James T. Yurkovich

12 papers Journal 10Unranked 1
YearRankTypeTitle / Venue / Authors
2024 J jnl
Frontiers Digit. Health
Yue Zhang, Guangrong Qin, Boris Aguilar, Noa Rappaport, James T. Yurkovich, Lance Pflieger, Sui Huang, Leroy Hood, Ilya Shmulevich
2021 J jnl
PLoS Comput. Biol.
Zachary B. Haiman, Daniel C. Zielinski, Yuko Koike, James T. Yurkovich, Bernhard O. Palsson
2020 J jnl
Nucleic Acids Res.
Charles J. Norsigian, Neha Pusarla, John Luke McConn, James T. Yurkovich, Andreas Dräger, Bernhard O. Palsson, Zachary A. King
2020 J jnl
BMC Bioinform.
Lea Buchweitz, James T. Yurkovich, Christoph Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A. King, Laurence Yang, Freyr Jóhannsson, Ólafur E. Sigurjónsson, Ottar Rolfsson, Julian Heinrich, Andreas Dräger
2018 J jnl
PLoS Comput. Biol.
James T. Yurkovich, Miguel A. Alcantar, Zachary B. Haiman, Bernhard O. Palsson
2018 J jnl
BMC Syst. Biol.
James T. Yurkovich, Aarash Bordbar, Ólafur E. Sigurjónsson, Bernhard O. Palsson
2018
James T. Yurkovich
2018 J jnl
BMC Syst. Biol.
Erol S. Kavvas, Yara Seif, James T. Yurkovich, Charles J. Norsigian, Saugat Poudel, William W. Greenwald, Sankha Ghatak, Bernhard O. Palsson, Jonathan M. Monk
2017 J jnl
PLoS Comput. Biol.
James T. Yurkovich, Laurence Yang, Bernhard O. Palsson
2017 conf
CCTA
James T. Yurkovich, Laurence Yang, Bernhard O. Palsson
2016 J jnl
Proc. IEEE
James T. Yurkovich, Bernhard O. Palsson
2016 J jnl
IEEE Trans. Biomed. Eng.
Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K. Aranganathan, Kambiz Baghalian, Arne T. Bittig, Paulo E. Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S. Costa, Joseph Cursons, Tobias Czauderna, Arthur P. Goldberg, Harold F. Gómez, Jens Hahn, Tuure Hameri, Daniel F. Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knüpfer, Matthias König, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J. Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K. Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J. Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Touré, Jannis Uhlendorf, Thawfeek M. Varusai, Leandro H. Watanabe, Florian Wendland, Markus Wolfien, James T. Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber
redb/extractors/decompiler/apk/library_filter.py
← Index redb/extractors/decompiler/apk/library_filter.py python
"""Package-based library filtering for APK DEX code analysis.

Determines whether a method belongs to a known library/framework package
and should be filtered out of content tables. This is the Android equivalent
of is_lib_or_thunk() in the Binary Ninja pipeline.
"""

import os
from typing import Dict, List


DEFAULT_LIBRARY_PREFIXES = [
    "android.",
    "androidx.",
    "com.google.android.",
    "com.google.firebase.",
    "com.google.gson.",
    "com.google.protobuf.",
    "kotlin.",
    "kotlinx.",
    "org.apache.",
    "com.squareup.",
    "io.reactivex.",
    "org.reactivestreams.",
    "com.facebook.",
    "com.crashlytics.",
    "io.fabric.",
    "org.junit.",
    "org.mockito.",
]


class LibraryFilter:
    """Filters library/framework classes from APK analysis."""

    def __init__(self, prefixes: List[str] = None):
        env_prefixes = os.getenv("APK_LIBRARY_PREFIXES")
        if env_prefixes:
            self._prefixes = [p.strip() for p in env_prefixes.split(",") if p.strip()]
        elif prefixes is not None:
            self._prefixes = prefixes
        else:
            self._prefixes = DEFAULT_LIBRARY_PREFIXES

        # Convert Dalvik-style prefixes to both formats for matching
        self._dot_prefixes = tuple(self._prefixes)

        self._stats = {"library": 0, "user": 0}

    def is_library(self, class_name: str) -> bool:
        """Check if a class belongs to a known library/framework package.

        Accepts both Java dot notation (com.example.Foo) and Dalvik
        descriptor notation (Lcom/example/Foo;).
        """
        # Normalize Dalvik descriptor to dot notation
        normalized = self._normalize_class_name(class_name)

        is_lib = normalized.startswith(self._dot_prefixes)
        if is_lib:
            self._stats["library"] += 1
        else:
            self._stats["user"] += 1
        return is_lib

    def get_filter_stats(self) -> Dict[str, int]:
        """Return counts of filtered vs. retained classes."""
        return dict(self._stats)

    @staticmethod
    def _normalize_class_name(class_name: str) -> str:
        """Convert Dalvik descriptor to dot notation.

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