Naama Menda

11 papers C 1Journal 10
YearRankTypeTitle / Venue / Authors
2025 J jnl
Database J. Biol. Databases Curation
Naama Menda, Bryan J. Ellerbrock, Christiano C. Simoes, Srikanth Kumar Karaikal, Christine Nyaga, Mirella Flores-Gonzalez, Isaak Y. Tecle, David Lyon, Afolabi Agbona, Paterne A. Agre, Prasad Peteti, Violet Akech, Amos Asiimwe, Eglantine Fauvelle, Karima Meghar, Thierry Tran, Dominique Dufour, Laurel Cooper, Marie-Angélique Laporte, Elizabeth Arnaud, Lukas A. Mueller
2020 J jnl
Patterns
Elizabeth Arnaud, Marie-Angélique Laporte, Soonho Kim, Céline Aubert, Sabina Leonelli, Berta Miro, Laurel Cooper, Pankaj Jaiswal, Gideon Kruseman, Rosemary Shrestha, Pier Luigi Buttigieg, Christopher J. Mungall, Julian Pietragalla, Afolabi Agbona, Jacqueline Muliro, Jeffrey Detras, Vilma Hualla, Abhishek Rathore, Roma Rani Das, Ibnou Dieng, Guillaume Bauchet, Naama Menda, Cyril Pommier, Felix Shaw, David Lyon, Leroy Mwanzia, Henry Juarez, Enrico Bonaiuti, Brian Chiputwa, Oluremi Olatunbosun, Sandrine Auzoux, Esther Dzalé Yeumo, Lukas A. Mueller, Kevin A. T. Silverstein, Alexandra Lafargue, Erick Antezana, Medha Devare, Brian King
2018 J jnl
Database J. Biol. Databases Curation
Lisa C. Harper, Jacqueline D. Campbell, Ethalinda K. S. Cannon, Sook Jung, Monica Poelchau, Ramona L. Walls, Carson M. Andorf, Elizabeth Arnaud, Tanya Z. Berardini, Clayton L. Birkett, Steven B. Cannon, James D. Carson, Bradford Condon, Laurel Cooper, Nathan A. Dunn, Christine G. Elsik, Andrew D. Farmer, Stephen P. Ficklin, David M. Grant, Emily S. Grau, Nic Herndon, Zhi-Liang Hu, Jodi L. Humann, Pankaj Jaiswal, Clément Jonquet, Marie-Angélique Laporte, Pierre Larmande, Gerard R. Lazo, Fiona McCarthy, Naama Menda, Christopher J. Mungall, Monica C. Munoz-Torres, Sushma Naithani, Rex T. Nelson, Daureen Nesdill, Carissa A. Park, James M. Reecy, Leonore Reiser, Lacey-Anne Sanderson, Taner Z. Sen, Margaret Staton, Sabarinath Subramaniam, Marcela Karey Tello-Ruiz, Victor Unda, Deepak R. Unni, Liya Wang, Doreen Ware, Jill L. Wegrzyn, Jason Williams, Margaret Woodhouse, Jing Yu, Doreen Main
2015 J jnl
Nucleic Acids Res.
Noé Fernández-Pozo, Naama Menda, Jeremy D. Edwards, Surya Saha, Isaak Y. Tecle, Susan R. Strickler, Aureliano Bombarely, Thomas Fisher-York, Anuradha Pujar, Hartmut Foerster, Aimin Yan, Lukas A. Mueller
2014 J jnl
BMC Bioinform.
Isaak Y. Tecle, Jeremy D. Edwards, Naama Menda, Chiedozie Egesi, Ismail Y. Rabbi, Peter Kulakow, Robert Kawuki, Jean-Luc Jannink, Lukas A. Mueller
2013 J jnl
Database J. Biol. Databases Curation
Anuradha Pujar, Naama Menda, Aureliano Bombarely, Jeremy D. Edwards, Susan Strickler, Lukas A. Mueller
2012 C conf
KEOD
Elizabeth Arnaud, Laurel Cooper, Rosemary Shrestha, Naama Menda, Rex T. Nelson, Luca Matteis, Milko Skofic, Ruth Bastow, Pankaj Jaiswal, Lukas A. Mueller, Graham McLaren
2011 J jnl
Database J. Biol. Databases Curation
Sook Jung, Naama Menda, Seth Redmond, Robert M. Buels, Maren Friesen, Yuri R. Bendaña, Lacey-Anne Sanderson, Hilmar Lapp, Taein Lee, Bob MacCallum, Kirstin E. Bett, Scott Cain, Dave Clements, Lukas A. Mueller, Dorrie Main
2011 J jnl
Nucleic Acids Res.
Aureliano Bombarely, Naama Menda, Isaak Y. Tecle, Robert M. Buels, Susan Strickler, Thomas Fischer-York, Anuradha Pujar, Jonathan Leto, Joseph Gosselin, Lukas A. Mueller
2010 J jnl
BMC Bioinform.
Isaak Y. Tecle, Naama Menda, Robert M. Buels, Esther van der Knaap, Lukas A. Mueller
2008 J jnl
Bioinform.
Lukas A. Mueller, Adri A. Mills, Beth Skwarecki, Robert M. Buels, Naama Menda, Steven D. Tanksley
redb/extractors/decompiler/bninja/analysis/cfg.py
← Index redb/extractors/decompiler/bninja/analysis/cfg.py python
from binaryninja.enums import LowLevelILOperation as LLIL_OP

