Walter Kolch

17 papers Journal 15Unranked 2
YearRankTypeTitle / Venue / Authors
2020 J jnl
PLoS Comput. Biol.
Vít Novácek, Gavin McGauran, David Matallanas, Adrián Vallejo Blanco, Piero Conca, Emir Muñoz, Luca Costabello, Kamalesh Kanakaraj, Muhammad Zeeshan Nawaz, Brian Walsh, Sameh K. Mohamed, Pierre-Yves Vandenbussche, Colm J. Ryan, Walter Kolch, Dirk Fey
2016 J jnl
BMC Bioinform.
Eleanor Stanley, Eleni Ioanna Delatola, Esther Nkuipou-Kenfack, William Spooner, Walter Kolch, Joost P. Schanstra, Harald Mischak, Thomas Koeck
2016 J jnl
Briefings Bioinform.
Goar Sánchez-Sanz, David Matallanas, Lan K. Nguyen, Boris N. Kholodenko, Edina Rosta, Walter Kolch, Nicolae-Viorel Buchete
2016 J jnl
PLoS Comput. Biol.
Goar Sánchez-Sanz, Bartlomiej Tywoniuk, David Matallanas, David Romano, Lan K. Nguyen, Boris N. Kholodenko, Edina Rosta, Walter Kolch, Nicolae-Viorel Buchete
2014 J jnl
PLoS Comput. Biol.
Tapesh Santra, Walter Kolch, Boris N. Kholodenko
2014 J jnl
PLoS Comput. Biol.
Junil Kim, Drieke Vandamme, Jeong-Rae Kim, Amaya Garcia Munoz, Walter Kolch, Kwang-Hyun Cho
2013 J jnl
BMC Syst. Biol.
Tapesh Santra, Walter Kolch, Boris N. Kholodenko
2012 J jnl
BMC Syst. Biol.
Marc R. Birtwistle, Jens Rauch, Anatoly Kiyatkin, Edita Aksamitiene, Maciej Dobrzynski, Jan B. Hoek, Walter Kolch, Babatunde A. Ogunnaike, Boris N. Kholodenko
2011 J jnl
PLoS Comput. Biol.
Lan K. Nguyen, Javier Muñoz-García, Helene Maccario, Aaron Ciechanover, Walter Kolch, Boris N. Kholodenko
2010 J jnl
BMC Bioinform.
Mohammed Dakna, Keith Harris, Alexandros Kalousis, Sebastien Carpentier, Walter Kolch, Joost P. Schanstra, Marion Haubitz, Antonia Vlahou, Harald Mischak, Mark A. Girolami
2009 J jnl
BMC Syst. Biol.
Richard J. Orton, Michiel E. Adriaens, Amelie Gormand, Oliver E. Sturm, Walter Kolch, David R. Gilbert
2009 J jnl
Int. J. Bioinform. Res. Appl.
Julio Vera, Taesoo Kwon, Ulf Schmitz, Walter Kolch, Olaf Wolkenhauer
2008 J jnl
BMC Syst. Biol.
Julio Vera, Thomas Millat, Walter Kolch, Olaf Wolkenhauer
2008 J jnl
Bioinform.
Simon Rogers, Mark A. Girolami, Walter Kolch, Katrina M. Waters, Tao Liu, Brian Thrall, H. Steven Wiley
2008 conf
SWAT4LS
Nadia Anwar, Ela Hunt, Walter Kolch, Andrew Pitt
2003 J jnl
Simul.
Kwang-Hyun Cho, Sung-Young Shin, Walter Kolch, Olaf Wolkenhauer
2003 conf
CMSB
Kwang-Hyun Cho, Sung-Young Shin, Hyun Woo Kim, Olaf Wolkenhauer, Brian McFerran, Walter Kolch
redb/extractors/apk_extractors/apk_resources.py
← Index redb/extractors/apk_extractors/apk_resources.py python
import hashlib
import inspect
import os
from datetime import datetime, timezone
from typing import Any

from redb.extractors.enum import Tag
from redb.extractors.apk_extractor import APKExtractor
from redb.models.dataclasses import APKResource


# ─── Suspicious file types ──────────────────────────────────────────────
# File types that are suspicious when found inside res/ or assets/.
# Excludes javascript/html (extremely common in legitimate hybrid apps)
# and common media/font types that are normal APK content.
SUSPICIOUS_TYPES = {
    # Executables — no legitimate reason in assets/res
    "elf", "pebin", "macho", "dex", "apk",
    # Java containers — DexClassLoader target
    "jar",
    # Archives — rare in legitimate assets (~135:1 malware-to-benign ratio)
    "zip", "gzip", "7z", "xz", "tar", "bzip2", "rar", "7zip", "lzma",
    # Scripts with system execution capability
    "shell", "python", "powershell", "batch",
}

