James G. Mork

55 papers Misc 25Journal 13Unranked 17
YearRankTypeTitle / Venue / Authors
2025 conf
MedInfo
Chris J. Lu, Amanda Payne, James G. Mork
2023 J jnl
J. Assoc. Inf. Sci. Technol.
Alastair R. Rae, James G. Mork, Dina Demner-Fushman
2023 J jnl
Frontiers Res. Metrics Anal.
Anastasia Krithara, James G. Mork, Anastasios Nentidis, Georgios Paliouras
2021 conf
CLEF (Working Notes)
Alastair R. Rae, James G. Mork, Dina Demner-Fushman
2021 conf
SDU@AAAI
Dina Demner-Fushman, Willie J. Rogers, James G. Mork
2021 Misc conf
AMIA
Daniel X. Le, James G. Mork, Sameer Antani
2021 Misc conf
AMIA
Chris J. Lu, Amanda Payne, James G. Mork
2021 J jnl
J. Am. Medical Informatics Assoc.
Chris J. Lu, Amanda Payne, James G. Mork
2021 Misc conf
AMIA
Victor Cid, James G. Mork
2020 Misc conf
AMIA
Alastair R. Rae, David O. Pritchard, James G. Mork, Dina Demner-Fushman
2020 Misc conf
AMIA
Chris J. Lu, Amanda Payne, James G. Mork
2020 J jnl
J. Am. Medical Informatics Assoc.
Chris J. Lu, Amanda Payne, James G. Mork
2019 Misc conf
AMIA
Alastair R. Rae, Max E. Savery, James G. Mork, Dina Demner-Fushman
2019 conf
PKDD/ECML Workshops (2)
Alastair R. Rae, James G. Mork, Dina Demner-Fushman
2019 Misc conf
AMIA
Max E. Savery, Melanie Huston, James G. Mork, Olga Printseva, Susan Schmidt, Alastair R. Rae, Dina Demner-Fushman
2018 Misc conf
AMIA
Dina Demner-Fushman, James G. Mork, Willie J. Rogers, Sonya E. Shooshan, Laritza M. Rodriguez, Alan R. Aronson
2018 Misc conf
AMIA
François-Michel Lang, James G. Mork, Dina Demner-Fushman, Alan R. Aronson
2017 J jnl
J. Biomed. Semant.
James G. Mork, Alan R. Aronson, Dina Demner-Fushman
2016 Misc conf
AMIA
James G. Mork, Dina Demner-Fushman
2015 Misc conf
AMIA
Dina Demner-Fushman, James G. Mork
2015 J jnl
BMC Bioinform.
Antonio Jimeno-Yepes, Laura Plaza, Jorge Carrillo de Albornoz, James G. Mork, Alan R. Aronson
2014 conf
CLEF (Working Notes)
James G. Mork, Dina Demner-Fushman, Susan Schmidt, Alan R. Aronson
2014 Misc conf
AMIA
James G. Mork, Dina Demner-Fushman, Susan Schmidt, Alan R. Aronson
2013 Misc conf
AMIA
Antonio Jimeno-Yepes, James G. Mork, Dina Demner-Fushman, Alan R. Aronson
2013 J jnl
BMC Bioinform.
Antonio Jimeno-Yepes, J. Caitlin Sticco, James G. Mork, Alan R. Aronson
2013 conf
BioASQ@CLEF
Antonio Jimeno-Yepes, James G. Mork, Alan R. Aronson
2013 J jnl
BMC Bioinform.
Antonio José Jimeno-Yepes, Laura Plaza, James G. Mork, Alan R. Aronson, Alberto Díaz
2013 Misc conf
AMIA
Dina Demner-Fushman, James G. Mork, Alan R. Aronson
2013 conf
BioASQ@CLEF
James G. Mork, Antonio Jimeno-Yepes, Alan R. Aronson
2013 conf
BioNLP@ACL
Antonio Jimeno-Yepes, James G. Mork, Alan R. Aronson
2012 J jnl
J. Comput. Sci. Eng.
Antonio Jimeno-Yepes, James G. Mork, Dina Demner-Fushman, Alan R. Aronson
2012 conf
IHI
Antonio Jimeno-Yepes, James G. Mork, Bartlomiej Wilkowski, Dina Demner-Fushman, Alan R. Aronson
2012 conf
TREC
Dina Demner-Fushman, Swapna Abhyankar, Antonio Jimeno-Yepes, Russell F. Loane, François-Michel Lang, James G. Mork, Nicolas Ide, Alan R. Aronson
