Catherine J. Staes

55 papers Misc 30Journal 22Unranked 3
YearRankTypeTitle / Venue / Authors
2023 J jnl
J. Am. Medical Informatics Assoc.
Catherine J. Staes, Anna C Beck, George Chalkidis, Carolyn H. Scheese, Teresa Taft, Jia-Wen Guo, Michael G. Newman, Kensaku Kawamoto, Elizabeth A. Sloss, Jordan P. McPherson
2023 J jnl
J. Am. Medical Informatics Assoc.
Brian E. Dixon, Catherine J. Staes, Jessica Acharya, Katie S. Allen, Joel Hartsell, Theresa Cullen, Leslie Lenert, Donald W. Rucker, Harold P. Lehmann
2023 J jnl
J. Am. Medical Informatics Assoc.
Catherine J. Staes, Saldi Yusuf, Medalit Hambly, Saifon Phengphoo, Jia-Wen Guo
2023 J jnl
J. Am. Medical Informatics Assoc.
Jessica C. Acharya, Catherine J. Staes, Katie S. Allen, Joel Hartsell, Theresa A. Cullen, Leslie Lenert, Donald W. Rucker, Harold P. Lehmann, Brian E. Dixon
2022 J jnl
J. Biomed. Informatics
Polina V. Kukhareva, Charlene R. Weir, Guilherme Del Fiol, Gregory A. Aarons, Teresa Taft, Chelsey R. Schlechter, Thomas J. Reese, Rebecca L. Curran, Claude J. Nanjo, Damian Borbolla, Catherine J. Staes, Keaton L. Morgan, Heidi Kramer, Carole H. Stipelman, Julie Shakib, Michael C. Flynn, Kensaku Kawamoto
2021 J jnl
Appl. Clin. Inform.
Brian J. Douthit, Guilherme Del Fiol, Catherine J. Staes, Sharron L. Docherty, Rachel L. Richesson
2021 J jnl
J. Biomed. Informatics
Peter Taber, Catherine J. Staes, Saifon Phengphoo, Elisa Rocha, Adria Lam, Guilherme Del Fiol, Saverio M. Maviglia, Roberto A. Rocha
2021 J jnl
Appl. Clin. Inform.
Victoria L. Tiase, Sarah E. Wawrzynski, Katherine A. Sward, Guilherme Del Fiol, Catherine J. Staes, Charlene R. Weir, Mollie R. Cummins
2020 Misc conf
AMIA
Damian A. Borbolla, Catherine J. Staes, Laura K. Heermann Langford, Viet Nguyen
2020 J jnl
J. Am. Medical Informatics Assoc.
Rachel L. Richesson, Catherine J. Staes, Brian J. Douthit, Traci Thoureen, Daniel J. Hatch, Kensaku Kawamoto, Guilherme Del Fiol
2020 J jnl
J. Am. Medical Informatics Assoc.
Catherine J. Staes, James Jellison, Mary Beth Kurilo, Rick Keller, Hadi Kharrazi
2020 Misc conf
AMIA
Saldi Yusuf, Medalit Hambly, Catherine J. Staes
2018 Misc conf
AMIA
Jean F. Louis, Leah R. Yingling, Guilherme Del Fiol, Catherine J. Staes
2018 Misc conf
AMIA
John W. Loonsk, Catherine J. Staes, Joe Jackson, John Stamm
2018 Misc conf
AMIA
Polina V. Kukhareva, Charlene R. Weir, Catherine J. Staes, Damian A. Borbolla, Stacey Slager, Kensaku Kawamoto
2017 Misc conf
AMIA
Catherine J. Staes, John W. Loonsk, Kathryn Turner, Noam H. Arzt, Patina Zarcone
2017 J jnl
J. Biomed. Informatics
Polina V. Kukhareva, Catherine J. Staes, Kevin Noonan, Heather Mueller, Phillip B. Warner, David Shields, Howard Weeks, Kensaku Kawamoto
2017 Misc conf
AMIA
Carl J. Grafe, Catherine J. Staes, Kensaku Kawamoto, Matthew H. Samore, R. Scott Evans
2016 Misc conf
AMIA
Jeffrey Duncan, Catherine J. Staes
2016 Misc conf
AMIA
Catherine J. Staes, Sunanda R. McGarvey, Shan He, Ryan Arnold, Laura A. Conn
2016 Misc conf
AMIA
Yik-Ki J. Wan, Catherine J. Staes
2016 Misc conf
AMIA
Michael Totzke, Catherine J. Staes, Julie Shakib
2016 Misc conf
AMIA
Prasad Unni, Catherine J. Staes, Howard Weeks, Heidi Kramer, Damian A. Borbolla, Stacey Slager, Teresa Taft, Valliammai Chidambaram, Charlene R. Weir
2015 J jnl
J. Am. Medical Informatics Assoc.
Jeffrey Duncan, Scott P. Narus, Stephen Clyde, Karen Eilbeck, Sidney N. Thornton, Catherine J. Staes
2015 Misc conf
AMIA
Tyler J. Tippetts, Phillip B. Warner, Polina V. Kukhareva, David Shields, Catherine J. Staes, Kensaku Kawamoto
2015 Misc conf
AMIA
Yanhua Lin, Catherine J. Staes, David Shields, Vijayabhaskar R. Kandula, Brandon M. Welch, Kensaku Kawamoto
2015 Misc conf
AMIA
Polina V. Kukhareva, Catherine J. Staes, Tyler J. Tippetts, Phillip B. Warner, David Shields, Heather Mueller, Kevin Noonan, Kensaku Kawamoto
2015 Misc conf
AMIA
Jason R. Jacobs, Scott P. Narus, R. Scott Evans, Catherine J. Staes
2015 Misc conf
AMIA
Sunanda R. McGarvey, Denisha Abrams, Janet Hui, Laura A. Conn, Catherine J. Staes
2015 J jnl