# ─── Entropy thresholds ─────────────────────────────────────────────────
# For unrecognized/unknown types: encrypted payloads typically land > 7.0
ENTROPY_HIGH_UNKNOWN = 7.0
# For recognized-but-non-image types: stricter threshold
ENTROPY_EXTREME = 7.85

# ─── Android-specific binary format magic bytes ─────────────────────────
# These formats are common in legitimate APKs but unknown to Magika,
# causing misclassification (e.g., AXML → "gzip", profm → "unknown").
AXML_MAGIC = b'\x03\x00\x08\x00'       # Android Binary XML (compiled res/*.xml)
ARSC_MAGIC = b'\x02\x00\x0c\x00'       # Android compiled resource table
ART_PROF_MAGIC = b'pro\x00'            # ART baseline profile
ART_PROFM_MAGIC = b'prm\x00'           # ART baseline profile metadata

# ─── Allowlisted paths ──────────────────────────────────────────────────
# Fixed, hardcoded paths in the Android build system that are always benign.
# ART profiles at these exact paths are shipped by Jetpack ProfileInstaller.
ALLOWLISTED_PATHS = {
    "assets/dexopt/baseline.prof",
    "assets/dexopt/baseline.profm",
}

# ─── Image handling ─────────────────────────────────────────────────────
# Magika-confirmed image types: high entropy is expected (lossy codecs
# like VP8/JPEG arithmetic-code toward entropy ~7.95-8.0 by design).
IMAGE_MAGIKA_TYPES = {"png", "webp", "jpeg", "gif", "bmp", "tiff", "ico"}
IMAGE_EXTENSIONS = {".png", ".webp", ".jpg", ".jpeg", ".gif", ".bmp", ".tiff", ".ico"}

# ─── Types Magika assigns when it can't identify the content ────────────
UNRECOGNIZED_MAGIKA_TYPES = {"unknown", "empty"}

# ─── Resource scan limits ───────────────────────────────────────────────
MAX_RESOURCE_FILES = 5000


class APKResourceExtractor(APKExtractor):

    def __init__(
        self, filepath, log, exporters=None, index_prefix=None,
        known_benign=False, known_malicious=False,
        apk=None,
    ):
        super().__init__(
            filepath, log, exporters, index_prefix,
            known_benign, known_malicious, apk,
        )
        self.resources = []
        self.suspicious_files = []
        self.log.debug(inspect.currentframe().f_code.co_name)

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

    # ─── Core classification logic ──────────────────────────────────────

    def _identify_android_format(self, header: bytes) -> str | None:
        """
        Identify Android-specific binary formats that Magika doesn't know.
        Returns a corrected type label, or None to fall through to Magika.
        """
        if len(header) < 4:
            return None

        magic4 = header[:4]

        # Android Binary XML — all res/*.xml in a compiled APK.
        # Magika often misclassifies this as "gzip".
        if magic4 == AXML_MAGIC:
            return "android_binary_xml"

        # Android compiled resource table (resources.arsc chunks)
        if magic4 == ARSC_MAGIC:
            return "android_resource_table"

        # ART baseline profiles — high entropy (zlib inside) but benign.
        # The format is inert (method reference bitmaps/metadata, not
        # executable code) and some build configs place them at varying paths.
        if magic4 == ART_PROF_MAGIC:
            return "android_art_profile"
        if magic4 == ART_PROFM_MAGIC:
            return "android_art_profile_metadata"

        return None

    def _is_suspicious_resource(
        self, path: str, magika_type: str, entropy: float,
        android_type: str | None,
    ) -> bool:
        """
        Determine if a resource file is suspicious.

        Detection layers:
        1. Allowlisted paths → always benign
        2. Android-specific format override → reclassify Magika mislabels
        3. Image extension vs Magika type mismatch → encrypted blob detection
        4. Magika-confirmed images → benign regardless of entropy
        5. Suspicious type match → flag known-dangerous types
        6. High-entropy unknown blobs → likely encrypted payloads
        """

        # ── Layer 1: Allowlisted paths (hardcoded Android build artifacts) ──
        if path in ALLOWLISTED_PATHS:
            return False

        # ── Layer 2: Android-specific format detection ──────────────────────
        # Override Magika's label for formats it doesn't recognize.
        # All Android-specific formats (AXML, ARSC, ART profiles) are
        # legitimate build artifacts — never suspicious.
        if android_type is not None:
            return False

        # ── Layer 3: Image extension / Magika type mismatch ─────────────────
        # If the file extension claims "image" but Magika's content analysis
        # disagrees, this is a strong signal for an encrypted payload with
        # a fake image extension (e.g., ErrorFather's "rbyypivsnw.png").
        ext = os.path.splitext(path)[1].lower()
        if ext in IMAGE_EXTENSIONS and magika_type not in IMAGE_MAGIKA_TYPES:
            # Exception: Magika might label a valid image as "unknown" if
            # the file is very small (< ~16 bytes). Don't flag tiny files.
            if entropy > 5.0:
                return True