2012 Misc conf
AMIA
Anna Ripple, Lou Knecht, John Rozier, James G. Mork
2010 J jnl
J. Am. Medical Informatics Assoc.
James G. Mork, Olivier Bodenreider, Dina Demner-Fushman, Rezarta Islamaj Dogan, François-Michel Lang, Zhiyong Lu, Aurélie Névéol, Lee B. Peters, Sonya E. Shooshan, Alan R. Aronson
2010 J jnl
J. Biomed. Informatics
Dina Demner-Fushman, James G. Mork, Sonya E. Shooshan, Alan R. Aronson
2009 J jnl
J. Biomed. Informatics
Aurélie Névéol, Sonya E. Shooshan, Susanne M. Humphrey, James G. Mork, Alan R. Aronson
2009 J jnl
Bioinform.
Aurélie Névéol, James G. Mork, Alan R. Aronson
2008 Misc conf
AMIA
Alan R. Aronson, James G. Mork, Aurélie Névéol, Sonya E. Shooshan, Dina Demner-Fushman
2007 conf
BioNLP@ACL
Aurélie Névéol, James G. Mork, Alan R. Aronson
2007 conf
TREC
Dina Demner-Fushman, Susanne M. Humphrey, Nicholas C. Ide, Russell F. Loane, James G. Mork, Patrick Ruch, Miguel E. Ruiz, Lawrence H. Smith, W. John Wilbur, Alan R. Aronson
2007 Misc conf
AMIA
Aurélie Névéol, Sonya E. Shooshan, James G. Mork, Alan R. Aronson
2007 conf
BioNLP@ACL
Alan R. Aronson, Olivier Bodenreider, Dina Demner-Fushman, Kin Wah Fung, Vivian K. Lee, James G. Mork, Aurélie Névéol, Lee B. Peters, Willie J. Rogers
2005 Misc conf
AMIA
Aurélie Névéol, James G. Mork, Alan R. Aronson, Stéfan Jacques Darmoni
2004 conf
MedInfo
George R. Kim, Alan R. Aronson, James G. Mork, Bernard A. Cohen, Christoph U. Lehmann
2004 conf
TREC
Alan R. Aronson, Susanne M. Humphrey, Nicholas C. Ide, Won Kim, Russell F. Loane, James G. Mork, Lawrence H. Smith, Lorraine K. Tanabe, W. John Wilbur, Natalie Xie, Dina Demner-Fushman, Hongfang Liu
2004 conf
MedInfo
Alan R. Aronson, James G. Mork, Clifford W. Gay, Susanne M. Humphrey, Willie J. Rogers
2003 Misc conf
AMIA
Joyce A. Mitchell, Alan R. Aronson, James G. Mork, Lillian C. Folk, Susanne M. Humphrey, Janice M. Ward
2003 conf
TREC
Mehmet Kayaalp, Alan R. Aronson, Susanne M. Humphrey, Nicholas C. Ide, Lorraine K. Tanabe, Lawrence H. Smith, Dina Demner-Fushman, Russell F. Loane, James G. Mork, Olivier Bodenreider
2002 Misc conf
AMIA
Suresh Srinivasan, Thomas C. Rindflesch, William T. Hole, Alan R. Aronson, James G. Mork
2001 Misc conf
AMIA
Marc Weeber, James G. Mork, Alan R. Aronson
2000 Misc conf
AMIA
Marc Weeber, Henny Klein, Alan R. Aronson, James G. Mork, Lolkje T. W. de Jong-van den Berg, Rein Vos
2000 Misc conf
AMIA
Alan R. Aronson, Olivier Bodenreider, Florence Chang, Susanne M. Humphrey, James G. Mork, Stuart J. Nelson, Thomas C. Rindflesch, W. John Wilbur
1999 Misc conf
AMIA
W. John Wilbur, George F. Hazard Jr., Guy Divita, James G. Mork, Alan R. Aronson, Allen C. Browne
1999 Misc conf
AMIA
Stuart J. Nelson, Alan R. Aronson, Tamas E. Doszkocs, W. John Wilbur, Olivier Bodenreider, H. Florence Chang, James G. Mork, Alexa T. McCray
redb/extractors/decompiler/bninja/analysis/medium_level.py
← Index redb/extractors/decompiler/bninja/analysis/medium_level.py python
import time

