Owen A. Johnson

38 papers Journal 12Unranked 26
YearRankTypeTitle / Venue / Authors
2025 conf
AIME (1)
Victoria Moglia, Lesley Smith, Gordon Cook, Marc de Kamps, Owen A. Johnson
2024 conf
ICPM Workshops
Abdulaziz Aljebreen, Allan Pang, Marc de Kamps, Owen A. Johnson
2024 conf
Nursing Informatics
Valentina Lichtner, Aleksandra Irnazarow, Owen A. Johnson, Stephen Bush, Stuart Macmillan, Mark Songhurst
2022 conf
HEALTHINF
Nik F. Farid, Marc de Kamps, Owen A. Johnson
2022 J jnl
J. Biomed. Informatics
Jorge Munoz-Gama, Niels Martin, Carlos Fernández-Llatas, Owen A. Johnson, Marcos Sepúlveda
2022 conf
ICPM Workshops
Christin Puthur, Abdulaziz Aljebreen, Ciarán McInerney, Teumzghi Mebrahtu, Tom Lawton, Owen A. Johnson
2022 J jnl
J. Biomed. Informatics
Jorge Munoz-Gama, Niels Martin, Carlos Fernández-Llatas, Owen A. Johnson, Marcos Sepúlveda, Emmanuel Helm, Victor Galvez-Yanjari, Eric Rojas, Antonio Martinez-Millana, Davide Aloini, Ilaria Angela Amantea, Robert Andrews, Michael Arias, Iris Beerepoot, Elisabetta Benevento, Andrea Burattin, Daniel Capurro, Josep Carmona, Marco Comuzzi, Benjamin Dalmas, Rene de la Fuente, Chiara Di Francescomarino, Claudio Di Ciccio, Roberto Gatta, Chiara Ghidini, Fernanda Gonzalez-Lopez, Gema Ibáñez-Sánchez, Hilda B. Klasky, Angelina Prima Kurniati, Xixi Lu, Felix Mannhardt, Ronny Mans, Mar Marcos, Renata Medeiros de Carvalho, Marco Pegoraro, Simon K. Poon, Luise Pufahl, Hajo A. Reijers, Simon Remy, Stefanie Rinderle-Ma, Lucia Sacchi, Fernando Seoane, Minseok Song, Alessandro Stefanini, Emilio Sulis, Arthur H. M. ter Hofstede, Pieter J. Toussaint, Vicente Traver, Zoe Valero-Ramon, Inge van de Weerd, Wil M. P. van der Aalst, Rob J. B. Vanwersch, Mathias Weske, Moe Thandar Wynn, Francesca Zerbato
2022 conf
ICPM Workshops
Alistair Bullward, Abdulaziz Aljebreen, Alexander Coles, Ciarán McInerney, Owen A. Johnson
2021 conf
MedInfo
Ciarán McInerney, Jonathan Benn, Dawn Dowding, Ibrahim Habli, David A. Jenkins, Carolyn McCrorie, Niels Peek, Rebecca Randell, Richard Williams, Owen A. Johnson
2021 conf
MIE
Guntur P. Kusuma, Angelina Prima Kurniati, Eric Rojas, Ciarán D. McInerney, Chris P. Gale, Owen A. Johnson
2021 conf
MIE
Angelina Prima Kurniati, Eric Rojas, Kieran Zucker, Geoff Hall, David C. Hogg, Owen A. Johnson
2020 J jnl
J. Biomed. Informatics
Jorge Munoz-Gama, Niels Martin, Carlos Fernández-Llatas, Owen A. Johnson, Marcos Sepúlveda
2020 conf
ICPM Workshops
Guntur P. Kusuma, Angelina Kurniati, Ciarán D. McInerney, Marlous S. Hall, Chris P. Gale, Owen A. Johnson
2020 conf
HEALTHINF
Guntur P. Kusuma, Samantha Sykes, Ciarán McInerney, Owen A. Johnson
2020 conf
ICPM Workshops
Angelina Prima Kurniati, Geoff Hall, David C. Hogg, Owen A. Johnson
2020 J jnl
Artif. Intell. Medicine
Niels Martin, Jochen De Weerdt, Carlos Fernández-Llatas, Avigdor Gal, Roberto Gatta, Gema Ibáñez, Owen A. Johnson, Felix Mannhardt, Luis Marco-Ruiz, Steven Mertens, Jorge Munoz-Gama, Fernando Seoane, Jan Vanthienen, Moe Thandar Wynn, David Baltar Boilève, Jochen Bergs, Mieke Joosten-Melis, Stijn Schretlen, Bram B. Van Acker
2019 conf
Business Process Management Workshops
Angelina Prima Kurniati, Ciarán McInerney, Kieran Zucker, Geoff Hall, David C. Hogg, Owen A. Johnson
