K. Anton Feenstra

35 papers B 1C 1Journal 27Unranked 5
YearRankTypeTitle / Venue / Authors
2024 J jnl
Bioinform.
Ting Liu, K. Anton Feenstra, Zhisheng Huang, Jaap Heringa
2022 conf
ICATCI (2)
Yi Ping, Laura Hoekstra, K. Anton Feenstra
2022 J jnl
Bioinform.
Bas Stringer, Hans de Ferrante, Sanne Abeln, Jaap Heringa, K. Anton Feenstra, Reza Haydarlou
2022 J jnl
PLoS Comput. Biol.
Qingzhen Hou, Katharina Waury, Dea Gogishvili, K. Anton Feenstra
2021 J jnl
Health Inf. Sci. Syst.
Ting Liu, Xueli Pan, Xu Wang, K. Anton Feenstra, Jaap Heringa, Zhisheng Huang
2021 J jnl
Bioinform.
Qingzhen Hou, Bas Stringer, Katharina Waury, Henriette Capel, Reza Haydarlou, Fuzhong Xue, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
2020 J jnl
Bioinform.
Annika Jacobsen, Olga Ivanova, Saman Amini, Jaap Heringa, Patrick Kemmeren, K. Anton Feenstra
2019 ch.
Encyclopedia of Bioinformatics and Computational Biology (2)
Sanne Abeln, K. Anton Feenstra, Jaap Heringa
2019 J jnl
Bioinform.
Qingzhen Hou, Paul F. G. De Geest, Christian J. Griffioen, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
2019 J jnl
Bioinform.
Maurits J. J. Dijkstra, Atze van der Ploeg, K. Anton Feenstra, Wan J. Fokkink, Sanne Abeln, Jaap Heringa
2019 J jnl
PLoS Comput. Biol.
Saman Amini, Annika Jacobsen, Olga Ivanova, Philip Lijnzaad, Jaap Heringa, Frank C. P. Holstege, K. Anton Feenstra, Patrick Kemmeren
2018 J jnl
PLoS Comput. Biol.
Maurits J. J. Dijkstra, Punto Bawono, Sanne Abeln, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa
2018 J jnl
Bioinform.
K. Anton Feenstra, Sanne Abeln, Johan A. Westerhuis, Filipe Brancos dos Santos, Douwe Molenaar, Bas Teusink, Huub C. J. Hoefsloot, Jaap Heringa
2017 J jnl
Bioinform.
Qingzhen Hou, Paul F. G. De Geest, Wim F. Vranken, Jaap Heringa, K. Anton Feenstra
2016 J jnl
Bioinform.
Reza Haydarlou, Annika Jacobsen, Nicola Bonzanni, K. Anton Feenstra, Sanne Abeln, Jaap Heringa
2015 conf
HPCS
Bas Stringer, Maurits J. J. Dijkstra, K. Anton Feenstra, Sanne Abeln, Jaap Heringa
2015 J jnl
BMC Bioinform.
Qingzhen Hou, Bas E. Dutilh, Martijn A. Huynen, Jaap Heringa, K. Anton Feenstra
2014 J jnl
Bioinform.
Ali May, René Pool, Erik van Dijk, Jochem Bijlard, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
2014 conf
FMMB
Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa
2013 J jnl
Briefings Bioinform.
Sanne Abeln, Douwe Molenaar, K. Anton Feenstra, Huub C. J. Hoefsloot, Bas Teusink, Jaap Heringa
2013 conf
LISC@ISWC
Timo Willemsen, K. Anton Feenstra, Paul Groth
2013 J jnl
Bioinform.
Nicola Bonzanni, Abhishek Garg, K. Anton Feenstra, Judith Schütte, Sarah Kinston, Diego Miranda-Saavedra, Jaap Heringa, Ioannis Xenarios, Berthold Göttgens
2012 J jnl
J. Comput. Chem.
René Pool, Jaap Heringa, Martin Hoefling, Roland Schulz, Jeremy C. Smith, K. Anton Feenstra
2010 J jnl
Nucleic Acids Res.
Bernd W. Brandt, K. Anton Feenstra, Jaap Heringa
2009 J jnl
Bioinform.
Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa
2009 J jnl
Bioinform.
Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa
2009 J jnl
BMC Bioinform.
Walter Pirovano, Anneke van der Reijden, K. Anton Feenstra, Jaap Heringa
2009 B conf
FM
Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Elzbieta Krepska
2008 conf
FMSB
Elzbieta Krepska, Nicola Bonzanni, K. Anton Feenstra, Wan J. Fokkink, Thilo Kielmann, Henri E. Bal, Jaap Heringa
2008 J jnl
Bioinform.
Kai Ye, K. Anton Feenstra, Jaap Heringa, Adriaan P. IJzerman, Elena Marchiori
2008 J jnl
Bioinform.
Walter Pirovano, K. Anton Feenstra, Jaap Heringa
2008 J jnl
BMC Bioinform.
Walter Pirovano, K. Anton Feenstra, Jaap Heringa
2007 J jnl
Nucleic Acids Res.
K. Anton Feenstra, Walter Pirovano, Klaas Krab, Jaap Heringa
2006 C conf
ICMLA
Elena Marchiori, Walter Pirovano, Jaap Heringa, K. Anton Feenstra
1999 J jnl
J. Comput. Chem.
K. Anton Feenstra, Berk Hess, Herman J. C. Berendsen
redb/extractors/decompiler/bninja/similarity/minhasher.py
← Index redb/extractors/decompiler/bninja/similarity/minhasher.py python
import logging
import random
from enum import Enum

