Karine Megy

11 papers Journal 11
YearRankTypeTitle / Venue / Authors
2016 J jnl
Nucleic Acids Res.
Robert Petryszak, Maria Keays, Y. Amy Tang, Nuno A. Fonseca, Elisabet Barrera, Tony Burdett, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Simon Jupp, Satu Koskinen, Oliver Mannion, Laura Huerta, Karine Megy, Catherine Snow, Eleanor Williams, Mitra Barzine, Emma Hastings, Hendrik Weisser, James C. Wright, Pankaj Jaiswal, Wolfgang Huber, Jyoti Choudhary, Helen E. Parkinson, Alvis Brazma
2014 J jnl
Nucleic Acids Res.
Robert Petryszak, Tony Burdett, Benedetto Fiorelli, Nuno A. Fonseca, Mar Gonzalez-Porta, Emma Hastings, Wolfgang Huber, Simon Jupp, Maria Keays, Nataliya Kryvych, Julie A. McMurry, John C. Marioni, James Malone, Karine Megy, Gabriella Rustici, Y. Amy Tang, Jan Taubert, Eleanor Williams, Oliver Mannion, Helen E. Parkinson, Alvis Brazma
2012 J jnl
Nucleic Acids Res.
Paul J. Kersey, Daniel M. Staines, Daniel Lawson, Eugene Kulesha, Paul S. Derwent, Jay C. Humphrey, Daniel S. T. Hughes, Stephen Keenan, Arnaud Kerhornou, Gautier Koscielny, Nicholas Langridge, Mark D. McDowall, Karine Megy, Uma Maheswari, Michael Nuhn, Michael Paulini, Helder Pedro, Iliana Toneva, Derek Wilson, Andrew D. Yates, Ewan Birney
2012 J jnl
Nucleic Acids Res.
Karine Megy, Scott J. Emrich, Daniel Lawson, David Campbell, Emmanuel Dialynas, Daniel S. T. Hughes, Gautier Koscielny, Christos Louis, Robert M. MacCallum, Seth Redmond, Andrew Sheehan, Pantelis Topalis, Derek Wilson
2010 J jnl
Nucleic Acids Res.
Paul J. Kersey, Daniel Lawson, Ewan Birney, Paul S. Derwent, Matthias Haimel, Javier Herrero, Stephen Keenan, Arnaud Kerhornou, Gautier Koscielny, Andreas Kähäri, Rhoda Kinsella, Eugene Kulesha, Uma Maheswari, Karine Megy, Michael Nuhn, Glenn Proctor, Daniel M. Staines, Franck Valentin, Albert J. Vilella, Andy Yates
2010 J jnl
Nucleic Acids Res.
Paul Flicek, Bronwen L. Aken, Benoît Ballester, Kathryn Beal, Eugene Bragin, Simon Brent, Yuan Chen, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Julio Fernandez-Banet, Leo Gordon, Stefan Gräf, Syed Haider, Martin Hammond, Kerstin Howe, Andrew M. Jenkinson, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Gautier Koscielny, Eugene Kulesha, Daniel Lawson, Ian Longden, Tim Massingham, William M. McLaren, Karine Megy, Bert Overduin, Bethan Pritchard, Daniel Rios, Magali Ruffier, Michael Schuster, Guy Slater, Damian Smedley, Giulietta Spudich, Y. Amy Tang, Stephen J. Trevanion, Albert J. Vilella, Jan Vogel, Simon White, Steven P. Wilder, Amonida Zadissa, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M. Fernández-Suárez, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, James A. Smith, Stephen M. J. Searle
2009 J jnl
Nucleic Acids Res.
Tim J. P. Hubbard, Bronwen L. Aken, Sarah C. Ayling, Benoît Ballester, Kathryn Beal, Eugene Bragin, Simon Brent, Yuan Chen, Peter Clapham, Laura Clarke, Guy Coates, Susan Fairley, Stephen Fitzgerald, Julio Fernandez-Banet, Leo Gordon, Stefan Gräf, Syed Haider, Martin Hammond, Richard C. G. Holland, Kevin L. Howe, Andrew M. Jenkinson, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, Ian Longden, Karine Megy, Patrick Meidl, Bert Overduin, Anne Parker, Bethan Pritchard, Daniel Rios, Michael Schuster, Guy Slater, Damian Smedley, William Spooner, Giulietta Spudich, Stephen J. Trevanion, Albert J. Vilella, Jan Vogel, Simon White, Steven P. Wilder, Arek Zadissa, Ewan Birney, Fiona Cunningham, Val Curwen, Richard Durbin, Xosé M. Fernández-Suárez, Javier Herrero, Arek Kasprzyk, Glenn Proctor, James A. Smith, Stephen M. J. Searle, Paul Flicek
