Olivier Lichtarge

33 papers A* 3B 1Misc 6Journal 22Unranked 1
YearRankTypeTitle / Venue / Authors
2023 J jnl
Bioinform.
Chen Wang, Harikumar Govindarajan, Panagiotis Katsonis, Olivier Lichtarge
2021 J jnl
Bioinform.
Chen Wang, Daniel M. Konecki, David C. Marciano, Harikumar Govindarajan, Amanda M. Williams, Brigitta Wastuwidyaningtyas, Thomas Bourquard, Panagiotis Katsonis, Olivier Lichtarge
2021 J jnl
Bioinform.
Chih-Hsu Lin, Olivier Lichtarge
2020 J jnl
PLoS Comput. Biol.
Ilya B. Novikov, Angela D. Wilkins, Olivier Lichtarge
2020 J jnl
Bioinform.
Minh Pham, Stephen J. Wilson, Harikumar Govindarajan, Chih-Hsu Lin, Olivier Lichtarge
2020 J jnl
Bioinform.
Minh Pham, Stephen J. Wilson, Harikumar Govindarajan, Chih-Hsu Lin, Olivier Lichtarge
2020 Misc conf
PSB
Minh Pham, Olivier Lichtarge
2019 J jnl
Bioinform.
Chih-Hsu Lin, Daniel M. Konecki, Meng Liu, Stephen J. Wilson, Huda Nassar, Angela D. Wilkins, David F. Gleich, Olivier Lichtarge
2017 Misc conf
PSB
Stephen J. Wilson, Angela D. Wilkins, Chih-Hsu Lin, Rhonald C. Lua, Olivier Lichtarge
2017 Misc conf
PSB
Jonathan Gallion, Angela D. Wilkins, Olivier Lichtarge
2016 Misc conf
PSB
Sam Regenbogen, Angela D. Wilkins, Olivier Lichtarge
2016 Misc conf
PSB
Amanda Koire, Panagiotis Katsonis, Olivier Lichtarge
2016 J jnl
Nucleic Acids Res.
Rhonald C. Lua, Stephen J. Wilson, Daniel M. Konecki, Angela D. Wilkins, Eric Venner, Daniel H. Morgan, Olivier Lichtarge
2015 A* conf
KDD
Meenakshi Nagarajan, Angela D. Wilkins, Benjamin J. Bachman, Ilya B. Novikov, Shenghua Bao, Peter J. Haas, María E. Terrón-Díaz, Sumit Bhatia, Anbu K. Adikesavan, Jacques J. Labrie, Sam Regenbogen, Christie M. Buchovecky, Curtis R. Pickering, Linda Kato, Andreas Martin Lisewski, Ana Lelescu, Houyin Zhang, Stephen Boyer, Griff Weber, Ying Chen, Lawrence A. Donehower, W. Scott Spangler, Olivier Lichtarge
2014 A* conf
KDD
W. Scott Spangler, Angela D. Wilkins, Benjamin J. Bachman, Meena Nagarajan, Tajhal Dayaram, Peter J. Haas, Sam Regenbogen, Curtis R. Pickering, Austin Comer, Jeffrey N. Myers, Ioana Stanoi, Linda Kato, Ana Lelescu, Jacques J. Labrie, Neha Parikh, Andreas Martin Lisewski, Lawrence A. Donehower, Ying Chen, Olivier Lichtarge
2013 J jnl
Bioinform.
Angela D. Wilkins, Eric Venner, David C. Marciano, Serkan Erdin, Benu Atri, Rhonald C. Lua, Olivier Lichtarge
2013 J jnl
BMC Bioinform.
Serkan Erdin, Eric Venner, Andreas Martin Lisewski, Olivier Lichtarge
2012 J jnl
Bioinform.
Benjamin J. Bachman, Eric Venner, Rhonald C. Lua, Serkan Erdin, Olivier Lichtarge
2010 J jnl
Bioinform.
Rhonald C. Lua, Olivier Lichtarge
2009 J jnl
Bioinform.
R. Matthew Ward, Eric Venner, Bryce Daines, Stephen Murray, Serkan Erdin, David M. Kristensen, Olivier Lichtarge
2008 J jnl
BMC Bioinform.
David M. Kristensen, R. Matthew Ward, Andreas Martin Lisewski, Serkan Erdin, Brian Y. Chen, Viacheslav Fofanov, Marek Kimmel, Lydia E. Kavraki, Olivier Lichtarge
2007 J jnl
BMC Bioinform.
Ivana Mihalek, I. Res, Olivier Lichtarge
2007 J jnl
J. Bioinform. Comput. Biol.
Brian Y. Chen, Drew H. Bryant, Viacheslav Fofanov, David M. Kristensen, Amanda E. Cruess, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
2007 J jnl
Bioinform.
Hyunjung Shin, Andreas Martin Lisewski, Olivier Lichtarge
2007 conf
BIOCOMP
Hyunjung Shin, Andreas Martin Lisewski, Olivier Lichtarge
2007 J jnl
J. Comput. Biol.
Brian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
2006 J jnl
Bioinform.
Ivana Mihalek, I. Res, Olivier Lichtarge
2006 J jnl
Bioinform.
Daniel H. Morgan, David M. Kristensen, David Mittelman, Olivier Lichtarge
2006 J jnl
Bioinform.
Ivana Mihalek, I. Res, Olivier Lichtarge
2006 B conf
RECOMB
Brian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
2005 Misc conf
Pacific Symposium on Biocomputing
Brian Y. Chen, Viacheslav Fofanov, David M. Kristensen, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
2005 J jnl
Bioinform.
I. Res, Ivana Mihalek, Olivier Lichtarge
1986 A* conf
AAAI
Barbara Hayes-Roth, Bruce G. Buchanan, Olivier Lichtarge, Mike Hewitt, Russ B. Altman, James F. Brinkley, Craig Cornelius, Bruce S. Duncan, Oleg Jardetzky
tests/unit/conftest_binja_stubs.py
← Index tests/unit/conftest_binja_stubs.py python
"""Stubs for binaryninja module so decompiler unit tests can import
without a Binary Ninja license."""