J. Am. Medical Informatics Assoc.
Kensaku Kawamoto, Cary J. Martin, Kip Williams, Ming-Chieh Tu, Charlton G. Park, Cheri Hunter, Catherine J. Staes, Bruce E. Bray, Vikrant G. Deshmukh, Reid A. Holbrook, Scott J. Morris, Matthew B. Fedderson, Amy Sletta, James Turnbull, Sean J. Mulvihill, Gordon L. Crabtree, David E. Entwistle, Quinn L. McKenna, Michael B. Strong, Robert C. Pendleton, Vivian S. Lee
2014 Misc conf
AMIA
Polina V. Kukhareva, Kensaku Kawamoto, David Shields, Darryl Barfuss, Anne Halley, Tyler J. Tippetts, Phillip B. Warner, Bruce E. Bray, Catherine J. Staes
2014 Misc conf
AMIA
Karen Eilbeck, Julie Lipstein, Sunanda R. McGarvey, Catherine J. Staes
2014 Misc conf
AMIA
Yanhua Lin, Brandon M. Welch, Tyler J. Tippetts, Polina V. Kukhareva, David Shields, Catherine J. Staes, Vijayabhaskar R. Kandula, Bruce E. Bray, Kensaku Kawamoto
2014 Misc conf
AMIA
Tyler J. Tippetts, Phillip B. Warner, David Shields, Salvador Rodriguez-Loya, Catherine J. Staes, Kensaku Kawamoto
2013 Misc conf
AMIA
Jitsupa Peelay, Jeffrey Duncan, Catherine J. Staes
2013 conf
ICBO
Karen Eilbeck, Jason R. Jacobs, Sunanda R. McGarvey, Cynthia Vinion, Catherine J. Staes
2013 conf
HICSS
Karen Eilbeck, Jason R. Jacobs, Catherine J. Staes
2013 Misc conf
AMIA
Jeffrey Duncan, Karen Eilbeck, Catherine J. Staes, Scott P. Narus, Stephen Clyde
2012 Misc conf
AMIA
Jason R. Jacobs, Catherine J. Staes, Kensaku Kawamoto, David Shields
2012 Misc conf
AMIA
Jeffrey Duncan, Todd Grey, Leslie Lenert, Brian C. Sauer, Catherine J. Staes
2012 Misc conf
AMIA
Richard L. Bradshaw, Catherine J. Staes, Guilherme Del Fiol, Nicholas Schultz, Scott P. Narus, Joyce A. Mitchell
2012 J jnl
BMC Medical Informatics Decis. Mak.
Kailah Davis, Catherine J. Staes, Jeffrey Duncan, Sean Igo, Julio C. Facelli
2012 Misc conf
AMIA
Kensaku Kawamoto, David Shields, Ming Tu, Jon Reid, Susan Mottice, Paul Sanders, Catherine J. Staes, Cheri Hunter, Bruce E. Bray
2011 J jnl
J. Am. Medical Informatics Assoc.
Aldo Tinoco, R. Scott Evans, Catherine J. Staes, James F. Lloyd, Jeffrey M. Rothschild, Peter J. Haug
2010 J jnl
J. Am. Medical Informatics Assoc.
Deepthi Rajeev, Catherine J. Staes, R. Scott Evans, Susan Mottice, Robert T. Rolfs, Matthew H. Samore, Jon Whitney, Richard Kurzban, Stanley M. Huff
2010 J jnl
J. Am. Medical Informatics Assoc.
Deepthi Rajeev, Catherine J. Staes, R. Scott Evans, Susan Mottice, Robert T. Rolfs, Matthew H. Samore, Jon Whitney, Richard Kurzban, Stanley M. Huff
2010 J jnl
BMC Medical Informatics Decis. Mak.
Nephi A. Walton, Mollie R. Poynton, Per H. Gesteland, Christopher G. Maloney, Catherine J. Staes, Julio C. Facelli
2009 J jnl
BMC Medical Informatics Decis. Mak.
Catherine J. Staes, Wu Xu, Samuel D. LeFevre, Ronald C. Price, Scott P. Narus, Adi V. Gundlapalli, Robert T. Rolfs, Barry Nangle, Matthew H. Samore, Julio C. Facelli
2009 Misc conf
AMIA
Yuling Jiang, Catherine J. Staes, Ted D. Adams, Steven C. Hunt
2008 J jnl
J. Am. Medical Informatics Assoc.
Catherine J. Staes, R. Scott Evans, Beatriz H. S. C. Rocha, John B. Sorensen, Stanley M. Huff, Joan Arata, Scott P. Narus
2008 Misc conf
AMIA
Per H. Gesteland, Mandy A. Allison, Catherine J. Staes, Matthew H. Samore, Michael A. Rubin, Marjorie Carter, Amyanne Wuthrich, Anita Y. Kinney, Susan Mottice, Carrie L. Byington
2007 conf
MedInfo
Catherine J. Staes, R. Scott Evans, Scott P. Narus, Stanley M. Huff, John B. Sorensen
2006 J jnl
J. Am. Medical Informatics Assoc.
Catherine J. Staes, Sterling T. Bennett, R. Scott Evans, Scott P. Narus, Stanley M. Huff, John B. Sorensen
2005 J jnl
J. Am. Medical Informatics Assoc.
Catherine J. Staes, Stanley M. Huff, R. Scott Evans, Scott P. Narus, Cyndalynn Tilley, John B. Sorensen
2003 Misc conf
AMIA
Catherine J. Staes, Stanley M. Huff, Cyndalynn Tilley, Scott P. Narus, John B. Sorensen, R. Scott Evans
redb/extractors/macho_extractors/macho_similarity_hashes.py
← Index redb/extractors/macho_extractors/macho_similarity_hashes.py python
import inspect
from datetime import datetime, timezone
from typing import Any