2009 J jnl
Nucleic Acids Res.
Daniel Lawson, Peter Arensburger, Peter Atkinson, Nora J. Besansky, Robert V. Bruggner, Ryan Butler, Kathryn S. Campbell, George K. Christophides, Scott Christley, Emmanuel Dialynas, Martin Hammond, Catherine A. Hill, Nathan Konopinski, Neil F. Lobo, Robert M. MacCallum, Gregory R. Madey, Karine Megy, Jason Meyer, Seth Redmond, David W. Severson, Eric O. Stinson, Pantelis Topalis, Ewan Birney, William M. Gelbart, Fotis C. Kafatos, Christos Louis, Frank H. Collins
2008 J jnl
Nucleic Acids Res.
Paul Flicek, Bronwen L. Aken, Kathryn Beal, Benoît Ballester, Mario Cáccamo, Yuan Chen, Laura Clarke, Guy Coates, Fiona Cunningham, Tim Cutts, Thomas A. Down, S. C. Dyer, T. Eyre, Stephen Fitzgerald, Julio Fernandez-Banet, Stefan Gräf, Syed Haider, Martin Hammond, Richard C. G. Holland, Kevin L. Howe, Kerstin Howe, Nathan Johnson, Andrew M. Jenkinson, Andreas Kähäri, Damian Keefe, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, Ian Longden, Karine Megy, Patrick Meidl, Bert Overduin, Anne Parker, Bethan Pritchard, Andreas Prlic, S. Rice, Daniel Rios, Michael Schuster, Ian Sealy, Guy Slater, Damian Smedley, Giulietta Spudich, Stephen J. Trevanion, Albert J. Vilella, Jan Vogel, Simon White, M. Wood, Ewan Birney, Tony Cox, Val Curwen, Richard Durbin, Xosé M. Fernández-Suárez, Javier Herrero, Tim J. P. Hubbard, Arek Kasprzyk, Glenn Proctor, James A. Smith, Abel Ureta-Vidal, Stephen M. J. Searle
2007 J jnl
Nucleic Acids Res.
Tim J. P. Hubbard, Bronwen L. Aken, Kathryn Beal, Benoît Ballester, Mario Cáccamo, Yuan Chen, Laura Clarke, Guy Coates, Fiona Cunningham, Tim Cutts, Thomas A. Down, S. C. Dyer, Stephen Fitzgerald, Julio Fernandez-Banet, Stefan Gräf, Syed Haider, Martin Hammond, Javier Herrero, Richard C. G. Holland, Kevin L. Howe, Kerstin Howe, Nathan Johnson, Andreas Kähäri, Damian Keefe, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, Ian Longden, Craig Melsopp, Karine Megy, Patrick Meidl, Bert Overduin, Anne Parker, Andreas Prlic, S. Rice, Daniel Rios, Michael Schuster, Ian Sealy, Jessica Severin, Guy Slater, Damian Smedley, Giulietta Spudich, Stephen J. Trevanion, Albert J. Vilella, Jan Vogel, Simon White, M. Wood, Tony Cox, Val Curwen, Richard Durbin, Xosé M. Fernández-Suárez, Paul Flicek, Arek Kasprzyk, Glenn Proctor, Stephen M. J. Searle, James A. Smith, Abel Ureta-Vidal, Ewan Birney
2007 J jnl
Nucleic Acids Res.
Daniel Lawson, Peter Arensburger, Peter Atkinson, Nora J. Besansky, Robert V. Bruggner, Ryan Butler, Kathryn S. Campbell, George K. Christophides, Scott Christley, Emmanuel Dialynas, David B. Emmert, Martin Hammond, Catherine A. Hill, Ryan C. Kennedy, Neil F. Lobo, Robert M. MacCallum, Gregory R. Madey, Karine Megy, Seth Redmond, Susan Russo, David W. Severson, Eric O. Stinson, Pantelis Topalis, Evgeni M. Zdobnov, Ewan Birney, William M. Gelbart, Fotis C. Kafatos, Christos Louis, Frank H. Collins
redb/extractors/decompiler/apk/method_extractor.py
← Index redb/extractors/decompiler/apk/method_extractor.py python
"""Per-method content extraction, hashing, and similarity computation.