from ..analysis.medium_level_normalization import MediumLevelNormalization

try:
    from .minhashcustom import MinHashCustom
    from ..analysis.low_level_normalization import LowLevelNormalization
except ImportError:
    # Fallback to absolute imports (for multiprocessing spawned processes)
    from redb.extractors.decompiler.bninja.similarity.minhashcustom import MinHashCustom
    from redb.extractors.decompiler.bninja.analysis.low_level_normalization import LowLevelNormalization

## Values for this configuration were extracted from https://github.com/danielplohmann/mcrit/blob/main/mcrit/config/MinHashConfig.py#L10
# Length in number of Shingles of which a minhash consists
# this value represents the length of sha256sum hash truncated
MINHASH_SIGNATURE_LENGTH: int = 64
# Number of bits per signature element (1-32 bits)
MINHASH_SIGNATURE_BITS: int = 8


class TokenKind(Enum):
    LLIL = "llil"
    TYPED_LLIL = "typed_llil"
    MLIL = "mlil"
    TYPED_MLIL = "typed_mlil"


class MinHasher:
    # stick to the default method
    MINHASH_STRATEGY_HASH_ALL = 1

    def __init__(self, seed, il_function, kind: TokenKind = TokenKind.LLIL):
        self._minhash_seeds = []
        self.il_func = il_function
        self.kind = kind
        self._minhash_permutation = []
        self._signature_segments = []
        self._initMinhashing(seed)

    def _initMinhashing(self, MINHASH_SEED=None):
        random.seed(MINHASH_SEED)
        # init sequence of seeds
        self._minhash_seeds = [
            random.randint(0, MinHashCustom.getHashMax()) for _ in range(MINHASH_SIGNATURE_LENGTH)
        ]

    def make_ngrams(self, tokens, n=3):
        """Take the ngrams of the IL we try to pass into the functions"""
        return [tuple(tokens[i:i+n]) for i in range(len(tokens) - n + 1)]

    def _extract_tokens(self):
        """Extract the IL tokens from the IL function, picking the right
        normalizer (LLIL/MLIL) and the right normalization mode
        (skeleton/typed) based on self.kind."""
        if self.kind in (TokenKind.LLIL, TokenKind.TYPED_LLIL):
            normalizer = LowLevelNormalization()
        elif self.kind in (TokenKind.MLIL, TokenKind.TYPED_MLIL):
            normalizer = MediumLevelNormalization()
        else:
            raise ValueError(f"Unsupported token kind: {self.kind}")

        # typed variants include operand type info, skeleton variants don't
        if self.kind in (TokenKind.TYPED_LLIL, TokenKind.TYPED_MLIL):
            normalize = normalizer.normalize_instr_with_operands
        else:
            normalize = normalizer.normalize_instruction_all_levels

        instructions = []
        for basic_block in self.il_func.basic_blocks:
            for il in basic_block:
                instructions.append(normalize(il))

        return instructions

    def calculateMinHash(self):
        """Calculate hash function every time, then take minimum shingle per shingler"""
        minhash_result = MinHashCustom(minhash_bits=MINHASH_SIGNATURE_BITS)
        minhash_signature = []

        tokens = self._extract_tokens()
        shingles = self.make_ngrams(tokens, n=3)

        # Functions with fewer than 3 IL instructions can't produce n-grams
        # Return empty minhash for such small functions (thunks, stubs, etc.)
        # Triggered by 39d8ad95b0323c37bd3134ab93ac4af44c66a1a8443a41c1ac02cec19bb2816a
        if not shingles:
            return []

        # Generate the MinHash
        for seed in self._minhash_seeds:
            hashed_shingles = [
                self.shingle_hash(shingle, seed) for shingle in shingles
            ]
            min_value = min(hashed_shingles)

            if MINHASH_SIGNATURE_BITS < 32:
                min_value %= (2 ** MINHASH_SIGNATURE_BITS)

            minhash_signature.append(min_value)

        minhash_result.setMinHash(minhash_signature)
        return minhash_result.getMinHashInt()

    def shingle_hash(self, shingle, hash_seed=0):
        """Produce a single 32bit UINT hash for a given shingle"""
        return MinHashCustom.hashData(shingle, hash_seed)