2019 J jnl
J. Biomed. Semant.
Alicja Piotrkowicz, Owen A. Johnson, Geoff Hall
2019 conf
HEALTHINF
Nik F. Farid, Marc de Kamps, Owen A. Johnson
2019 conf
MedInfo
Richard Williams, Darren M. Ashcroft, Benjamin Brown, Eric Rojas, Niels Peek, Owen A. Johnson
2019 J jnl
BMC Medical Informatics Decis. Mak.
Carolyn McCrorie, Jonathan Benn, Owen A. Johnson, Arabella Scantlebury
2019 J jnl
Health Informatics J.
Angelina Prima Kurniati, Eric Rojas, David C. Hogg, Geoff Hall, Owen A. Johnson
2018 conf
ICHI
Frank Fox, Vishal R. Aggarwal, Helen Whelton, Owen A. Johnson
2018 conf
MIE
Richard Williams, Eric Rojas, Niels Peek, Owen A. Johnson
2018 conf
Business Process Management Workshops
Owen A. Johnson, Thamer Ba Dhafari, Angelina Kurniati, Frank Fox, Eric Rojas
2018 conf
MIE
Amirah Alharbi, Andy Bulpitt, Owen A. Johnson
2017 conf
BPM (Forum)
Amirah Alharbi, Andy Bulpitt, Owen A. Johnson
2017 J jnl
Int. J. Medical Informatics
Karl Baker, Elaine Dunwoodie, Richard G. Jones, Alex Newsham, Owen A. Johnson, Christopher P. Price, Jane Wolstenholme, Jose Leal, Patrick McGinley, Chris Twelves, Geoff Hall
2016 conf
ICHI
Samantha Crossfield, Owen A. Johnson, Thomas Fleming
2014 J jnl
CoRR
Samuel Danso, Eric Atwell, Owen A. Johnson
2013 conf
SGAI Conf.
Juliana Jaafar, Eric Atwell, Owen A. Johnson, Susan Clamp, Wan Azman Wan Ahmad
2013 conf
SOSE
Rob Smith, Jie Xu, Saman Hina, Owen A. Johnson
2013 conf
MedInfo
Dawn Dowding, Leanne M. Currie, Elizabeth M. Borycki, Susan Clamp, Jesús Favela, Geraldine Fitzpatrick, Peter Gardner, Susan Hamer, Nicholas R. Hardiker, Owen A. Johnson, Rebecca Lawton, Ann O'Brien, Rebecca Randell, Johanna I. Westbrook, Zac Whitewood-Moores, Patricia C. Dykes
2013 conf
GSCL
Samuel Danso, Eric Atwell, Owen A. Johnson
2013 J jnl
Int. J. Comput. Linguistics Appl.
Saman Hina, Eric Atwell, Owen A. Johnson
2010 conf
ICITST
Saman Hina, Eric Atwell, Owen A. Johnson
2009 J jnl
Comput. Hum. Behav.
Mary Godfrey, Owen A. Johnson
2006 J jnl
Inf. Softw. Technol.
Stephen F. King, Owen A. Johnson
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)