from redb.extractors.enum import Tag
from redb.extractors.macho_extractor import MachOExtractor


class MachOSimilarityHashExtractor(MachOExtractor):
    """Extract Mach-O similarity hashes using machofile API.

    Similarity hashes are MD5 fingerprints of sorted, deduplicated binary components:
    - dylib_hash: MD5 of dynamic library names
    - import_hash: MD5 of imported function names
    - export_hash: MD5 of exported symbol names
    - entitlement_hash: MD5 of entitlement names and array values
    - symhash: MD5 of external undefined symbols

    For FAT binaries:
    - Inserts one row per architecture slice with per-slice hashes
    - Inserts one row for the FAT container with combined hashes

    For single-arch binaries:
    - Inserts one row with that architecture's hashes

    Note: parent_sha256 and architecture relationships are tracked in redb_basic_properties,
    not duplicated here. Use JOIN with redb_basic_properties when needed.
    """

    def __init__(
        self,
        filepath,
        log,
        exporters=None,
        index_prefix=None,
        elastic_index=None,
        known_benign=False,
        known_malicious=False,
        macho=None,
    ):
        super().__init__(
            filepath,
            log,
            exporters,
            index_prefix,
            elastic_index,
            known_benign,
            known_malicious,
            macho,
        )
        self.elastic_index = self.index_prefix + "-macho_hashes"
        self.log.debug(inspect.currentframe().f_code.co_name)