import sys
from unittest.mock import MagicMock
from enum import IntEnum


# Stub binaryninja.enums
class BranchType(IntEnum):
    UnconditionalBranch = 0
    FalseBranch = 1
    TrueBranch = 2
    CallDestination = 3
    FunctionReturn = 4
    SystemCall = 5
    IndirectBranch = 6
    ExceptionBranch = 7
    UnresolvedBranch = 8
    UserDefinedBranch = 9


class InstructionTextTokenType(IntEnum):
    TextToken = 0
    InstructionToken = 1
    RegisterToken = 2
    IntegerToken = 3
    PossibleAddressToken = 4
    BeginMemoryOperandToken = 10
    EndMemoryOperandToken = 11
    FloatingPointToken = 12
    AnnotationToken = 13
    CodeRelativeAddressToken = 14
    ArgumentNameToken = 15
    HexDumpByteValueToken = 16
    HexDumpSkippedByteToken = 17
    HexDumpInvalidByteToken = 18
    HexDumpTextToken = 19
    OpcodeToken = 20
    StringToken = 21
    CharacterConstantToken = 22
    KeywordToken = 23
    TypeNameToken = 24
    FieldNameToken = 25
    NameSpaceToken = 26
    NameSpaceSeparatorToken = 27
    TagToken = 28
    StructOffsetToken = 29
    StructOffsetByteValueToken = 30
    StructureHexDumpTextToken = 31
    GotoLabelToken = 32
    CommentToken = 33
    PossibleValueToken = 34
    PossibleValueTypeToken = 35
    ArrayIndexToken = 36
    IndentationToken = 37
    UnknownMemoryToken = 38
    EnumerationMemberToken = 39
    OperationToken = 40
    BaseStructureOffsetToken = 41
    BaseStructureSeparatorToken = 42
    BraceToken = 43
    PlainTextToken = 44
    CollapsedInformationToken = 45


