James R. Faeder

42 papers A* 1A 1C 1Misc 2Journal 22Unranked 14
YearRankTypeTitle / Venue / Authors
2025 J jnl
PLoS Comput. Biol.
Caroline I. Larkin, Matthew D. Dunn, Jason E. Shoemaker, William B. Klimstra, James R. Faeder
2024 J jnl
PLoS Comput. Biol.
Adam Husár, Mariam Ordyan, Guadalupe C. Garcia, Joel G. Yancey, Ali Sinan Saglam, James R. Faeder, Thomas M. Bartol, Mary B. Kennedy, Terrence J. Sejnowski
2022 J jnl
CoRR
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
2022 J jnl
Nucleic Acids Res.
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
2021 J jnl
PLoS Comput. Biol.
Robin Schmucker, Gabriele Farina, James R. Faeder, Fabian Fröhlich, Ali Sinan Saglam, Tuomas Sandholm
2020 J jnl
PLoS Comput. Biol.
Sanjana Gupta, Robin E. C. Lee, James R. Faeder
2020 J jnl
J. Integr. Bioinform.
Fengkai Zhang, Lucian P. Smith, Michael L. Blinov, James R. Faeder, William S. Hlavacek, José Juan Tapia, Sarah M. Keating, Nicolas Rodriguez, Andreas Dräger, Leonard A. Harris, Andrew Finney, Bin Hu, Michael Hucka, Martin Meier-Schellersheim
2018 C conf
PDP
Sanjana Gupta, Liam Hainsworth, Justin S. Hogg, Robin Lee, James R. Faeder
2017 J jnl
PLoS Comput. Biol.
John A. P. Sekar, José Juan Tapia, James R. Faeder
2016 J jnl
Bioinform.
Leonard A. Harris, Justin S. Hogg, José Juan Tapia, John A. P. Sekar, Sanjana Gupta, Ilya Korsunsky, Arshi Arora, Dipak Barua, Robert P. Sheehan, James R. Faeder
2016 conf
BIBM
John A. P. Sekar, Justin S. Hogg, James R. Faeder
2016 conf
CMSB
Qinsi Wang, Natasa Miskov-Zivanov, Bing Liu, James R. Faeder, Michael Lotze, Edmund M. Clarke
2016 conf
HLDVT
Natasa Miskov-Zivanov, Paolo Zuliani, Qinsi Wang, Edmund M. Clarke, James R. Faeder
2016 conf
BIBM
Bing Liu, James R. Faeder
2016 J jnl
PLoS Comput. Biol.
Rory M. Donovan, José Juan Tapia, Devin P. Sullivan, James R. Faeder, Robert F. Murphy, Markus Dittrich, Daniel M. Zuckerman
2015 conf
ACM Great Lakes Symposium on VLSI
Devin P. Sullivan, Rohan Arepally, Robert F. Murphy, José Juan Tapia, James R. Faeder, Markus Dittrich, Jacob Czech
2014 J jnl
PLoS Comput. Biol.
Justin S. Hogg, Leonard A. Harris, Lori J. Stover, Niketh S. Nair, James R. Faeder
2014 ch.
Encyclopedia of Computational Neuroscience
Thomas M. Bartol, Markus Dittrich, James R. Faeder
2014 J jnl
BMC Bioinform.
John E. Wenskovitch, Leonard A. Harris, José Juan Tapia, James R. Faeder, G. Elisabeta Marai
2013 A* conf
DAC
Natasa Miskov-Zivanov, Diana Marculescu, James R. Faeder
2013 conf
BCB
Natasa Miskov-Zivanov, Paolo Zuliani, Edmund M. Clarke, James R. Faeder
2013 conf
BCB
José Juan Tapia, James R. Faeder
2012 conf
CDC
José Juan Tapia, James R. Faeder, Brian Munsky
2012 A conf
ICCAD
Natasa Miskov-Zivanov, James R. Faeder, Chris J. Myers, Herbert M. Sauro
2012 J jnl
BMC Bioinform.
Adam M. Smith, Wen Xu, Yao Sun, James R. Faeder, G. Elisabeta Marai
2011 conf
BCB
Natasa Miskov-Zivanov, Andrew Bresticker, Deepa Krishnaswamy, Sreesan Venkatakrishnan, Diana Marculescu, James R. Faeder
2011 conf
EMBC
Natasa Miskov-Zivanov, Andrew Bresticker, Deepa Krishnaswamy, Sreesan Venkatakrishnan, Prashant Kashinkunti, Diana Marculescu, James R. Faeder
2011 conf
BioVis
Adam M. Smith, Wen Xu, Yao Sun, James R. Faeder, G. Elisabeta Marai
2011 J jnl
Bioinform.
Wen Xu, Adam M. Smith, James R. Faeder, G. Elisabeta Marai
2011 conf
BICoB
Haijun Gong, Qinsi Wang, Paolo Zuliani, James R. Faeder, Michael Lotze
2010 J jnl
BMC Bioinform.
Haijun Gong, Paolo Zuliani, Anvesh Komuravelli, James R. Faeder, Edmund M. Clarke
2010 conf
ANB
Haijun Gong, Paolo Zuliani, Anvesh Komuravelli, James R. Faeder, Edmund M. Clarke
2009 J jnl
PLoS Comput. Biol.
Dipak Barua, James R. Faeder, Jason M. Haugh
2009 Misc conf
WSC
Leonard A. Harris, Justin S. Hogg, James R. Faeder
2009 J jnl
Bioinform.
Bin Hu, G. Matthew Fricke, James R. Faeder, Richard G. Posner, William S. Hlavacek
2009 J jnl
Bioinform.
Joshua Colvin, Michael I. Monine, James R. Faeder, William S. Hlavacek, Daniel D. Von Hoff, Richard G. Posner
2008 conf
CMSB
Edmund M. Clarke, James R. Faeder, Christopher James Langmead, Leonard A. Harris, Sumit Kumar Jha, Axel Legay
2007 J jnl
Bioinform.
Fangping Mu, Robert F. Williams, Clifford J. Unkefer, Pat J. Unkefer, James R. Faeder, William S. Hlavacek
2006 J jnl
Trans. Comp. Sys. Biology
Michael L. Blinov, Jin Yang, James R. Faeder, William S. Hlavacek
2005 Misc conf
SAC
James R. Faeder, Michael L. Blinov, William S. Hlavacek
2005 J jnl
Complex.
James R. Faeder, Michael L. Blinov, Byron Goldstein, William S. Hlavacek
2004 J jnl
Bioinform.
Michael L. Blinov, James R. Faeder, Byron Goldstein, William S. Hlavacek
redb/extractors/macho_extractors/macho_imports.py
← Index redb/extractors/macho_extractors/macho_imports.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
from redb.models.dataclasses import MachOImport


