
            occurences = Counter(bytearray(data))
            entropy = 0
            for x in occurences.values():
                p_x = float(x) / len(data)
                entropy -= p_x * math.log(p_x, 2)
            return entropy

    @abstractmethod
    def prepare_export_data(self, exporter_type: str) -> Tuple[List[Any], List[str], List[str]]:
        """
        Prepare data for specific export type
        Returns:
            Tuple containing:
            - data: List of values to insert
            - column_names: List of column names
            - column_type_names: List of column types
        """
        pass

    def export_data(self):
        """Export data to all configured exporters

        Returns:
            True: Export succeeded
            False: Export failed (actual error)
            None: No data to export (not an error, e.g., no overlay, no signature)
        """
        self.log.debug(inspect.currentframe().f_code.co_name)
        success = True
        extracted_data = self.extract()

        if extracted_data is None:
            self.log.debug("extract() returned None, skipping export")
            return None  # No data to export, not a failure
            
        for exporter in self.exporters:
            if isinstance(exporter, PrintExporter):
                # For PrintExporter, we pass the extracted data directly
                success &= exporter.export(extracted_data)
            else:
                # Get the data prepared for this specific exporter type
                export_data = self.prepare_export_data(exporter.__class__.__name__)
                
                if export_data is None:
                    self.log.debug(f"prepare_export_data returned None for {exporter.__class__.__name__}")
                    return False
                
                if isinstance(exporter, ElasticsearchExporter):
                    success &= exporter.export(
                        export_data,
                        index=self.elastic_index,
                        tag=self.tag(),
                        hashes=asdict(self.hash),
                        known_benign=self.known_benign,
                        known_malicious=self.known_malicious
                    )
                elif isinstance(exporter, ClickHouseExporter):
                    # For ClickHouse, we need to pass the table name and the prepared data
                    success &= exporter.export(
                        export_data,
                        table=self.get_clickhouse_table(),
                        # Add these parameters explicitly
                        column_names=export_data[1] if isinstance(export_data, tuple) else None,
                        column_type_names=export_data[2] if isinstance(export_data, tuple) else None
                    )
                
        return success

    @abstractmethod
    def get_clickhouse_table(self) -> str:
        """Return the appropriate ClickHouse table name"""
        pass
    # def export_to_elastic(self, list_of_dataclasses, tag=None):
    #     self.log.debug(inspect.currentframe().f_code.co_name)

    #     if not isinstance(list_of_dataclasses, list):
    #         self.log.error("Called export_to_elastic wrongly")

    #     now_t = datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M:%S")
    #     for dataclass_ in list_of_dataclasses:
    #         if not settings.ELASTIC_CLIENT.ping():
    #             self.log.error("[CONNECTION ERROR] ping to elastic failed")
            
    #         # Convert dataclass to dict and filter out None values
    #         document = {k: v for k, v in asdict(dataclass_).items() if v is not None}
            
    #         if tag:
    #             document["tag"] = [tag, self.tag()]
    #         else:
    #             document["tag"] = self.tag()
    #         hashes = asdict(self.hash)
    #         document |= hashes
    #         document["timestamp_utc"] = now_t
    #         # document["source"] = self.source
    #         document["known_benign"] = self.known_benign
    #         document["known_malicious"] = self.known_malicious

    #         if "_id" in document:
    #             tmp_id = document.pop("_id") + document["sha256"]
    #             _id = hashlib.sha256(tmp_id.encode()).hexdigest()
    #         else:
    #             _id = document["sha256"]

    #         # self.log.debug(f"[DEBUG] about to export {type(document)} {document}")
    #         try:
    #             doc_dump = json.dumps(document)
    #         except TypeError as e:
    #             self.log.error(
    #                 f"Failed export of document. " f"full document: {document}"
    #             )
    #             raise e

    #         # body={"doc": doc_dump,
    #         #       "doc_as_upsert": True  # Create the document if it doesn't exist
    #         # }

    #         # Check if the index exists, and create it if it doesn't
    #         # if not settings.ELASTIC_CLIENT.indices.exists(index=self.elastic_index):
    #         #     settings.ELASTIC_CLIENT.indices.create(index=self.elastic_index)
    #         # pprint(doc_dump) #DEBUG
    #         # print("[DEBUG] _id: " + _id)
    #         # print("[DEBUG] index: " + self.elastic_index)
    #         settings.ELASTIC_CLIENT.index(
    #             index=self.elastic_index, id=_id, document=doc_dump
    #         )