    def tag(self):
        return Tag.MACHO_HASHES.value

    def _extract_similarity_hashes(self, arch_name=None):
        """Extract similarity hashes for a specific architecture."""
        self.log.debug(inspect.currentframe().f_code.co_name)

        if not self.macho:
            return None

        try:
            similarity_hashes = self.macho.get_similarity_hashes(arch=arch_name)
            return similarity_hashes if similarity_hashes else None
        except Exception as e:
            self.log.error(f"Error extracting similarity hashes for arch {arch_name}: {e}")
            return None

    def extract(self):
        self.log.debug(inspect.currentframe().f_code.co_name)
        try:
            if not self.macho:
                return None

            architectures = self.macho.get_architectures()
            if not architectures:
                return None

            if len(architectures) > 1:
                # FAT binary - return combined hashes + per-arch hashes
                results = []

                # First add combined hashes for the FAT container
                all_hashes = self.macho.get_similarity_hashes()
                combined_hashes = all_hashes.get('combined', {}) if all_hashes else {}
                if combined_hashes:
                    combined_hashes['arch_identifier'] = 'fat'
                    results.append(combined_hashes)

                # Then add per-arch hashes
                for arch_name in architectures:
                    hashes = self._extract_similarity_hashes(arch_name)
                    if hashes:
                        hashes['arch_identifier'] = arch_name
                        results.append(hashes)
                return results
            else:
                # Single architecture - return single result
                return self._extract_similarity_hashes(architectures[0])
        except Exception as e:
            self.log.error(f"Error extracting similarity hashes: {e}")
            return None

    def prepare_export_data(self, exporter_type: str) -> Any:
        if exporter_type == "ElasticsearchExporter":
            return self.extract()
        elif exporter_type == "ClickHouseExporter":
            if not self.macho:
                return None

            try:
                architectures = self.macho.get_architectures()
                is_fat = len(architectures) > 1
            except Exception as e:
                self.log.error(f"Could not get architectures: {e}")
                return None

            data = []
            current_time = datetime.now(timezone.utc)

            # For FAT binaries, first insert a row for the container with combined hashes
            if is_fat:
                all_hashes = self.macho.get_similarity_hashes()  # Without arch returns all including 'combined'
                combined_hashes = all_hashes.get('combined', {}) if all_hashes else {}
                if combined_hashes:
                    data.append([
                        self.sha256,                                    # sha256 (FAT container)
                        combined_hashes.get('dylib_hash'),              # dylib_hash
                        combined_hashes.get('import_hash'),             # import_hash
                        combined_hashes.get('export_hash'),             # export_hash
                        combined_hashes.get('entitlement_hash'),        # entitlement_hash
                        combined_hashes.get('symhash'),                 # symhash
                        current_time,                                   # analysis_date
                    ])

            # Insert rows for each architecture slice
            for arch_name in architectures:
                # Get architecture-specific sha256
                try:
                    arch_general_info = self.macho.get_general_info(arch=arch_name)
                    arch_sha256 = arch_general_info.get('SHA256', self.sha256)
                except Exception as e:
                    self.log.warning(f"Could not get arch-specific sha256 for {arch_name}: {e}")
                    arch_sha256 = self.sha256

                # Get similarity hashes for this architecture
                similarity_hashes = self._extract_similarity_hashes(arch_name)
                if not similarity_hashes:
                    continue

                data.append([
                    arch_sha256,                                    # sha256 (arch-specific)
                    similarity_hashes.get('dylib_hash'),            # dylib_hash
                    similarity_hashes.get('import_hash'),           # import_hash
                    similarity_hashes.get('export_hash'),           # export_hash
                    similarity_hashes.get('entitlement_hash'),      # entitlement_hash
                    similarity_hashes.get('symhash'),               # symhash
                    current_time,                                   # analysis_date
                ])

            if not data:
                return None

            column_names = [
                'sha256',
                'macho_dylib_hash', 'macho_import_hash', 'macho_export_hash',
                'macho_entitlement_hash', 'macho_symhash',
                'analysis_date'
            ]

            column_type_names = [
                'FixedString(64)',
                'Nullable(FixedString(32))', 'Nullable(FixedString(32))', 'Nullable(FixedString(32))',
                'Nullable(FixedString(32))', 'Nullable(FixedString(32))',
                'DateTime64(3, \'UTC\')'
            ]

            return (data, column_names, column_type_names)

        return None

    def get_clickhouse_table(self) -> str:
        return "redb_hashes"