class MachOImportExtractor(MachOExtractor):

    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_imports"
        self.log.debug(inspect.currentframe().f_code.co_name)

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

    def _extract_imports(self, arch_name=None):
        """Extract import information from the MachO binary for a specific architecture.

        Handles machofile v2026.2.4+ API where get_imported_functions() returns:
        Dict[str, List[Dict]] where each dict has {'name': str, 'sources': [str, ...]}
        """
        self.log.debug(inspect.currentframe().f_code.co_name)

        if not self.macho:
            return None

        try:
            # Get imported functions using API for specific architecture
            imported_functions = self.macho.get_imported_functions(arch=arch_name)
            if not imported_functions:
                return None

            # Keep the library→functions mapping (like PE does)
            library_names = []
            imports_with_mapping = []  # List of {library: [(name, source), ...]}

            for dylib_name, functions in imported_functions.items():
                # v2026.2.4+: dylib_name is already str, but handle bytes for compatibility
                if isinstance(dylib_name, bytes):
                    dylib_name = dylib_name.decode('utf-8', errors='replace')
                library_names.append(dylib_name)

                # Process function entries
                func_list = []
                for func_entry in functions:
                    # v2026.2.4+: func_entry is {'name': str, 'sources': [str, ...]}
                    if isinstance(func_entry, dict):
                        func_name = func_entry.get('name', '')
                        # Join sources if multiple, take first if single
                        sources = func_entry.get('sources', [])
                        import_source = sources[0] if sources else None
                        func_list.append((func_name, import_source))
                    else:
                        # Legacy format: func_entry is str or bytes
                        if isinstance(func_entry, bytes):
                            func_entry = func_entry.decode('utf-8', errors='replace')
                        func_list.append((func_entry, None))

                imports_with_mapping.append({dylib_name: func_list})

            # Count total functions
            total_functions = sum(len(list(d.values())[0]) for d in imports_with_mapping)

            # Create import dataclass with mapping preserved
            macho_import = MachOImport(
                macho_imports_total=total_functions,
                macho_import_libraryName=library_names if library_names else None,
                macho_import_functions=imports_with_mapping if imports_with_mapping else None
            )

            return macho_import

        except Exception as e:
            self.log.error(f"Error extracting MachO imports for arch {arch_name}: {e}")
            return None

    def extract(self):
        self.log.debug(inspect.currentframe().f_code.co_name)
        try:
            # Get architectures (macho is already parsed in base class)
            architectures = self.macho.get_architectures()
            if len(architectures) > 1:
                # FAT binary - return list of imports for each architecture
                results = []
                for arch_name in architectures:
                    imports = self._extract_imports(arch_name)
                    if imports:
                        imports.arch_identifier = arch_name
                        results.append(imports)
                return results
            else:
                # Single architecture - return single result
                return self._extract_imports(architectures[0] if architectures else None)
        except Exception as e:
            self.log.error(f"Error extracting MachO imports: {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

            # Get architectures (macho is already parsed in base class)
            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

            # Flatten the data - one row per function import (like PE imports)
            data = []
            current_time = datetime.now(timezone.utc)

            # Loop through each architecture (1 for single, multiple for FAT)
            for arch_name in architectures:
                # Get architecture-specific sha256
                try:
                    arch_general_info = self.macho.get_general_info(arch=arch_name)
                    arch_header_raw = self.macho.get_macho_header(arch=arch_name)
                    arch_sha256 = arch_general_info.get('SHA256', self.sha256)
                    arch_cputype_raw = arch_header_raw.get('cputype', 0) if arch_header_raw else 0
                except Exception as e:
                    self.log.warning(f"Could not get arch-specific data for {arch_name}: {e}")
                    arch_sha256 = self.sha256
                    arch_cputype_raw = 0

                # Get imports for this architecture
                macho_import = self._extract_imports(arch_name)
                if not macho_import or not macho_import.macho_import_functions:
                    continue

                # Flatten to one row per (library, function) pair
                for lib_funcs in macho_import.macho_import_functions:
                    for lib, funcs in lib_funcs.items():
                        for func_name, import_source in funcs:
                            data.append([
                                arch_sha256,        # sha256 (arch-specific)
                                lib,                # library_name
                                func_name,          # function_name
                                import_source,      # import_source (chained_fixups, bind_opcodes, symtab)
                                current_time,       # analysis_date
                            ])

            column_names = [
                'sha256',
                'library_name', 'function_name', 'import_source',
                'analysis_date'
            ]

            if not data:
                return None

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

            return (data, column_names, column_type_names)

        return None

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