Handles SHA-256 content hashing, ssdeep/TLSH fuzzy hashing, MinHash
computation, and obfuscation indicator detection for APK methods.
"""

import hashlib
import re
from typing import Dict, List, Optional

from redb.extractors.decompiler.apk.smali_normalization import (
    categorize_opcode,
    normalize_method_body,
)
from redb.extractors.decompiler.apk.smali_parser import SmaliParser


# ---------------------------------------------------------------------------
# Smali Prime Product — semantic primes matching Binary Ninja's LLIL primes
# ---------------------------------------------------------------------------
# Each Dalvik semantic category maps to the same prime its LLIL counterpart
# uses in cfg_features.py. This makes prime products semantically comparable
# for APK-vs-APK similarity (not numerically comparable to Binja values).

SMALI_OP_PRIMES = {
    "ALU": 37,       # ADD/SUB → same prime as LLIL_ADD
    "CONV": 131,     # Type conversions → same as LLIL_SX
    "CMP": 103,      # Comparisons → same as LLIL_CMP_E
    "MOV": 2,        # Register moves → same as LLIL_SET_REG
    "CONST": 2,      # Constants → SET_REG equivalent
    "LOAD": 5,       # Field/array reads → same as LLIL_LOAD
    "STORE": 7,      # Field/array writes → same as LLIL_STORE
    "CALL": 17,      # invoke-* → same as LLIL_CALL
    "BRANCH": 29,    # if-* → same as LLIL_IF
    "JMP": 31,       # goto → same as LLIL_GOTO
    "SWITCH": 151,   # switch → same as LLIL_JUMP_TO
    "RET": 23,       # return → same as LLIL_RET
    "ALLOC": 5,      # new-instance/new-array → LOAD-adjacent (heap access)
    "TYPE": 1,       # check-cast/instance-of → identity (metadata)
    "ARR": 5,        # array-length/fill-array → LOAD-adjacent
    "EXC": 23,       # throw → RET-adjacent (control transfer out)
    "SYNC": 1,       # monitor → identity (no LLIL equivalent)
    "OTHER": 1,      # Unknown → identity
}


def compute_prime_product_smali(smali_body: str) -> int:
    """Multiplicative hash of normalized Dalvik opcodes. Mod 2^64.

    Same algorithm as cfg_features.compute_prime_product but using
    Dalvik semantic categories instead of LLIL operation enums.
    """
    if not smali_body:
        return 0

    product = 1
    for line in smali_body.splitlines():
        stripped = line.strip()
        if not stripped or stripped.startswith((".", ":", "#")):
            continue
        opcode = stripped.split()[0].split("/")[0] if stripped else ""
        category = categorize_opcode(opcode)
        prime = SMALI_OP_PRIMES.get(category, 1)
        product = (product * prime) % (2**64)

    return product


def count_call_instructions(smali_body: str) -> int:
    """Count invoke-* instructions in a smali method body."""
    if not smali_body:
        return 0
    count = 0
    for line in smali_body.splitlines():
        stripped = line.strip()
        if stripped.startswith("invoke-"):
            count += 1
    return count


def compute_sha256(content: str) -> str:
    """Compute SHA-256 hash of normalized content."""
    return hashlib.sha256(content.encode("utf-8")).hexdigest()


def compute_ssdeep(content: str) -> Optional[str]:
    """Compute ssdeep fuzzy hash of content."""
    try:
        import ppdeep
        data = content.encode("utf-8")
        if len(data) < 50:
            return None
        result = ppdeep.hash(data)
        return result if result else None
    except (ImportError, Exception):
        return None