class SymbolType(IntEnum):
    FunctionSymbol = 0
    ImportAddressSymbol = 1
    ImportedFunctionSymbol = 2
    DataSymbol = 3
    ImportedDataSymbol = 4
    ExternalSymbol = 5
    LibraryFunctionSymbol = 6
    SymbolicFunctionSymbol = 7
    LocalLabelSymbol = 8


class HighLevelILOperation(IntEnum):
    HLIL_NOP = 0
    HLIL_ADD = 1
    HLIL_SUB = 2
    HLIL_MUL = 3
    HLIL_DIVS = 4
    HLIL_NEG = 5
    HLIL_NOT = 6
    HLIL_AND = 7
    HLIL_OR = 8
    HLIL_XOR = 9
    HLIL_LSR = 10
    HLIL_LSL = 11
    HLIL_MODS = 12
    HLIL_IF = 13
    HLIL_GOTO = 14
    HLIL_RET = 15
    HLIL_ASSIGN = 16
    HLIL_CALL = 17
    HLIL_VAR = 18
    HLIL_CONST = 19
    HLIL_BLOCK = 20


class LowLevelILOperation(IntEnum):
    LLIL_NOP = 0
    LLIL_SET_REG = 1
    LLIL_SET_REG_SPLIT = 2
    LLIL_SET_FLAG = 3
    LLIL_LOAD = 4
    LLIL_STORE = 5
    LLIL_PUSH = 6
    LLIL_POP = 7
    LLIL_REG = 8
    LLIL_CONST = 9
    LLIL_CONST_PTR = 10
    LLIL_FLAG = 11
    LLIL_FLAG_BIT = 12
    LLIL_ADD = 13
    LLIL_ADC = 14
    LLIL_SUB = 15
    LLIL_SBB = 16
    LLIL_AND = 17
    LLIL_OR = 18
    LLIL_XOR = 19
    LLIL_LSL = 20
    LLIL_LSR = 21
    LLIL_ASR = 22
    LLIL_ROL = 23
    LLIL_RLC = 24
    LLIL_ROR = 25
    LLIL_RRC = 26
    LLIL_MUL = 27
    LLIL_MULU_DP = 28
    LLIL_MULS_DP = 29
    LLIL_DIVU = 30
    LLIL_DIVU_DP = 31
    LLIL_DIVS = 32
    LLIL_DIVS_DP = 33
    LLIL_MODU = 34
    LLIL_MODS = 35
    LLIL_NEG = 36
    LLIL_NOT = 37
    LLIL_SX = 38
    LLIL_ZX = 39
    LLIL_LOW_PART = 40
    LLIL_JUMP = 41
    LLIL_JUMP_TO = 42
    LLIL_CALL = 43
    LLIL_CALL_SSA = 44
    LLIL_RET = 45
    LLIL_NORET = 46
    LLIL_IF = 47
    LLIL_GOTO = 48
    LLIL_FLAG_COND = 49
    LLIL_CMP_E = 50
    LLIL_CMP_NE = 51
    LLIL_CMP_SLT = 52
    LLIL_CMP_ULT = 53
    LLIL_CMP_SLE = 54
    LLIL_CMP_ULE = 55
    LLIL_CMP_SGE = 56
    LLIL_CMP_UGE = 57
    LLIL_CMP_SGT = 58
    LLIL_CMP_UGT = 59
    LLIL_TEST_BIT = 60
    LLIL_BOOL_TO_INT = 61
    LLIL_TAILCALL = 62
    LLIL_SYSCALL = 63
    LLIL_BP = 64
    LLIL_TRAP = 65
    LLIL_UNDEF = 66
    LLIL_UNIMPL = 67
    LLIL_UNIMPL_MEM = 68


class AnalysisState(IntEnum):
    IdleState = 0
    DisassembleState = 1
    AnalyzeState = 2


def install_binja_stubs():
    """Install binaryninja module stubs into sys.modules.
    Call this BEFORE importing any decompiler modules.
    Idempotent — returns the existing mock if already installed.
    """
    if "binaryninja" in sys.modules and not isinstance(sys.modules["binaryninja"], MagicMock):
        return sys.modules["binaryninja"]
    if "binaryninja" in sys.modules and hasattr(sys.modules["binaryninja"], "_redb_stub"):
        return sys.modules["binaryninja"]