        # ── Layer 4: Magika-confirmed images → benign ───────────────────────
        # Lossy codecs (VP8, JPEG) produce entropy up to ~8.0 by design.
        # If Magika confirms image structure, high entropy is expected.
        if magika_type in IMAGE_MAGIKA_TYPES:
            return False

        # ── Layer 5: Known suspicious file types ────────────────────────────
        if magika_type in SUSPICIOUS_TYPES:
            return True

        # ── Layer 6: High-entropy unrecognized blobs ────────────────────────
        # Files Magika can't identify with high entropy are likely encrypted
        # payloads. Most Android malware packers store encrypted DEX/SO
        # payloads as opaque blobs with random names and no valid magic.
        if magika_type in UNRECOGNIZED_MAGIKA_TYPES and entropy > ENTROPY_HIGH_UNKNOWN:
            return True

        # ── Layer 7: Extreme entropy on any non-image recognized type ───────
        # Catches edge cases where Magika assigns a benign label (e.g.,
        # "xml", "txt") but the entropy is impossibly high for that format.
        if magika_type not in IMAGE_MAGIKA_TYPES and entropy > ENTROPY_EXTREME:
            return True

        return False

    # ─── Extraction pipeline ────────────────────────────────────────────

    def extract(self):
        if not self._is_valid_apk():
            self.log.error(f"Invalid APK for {self.hash.sha256}")
            return None

        try:
            from magika import Magika
            magika = Magika()
        except Exception as e:
            self.log.error(f"Failed to initialize Magika for {self.hash.sha256}: {e}")
            magika = None

        self.resources = []
        self.suspicious_files = []
        scanned = 0

        zf = self._get_zip_file()
        if not zf:
            return None

        with zf:
            for info in zf.infolist():
                if info.is_dir():
                    continue
                if not (info.filename.startswith("res/") or
                        info.filename.startswith("assets/")):
                    continue

                if scanned >= MAX_RESOURCE_FILES:
                    self.log.warning(
                        f"Resource scan limit reached ({MAX_RESOURCE_FILES}), "
                        f"stopping resource enumeration"
                    )
                    break
                scanned += 1

                try:
                    data = zf.read(info.filename)
                except Exception as e:
                    self.log.warning(
                        f"Error reading resource {info.filename}: {e}"
                    )
                    continue

                try:
                    file_sha256 = hashlib.sha256(data).hexdigest()
                    file_entropy = round(self.calculate_entropy(data), 3)

                    # Read first bytes for Android-specific format detection
                    header = data[:16] if len(data) >= 16 else data

                    if magika:
                        try:
                            filetype = magika.identify_bytes(data).output.label
                        except Exception:
                            filetype = "unknown"
                    else:
                        filetype = "unknown"

                    # Identify Android-specific formats once, reuse for
                    # both stored type and suspicion classification
                    android_type = self._identify_android_format(header)
                    stored_type = android_type if android_type else filetype

                    suspicious = self._is_suspicious_resource(
                        path=info.filename,
                        magika_type=filetype,
                        entropy=file_entropy,
                        android_type=android_type,
                    )

                    resource = APKResource(
                        path=info.filename,
                        size=info.file_size,
                        sha256=file_sha256,
                        filetype_magika=stored_type,
                        entropy=file_entropy,
                    )

                    if suspicious:
                        resource.is_suspicious = True
                        self.suspicious_files.append(resource)

                    self.resources.append(resource)
                except Exception as e:
                    self.log.warning(
                        f"Error processing resource {info.filename}: {e}"
                    )
                    continue

        if not self.resources:
            return None

        return {
            "total_resource_count": len(self.resources),
            "total_resource_size": sum(r.size for r in self.resources),
            "suspicious_file_count": len(self.suspicious_files),
            "resources": self.resources,
            "suspicious_files": self.suspicious_files,
        }

    # ─── Export ──────────────────────────────────────────────────────────

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

            current_time = datetime.now(timezone.utc)
            data = []
            for res in self.resources:
                data.append([
                    self.sha256,
                    res.path,
                    res.size,
                    res.sha256,
                    res.filetype_magika,
                    res.entropy,
                    int(res.is_suspicious),
                    current_time,
                ])

            column_names = [
                'sha256', 'resource_path', 'resource_size',
                'resource_sha256', 'resource_magika', 'resource_entropy',
                'is_suspicious', 'analysis_date',
            ]

            column_type_names = [
                'FixedString(64)', 'String', 'UInt64',
                'FixedString(64)', 'LowCardinality(String)', 'Float32',
                'UInt8', "DateTime64(3, 'UTC')",
            ]

            return (data, column_names, column_type_names)

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