from binaryninja import (
    MediumLevelILOperation as MLIL_OP,
)

try:
    from ..function_type import FunctionTypeAnalysis
    from ..similarity.minhasher import MinHasher, TokenKind
    from ..utils.hashes import calculate_sha256, calculate_tlsh
    from .medium_level_normalization import MediumLevelNormalization
except ImportError:
    from redb.extractors.decompiler.bninja.analysis.medium_level_normalization import MediumLevelNormalization
    from redb.extractors.decompiler.bninja.similarity.minhasher import MinHasher
    from redb.extractors.decompiler.bninja.function_type import FunctionTypeAnalysis
    from redb.extractors.decompiler.bninja.utils.hashes import calculate_sha256, calculate_tlsh


_MLIL_CALL_OPS = (
    MLIL_OP.MLIL_CALL,
    MLIL_OP.MLIL_CALL_SSA,
    MLIL_OP.MLIL_CALL_UNTYPED,
    MLIL_OP.MLIL_CALL_UNTYPED_SSA,
    MLIL_OP.MLIL_TAILCALL,
    MLIL_OP.MLIL_TAILCALL_SSA,
    MLIL_OP.MLIL_TAILCALL_UNTYPED,
    MLIL_OP.MLIL_TAILCALL_UNTYPED_SSA,
)

_MLIL_CONTROL_FLOW_OPS = (
    MLIL_OP.MLIL_IF,
    MLIL_OP.MLIL_GOTO,
    MLIL_OP.MLIL_JUMP,
    MLIL_OP.MLIL_JUMP_TO,
    MLIL_OP.MLIL_RET,
    MLIL_OP.MLIL_RET_HINT,
    MLIL_OP.MLIL_NORET,
) + _MLIL_CALL_OPS


class MediumLevelAnalysis:
    def __init__(self, function, bv, logger):
        self.function = function
        self.name = function.name
        self.start = function.start
        self.mlil_func = function.mlil
        self.bv = bv
        self.logger = logger
        self.errors = []

    def log_error(self, message, function_name, address, exception=None, error_location="unknown"):
        error_msg = f"Error in function {function_name} at {address}: {message}"
        if exception:
            error_msg += f" - {str(exception)}"
        self.logger.error(error_msg)

        error = {
            "function_name": function_name,
            "function_address": str(address),
            "error_location": error_location,
            "error_message": message,
            "error_details": str(exception) if exception else "",
            "error_type": type(exception).__name__ if exception else "Unknown",
            "timestamp": int(time.time() * 1000),
        }
        self.errors.append(error)

    def _collect_mlil_skeleton_and_typed(self):
        mlil = self.mlil_func
        if not mlil:
            return [], [], [], []

        start = self.start
        norm = MediumLevelNormalization()

        skeleton = []
        skeleton_with_addr = []
        typed = []
        typed_with_addr = []

        for il in mlil.instructions:
            skel_norm = norm.normalize_instruction_all_levels(il)
            typed_norm = norm.normalize_instr_with_operands(il)

            skeleton.append(skel_norm)
            typed.append(typed_norm)

            offset = il.address - start
            if offset < 0:
                offset = 0

            skeleton_with_addr.append((offset, skel_norm))
            typed_with_addr.append((offset, typed_norm))

        return skeleton, skeleton_with_addr, typed, typed_with_addr

    def analyze(self):
        (
            instr_skeleton,
            body_mlil_skeleton_vector,
            instr_typed,
            body_mlil_typed_vector,
        ) = self._collect_mlil_skeleton_and_typed()

        instr_skeleton_str = str(instr_skeleton)
        sha256_skeleton = calculate_sha256(instr_skeleton_str)
        tlsh_skeleton = calculate_tlsh(instr_skeleton_str)

        instr_typed_str = str(instr_typed)
        sha256_typed = calculate_sha256(instr_typed_str)
        tlsh_typed = calculate_tlsh(instr_typed_str)

        seed = 0xdeadbeef
        minhash_mlil_skeleton = MinHasher(seed, self.mlil_func, TokenKind.MLIL).calculateMinHash()
        minhash_mlil_typed = MinHasher(seed, self.mlil_func, TokenKind.TYPED_MLIL).calculateMinHash()

        medium_level_json = {
            "function_address": self.start,
            "body_mlil_skeleton_vector": body_mlil_skeleton_vector,
            "sha256_mlil_skeleton": sha256_skeleton,
            "tlsh_mlil_skeleton": tlsh_skeleton,
            "minhash_mlil_skeleton": minhash_mlil_skeleton,
            "body_mlil_typed_vector": body_mlil_typed_vector,
            "sha256_mlil_typed": sha256_typed,
            "tlsh_mlil_typed": tlsh_typed,
            "minhash_mlil_typed": minhash_mlil_typed,
        }

        return medium_level_json, self.errors