def compute_tlsh(content: str) -> Optional[str]:
    """Compute TLSH fuzzy hash of content."""
    try:
        import tlsh
        data = content.encode("utf-8")
        if len(data) < 50:
            return None
        result = tlsh.hash(data)
        return result if result else None
    except (ImportError, Exception):
        return None


def compute_minhash(
    content: str,
    n: int = 3,
    normalization_level: str = "opcode_api",
) -> Optional[List[int]]:
    """Compute MinHash signature from semantically normalized smali n-grams.

    Applies semantic normalization (analogous to Binary Ninja's LLIL) before
    computing the MinHash. This strips register allocation noise and
    instruction encoding variants while preserving operation semantics and
    API references.

    Uses the same algorithm and parameters as the Binary Ninja MinHasher
    (64 seeds from master seed 0xdeadbeef, 8-bit signature elements, mmh3)
    to ensure cross-platform similarity comparisons are compatible.

    Args:
        content: Raw smali method body.
        n: N-gram size (default 3).
        normalization_level: Normalization level for instructions.
            'opcode_api' (default) preserves API call/field references.
            'category' uses only semantic categories.
            'opcode' uses base opcodes without operands.
    """
    try:
        import mmh3
    except ImportError:
        return None

    HASH_MAX = 0xFFFFFFFF
    SIGNATURE_LENGTH = 64
    SIGNATURE_BITS = 8

    # Semantically normalize instructions (like LLIL for native code)
    lines = normalize_method_body(content, level=normalization_level)

    if len(lines) < n:
        return None

    # Build n-grams (tuples of normalized instruction strings)
    shingles = [tuple(lines[i:i + n]) for i in range(len(lines) - n + 1)]

    if not shingles:
        return None

    # Generate deterministic seeds matching the Binary Ninja pipeline
    import random
    rng = random.Random(0xDEADBEEF)
    seeds = [rng.randint(0, HASH_MAX) for _ in range(SIGNATURE_LENGTH)]

    # For each seed, hash all shingles and take the minimum
    signature = []
    for seed in seeds:
        min_val = HASH_MAX
        for shingle in shingles:
            text = "|".join(str(elem) for elem in shingle)
            h = mmh3.hash(text, seed) & HASH_MAX
            if h < min_val:
                min_val = h
        # Truncate to signature bits
        if SIGNATURE_BITS < 32:
            min_val %= (2 ** SIGNATURE_BITS)
        signature.append(min_val)

    return signature


def detect_obfuscation_indicators(
    method_name: str,
    class_name: str,
    smali_body: str,
    instruction_count: int,
) -> Dict[str, bool]:
    """Compute obfuscation indicators for a method.

    Returns dict with boolean indicators.
    """
    indicators = {}

    # Short method name (typical R8/ProGuard output)
    indicators["short_method_name"] = len(method_name) <= 2

    # Short class name — extract simple name from Dalvik descriptor
    simple_class = class_name
    if "/" in simple_class:
        simple_class = simple_class.rsplit("/", 1)[-1]
    simple_class = simple_class.rstrip(";")
    indicators["short_class_name"] = len(simple_class) <= 2

    # String encryption: const-string followed by decryption-pattern call
    indicators["has_string_encryption"] = _detect_string_encryption(smali_body)

    # Reflection calls
    indicators["has_reflection_calls"] = _detect_reflection_calls(smali_body)

    # Excessive goto count (control flow flattening)
    goto_count = _count_goto_instructions(smali_body)
    threshold = max(5, int(instruction_count * 0.15))
    indicators["excessive_goto_count"] = goto_count > threshold

    return indicators


def _detect_string_encryption(smali_body: str) -> bool:
    """Detect const-string followed by decryption-pattern calls."""
    lines = smali_body.split("\n")
    for i, line in enumerate(lines):
        stripped = line.strip()
        if stripped.startswith("const-string"):
            # Check the next 3 lines for invoke-* to potential decryption
            for j in range(i + 1, min(i + 4, len(lines))):
                next_line = lines[j].strip()
                if next_line.startswith("invoke-"):
                    # Common decryption patterns
                    if any(
                        pat in next_line
                        for pat in [
                            "decrypt",
                            "decode",
                            "Cipher",
                            "DES",
                            "AES",
                            "Base64",
                            "getBytes",
                        ]
                    ):
                        return True
    return False