    # Create the main mock
    bn_mock = MagicMock()
    bn_mock._redb_stub = True

    # Wire up enums as real enums (not mocks)
    enums_mod = MagicMock()
    enums_mod.BranchType = BranchType
    enums_mod.InstructionTextTokenType = InstructionTextTokenType
    enums_mod.SymbolType = SymbolType
    enums_mod.HighLevelILOperation = HighLevelILOperation
    enums_mod.LowLevelILOperation = LowLevelILOperation
    enums_mod.AnalysisState = AnalysisState

    bn_mock.enums = enums_mod
    bn_mock.enums.BranchType = BranchType
    bn_mock.enums.InstructionTextTokenType = InstructionTextTokenType
    bn_mock.enums.SymbolType = SymbolType
    bn_mock.enums.HighLevelILOperation = HighLevelILOperation
    bn_mock.enums.LowLevelILOperation = LowLevelILOperation
    bn_mock.enums.AnalysisState = AnalysisState

    # LowLevelILOperation on the top-level module
    bn_mock.LowLevelILOperation = LowLevelILOperation
    bn_mock.LowLevelILInstruction = MagicMock

    # highlevelil sub-module
    hlil_mod = MagicMock()
    hlil_mod.HighLevelILInstruction = type("HighLevelILInstruction", (), {})
    bn_mock.highlevelil = hlil_mod

    # lowlevelil sub-module
    llil_mod = MagicMock()
    llil_mod.LowLevelILAdd = type("LowLevelILAdd", (), {})
    llil_mod.LowLevelILConst = type("LowLevelILConst", (), {})
    llil_mod.LowLevelILConstPtr = type("LowLevelILConstPtr", (), {})
    llil_mod.LowLevelILLoad = type("LowLevelILLoad", (), {})
    llil_mod.LowLevelILLsl = type("LowLevelILLsl", (), {})
    llil_mod.LowLevelILMul = type("LowLevelILMul", (), {})
    llil_mod.LowLevelILPop = type("LowLevelILPop", (), {})
    llil_mod.LowLevelILPush = type("LowLevelILPush", (), {})
    llil_mod.LowLevelILReg = type("LowLevelILReg", (), {})
    llil_mod.LowLevelILStore = type("LowLevelILStore", (), {})
    llil_mod.LowLevelILSub = type("LowLevelILSub", (), {})
    bn_mock.lowlevelil = llil_mod

    # mediumlevelil sub-module
    mlil_mod = MagicMock()
    mlil_mod.MediumLevelILConst = type("MediumLevelILConst", (), {})
    mlil_mod.MediumLevelILConstPtr = type("MediumLevelILConstPtr", (), {})
    bn_mock.mediumlevelil = mlil_mod

    sys.modules["binaryninja"] = bn_mock
    sys.modules["binaryninja.enums"] = enums_mod
    sys.modules["binaryninja.lowlevelil"] = llil_mod
    sys.modules["binaryninja.highlevelil"] = hlil_mod
    sys.modules["binaryninja.mediumlevelil"] = mlil_mod

    return bn_mock


# ============================================================================
# Mock Factories
# ============================================================================

class MockToken:
    """Mock for instruction text tokens."""
    def __init__(self, text, token_type=None):
        self.text = text
        if token_type is None:
            self.type = InstructionTextTokenType.TextToken
        else:
            self.type = token_type

    def __str__(self):
        return self.text


class MockDisassemblyLine:
    """Mock for a disassembly text line."""
    def __init__(self, tokens=None):
        self.tokens = tokens or []