def _detect_reflection_calls(smali_body: str) -> bool:
    """Detect use of Java reflection APIs."""
    reflection_patterns = [
        "Ljava/lang/reflect/",
        "Ljava/lang/Class;->forName",
        "Ljava/lang/Class;->getMethod",
        "Ljava/lang/Class;->getDeclaredMethod",
        "Ljava/lang/Class;->getField",
        "Ljava/lang/Class;->getDeclaredField",
    ]
    for pattern in reflection_patterns:
        if pattern in smali_body:
            return True
    return False


def _count_goto_instructions(smali_body: str) -> int:
    """Count goto/goto_16/goto_32 instructions."""
    count = 0
    for line in smali_body.split("\n"):
        stripped = line.strip()
        if stripped.startswith(("goto ", "goto/16 ", "goto/32 ")):
            count += 1
        elif stripped in ("goto", "goto/16", "goto/32"):
            count += 1
    return count


def dalvik_to_java_class(descriptor: str) -> str:
    """Convert Dalvik class descriptor to Java dot notation.

    Lcom/example/Foo; -> com.example.Foo
    """
    if descriptor.startswith("L") and descriptor.endswith(";"):
        return descriptor[1:-1].replace("/", ".")
    return descriptor.replace("/", ".")


def dalvik_type_to_java(type_desc: str) -> str:
    """Convert a Dalvik type descriptor to Java type name."""
    type_map = {
        "V": "void",
        "Z": "boolean",
        "B": "byte",
        "S": "short",
        "C": "char",
        "I": "int",
        "J": "long",
        "F": "float",
        "D": "double",
    }

    if not type_desc:
        return "void"

    if type_desc in type_map:
        return type_map[type_desc]

    if type_desc.startswith("["):
        return dalvik_type_to_java(type_desc[1:]) + "[]"

    if type_desc.startswith("L") and type_desc.endswith(";"):
        full = type_desc[1:-1].replace("/", ".")
        # Return simple name
        return full.rsplit(".", 1)[-1] if "." in full else full

    return type_desc


def dalvik_to_java_prototype(
    method_name: str, signature: str, class_name: str = ""
) -> str:
    """Convert Dalvik method signature to Java-style prototype.

    Input: method_name='onCreate', signature='(Landroid/os/Bundle;)V'
    Output: 'void onCreate(Bundle)'
    """
    # Parse return type and param types from signature
    if not signature or not signature.startswith("("):
        return f"void {method_name}()"

    close_paren = signature.find(")")
    if close_paren == -1:
        return f"void {method_name}()"

    params_str = signature[1:close_paren]
    return_type_str = signature[close_paren + 1:]

    return_type = dalvik_type_to_java(return_type_str)
    params = _parse_dalvik_params(params_str)
    param_java = ", ".join(dalvik_type_to_java(p) for p in params)

    return f"{return_type} {method_name}({param_java})"


def _parse_dalvik_params(params_str: str) -> List[str]:
    """Parse Dalvik parameter descriptor string into individual types."""
    params = []
    i = 0
    while i < len(params_str):
        ch = params_str[i]
        if ch in "VZBSCIJFD":
            params.append(ch)
            i += 1
        elif ch == "[":
            # Array — find the base type
            array_prefix = "["
            i += 1
            while i < len(params_str) and params_str[i] == "[":
                array_prefix += "["
                i += 1
            if i < len(params_str):
                if params_str[i] == "L":
                    end = params_str.find(";", i)
                    if end != -1:
                        params.append(array_prefix + params_str[i : end + 1])
                        i = end + 1
                    else:
                        break
                else:
                    params.append(array_prefix + params_str[i])
                    i += 1
        elif ch == "L":
            end = params_str.find(";", i)
            if end != -1:
                params.append(params_str[i : end + 1])
                i = end + 1
            else:
                break
        else:
            i += 1
    return params