    def __str__(self):
        return "".join(t.text for t in self.tokens)


class MockEdge:
    """Mock for a basic block edge."""
    def __init__(self, source=None, target=None, edge_type=None):
        self.source = source
        self.target = target
        self.type = edge_type


class MockBasicBlock:
    """Mock for a basic block."""
    def __init__(
        self,
        start=0,
        end=0,
        disassembly_text=None,
        outgoing_edges=None,
        incoming_edges=None,
        dominators=None,
        post_dominators=None,
        dominance_frontier=None,
        dominator_tree_children=None,
        instruction_count=None,
    ):
        self.start = start
        self.end = end
        self.disassembly_text = disassembly_text or []
        self.outgoing_edges = outgoing_edges or []
        self.incoming_edges = incoming_edges or []
        self.dominators = dominators if dominators is not None else [self]
        self.post_dominators = post_dominators if post_dominators is not None else [self]
        self.dominance_frontier = dominance_frontier if dominance_frontier is not None else set()
        self.dominator_tree_children = dominator_tree_children or []
        self.instruction_count = instruction_count if instruction_count is not None else len(self.disassembly_text)

    def __iter__(self):
        return iter(self.disassembly_text)


class MockFunction:
    """Mock for a Binary Ninja function."""
    def __init__(
        self,
        name="sub_1000",
        start=0x1000,
        basic_blocks=None,
        instructions=None,
        hlil=None,
        llil=None,
        mlil=None,
        symbol=None,
        is_thunk=False,
        stack_adjustment=0,
        call_sites=None,
        caller_sites=None,
        low_level_il=None,
    ):
        self.name = name
        self.start = start
        self.basic_blocks = basic_blocks or []
        self._instructions = instructions or []
        self.hlil = hlil
        self.llil = llil
        self.mlil = mlil
        self.symbol = symbol
        self.is_thunk = is_thunk
        self.stack_adjustment = stack_adjustment
        self.call_sites = call_sites or []
        self.caller_sites = caller_sites or []
        self.low_level_il = low_level_il

    @property
    def instructions(self):
        return iter(self._instructions)

    def get_basic_block_at(self, addr):
        for bb in self.basic_blocks:
            if bb.start <= addr < bb.end or bb.start == addr:
                return bb
        return self.basic_blocks[0] if self.basic_blocks else None

    def get_regs_read_by(self, addr, arch):
        return []

    def get_regs_written_by(self, addr, arch):
        return []

    def __str__(self):
        return f"uint64_t {self.name}()"


class MockBinaryView:
    """Mock for a Binary Ninja binary view."""
    def __init__(
        self,
        functions=None,
        strings=None,
        arch=None,
    ):
        self.functions = functions or []
        self.strings = strings or []
        self.arch = arch

    def get_segment_at(self, addr):
        return None

    def get_section_at(self, addr):
        return None

    def get_symbol_at(self, addr):
        return None

    def get_functions_at(self, addr):
        return []

    def get_string_at(self, addr):
        return None

    def get_data_var_at(self, addr):
        return None


class MockSymbol:
    """Mock for a Binary Ninja symbol."""
    def __init__(self, symbol_type=None, name="unknown"):
        self.type = symbol_type if symbol_type is not None else SymbolType.FunctionSymbol
        self.name = name
        self.full_name = name


class MockILInstruction:
    """Mock for an IL instruction (LLIL/HLIL)."""
    def __init__(self, operation, operands=None, address=0):
        self.operation = operation
        self.operands = operands or []
        self.address = address


class MockStringEntry:
    """Mock for a Binary Ninja string reference."""
    def __init__(self, value, raw=None, start=0, length=0, string_type=None):
        self.value = value
        self.raw = raw if raw is not None else value.encode("utf-8") if isinstance(value, str) else value
        self.start = start
        self.length = length if length else len(self.raw)
        self.type = string_type or MockStringType("Utf8String")


class MockStringType:
    """Mock for string type."""
    def __init__(self, name="Utf8String"):
        self.name = name