# Support both package and standalone imports
try:
    from . import cfg_features
except ImportError:
    from redb.extractors.decompiler.bninja.analysis import cfg_features


# ---------------------------------------------------------------------------
# Task 2.2: Build LLIL operation maps at import time using real enum values
# ---------------------------------------------------------------------------

# Prime product map: LLIL operation integer value -> small prime
cfg_features.LLIL_OP_PRIMES = {
    # SET_REG, SET_REG_SPLIT
    LLIL_OP.LLIL_SET_REG.value: 2,
    LLIL_OP.LLIL_SET_REG_SPLIT.value: 2,
    # SET_FLAG
    LLIL_OP.LLIL_SET_FLAG.value: 3,
    # LOAD
    LLIL_OP.LLIL_LOAD.value: 5,
    # STORE
    LLIL_OP.LLIL_STORE.value: 7,
    # PUSH, POP
    LLIL_OP.LLIL_PUSH.value: 11,
    LLIL_OP.LLIL_POP.value: 13,
    # CALL, TAILCALL, SYSCALL
    LLIL_OP.LLIL_CALL.value: 17,
    LLIL_OP.LLIL_TAILCALL.value: 17,
    LLIL_OP.LLIL_SYSCALL.value: 19,
    # RET, NORET
    LLIL_OP.LLIL_RET.value: 23,
    LLIL_OP.LLIL_NORET.value: 23,
    # IF, GOTO
    LLIL_OP.LLIL_IF.value: 29,
    LLIL_OP.LLIL_GOTO.value: 31,
    # ADD, SUB
    LLIL_OP.LLIL_ADD.value: 37,
    LLIL_OP.LLIL_SUB.value: 41,
    # AND, OR, XOR
    LLIL_OP.LLIL_AND.value: 43,
    LLIL_OP.LLIL_OR.value: 47,
    LLIL_OP.LLIL_XOR.value: 53,
    # LSL, LSR, ASR, ROL, ROR
    LLIL_OP.LLIL_LSL.value: 59,
    LLIL_OP.LLIL_LSR.value: 61,
    LLIL_OP.LLIL_ASR.value: 67,
    LLIL_OP.LLIL_ROL.value: 71,
    LLIL_OP.LLIL_ROR.value: 73,
    # MUL, DIVU, DIVS, MODU, MODS
    LLIL_OP.LLIL_MUL.value: 79,
    LLIL_OP.LLIL_DIVU.value: 83,
    LLIL_OP.LLIL_DIVS.value: 83,
    LLIL_OP.LLIL_MODU.value: 89,
    LLIL_OP.LLIL_MODS.value: 89,
    # NEG, NOT
    LLIL_OP.LLIL_NEG.value: 97,
    LLIL_OP.LLIL_NOT.value: 101,
    # CMP_E, CMP_NE, CMP_SLT, CMP_ULT, CMP_SLE, CMP_ULE
    # CMP_SGT, CMP_UGT, CMP_SGE, CMP_UGE
    LLIL_OP.LLIL_CMP_E.value: 103,
    LLIL_OP.LLIL_CMP_NE.value: 103,
    LLIL_OP.LLIL_CMP_SLT.value: 107,
    LLIL_OP.LLIL_CMP_ULT.value: 107,
    LLIL_OP.LLIL_CMP_SLE.value: 109,
    LLIL_OP.LLIL_CMP_ULE.value: 109,
    LLIL_OP.LLIL_CMP_SGT.value: 113,
    LLIL_OP.LLIL_CMP_UGT.value: 113,
    LLIL_OP.LLIL_CMP_SGE.value: 127,
    LLIL_OP.LLIL_CMP_UGE.value: 127,
    # NOP
    LLIL_OP.LLIL_NOP.value: 1,
    # SX, ZX, LOW_PART, BOOL_TO_INT
    LLIL_OP.LLIL_SX.value: 131,
    LLIL_OP.LLIL_ZX.value: 137,
    LLIL_OP.LLIL_LOW_PART.value: 139,
    LLIL_OP.LLIL_BOOL_TO_INT.value: 149,
    # JUMP, JUMP_TO
    LLIL_OP.LLIL_JUMP.value: 151,
    LLIL_OP.LLIL_JUMP_TO.value: 151,
}

# Category map: LLIL operation integer value -> category index
_ARITHMETIC = {
    LLIL_OP.LLIL_ADD, LLIL_OP.LLIL_ADC, LLIL_OP.LLIL_SUB, LLIL_OP.LLIL_SBB,
    LLIL_OP.LLIL_MUL, LLIL_OP.LLIL_MULU_DP, LLIL_OP.LLIL_MULS_DP,
    LLIL_OP.LLIL_DIVU, LLIL_OP.LLIL_DIVU_DP, LLIL_OP.LLIL_DIVS,
    LLIL_OP.LLIL_DIVS_DP, LLIL_OP.LLIL_MODU, LLIL_OP.LLIL_MODS,
    LLIL_OP.LLIL_NEG,
}
_LOGIC = {
    LLIL_OP.LLIL_AND, LLIL_OP.LLIL_OR, LLIL_OP.LLIL_XOR, LLIL_OP.LLIL_NOT,
    LLIL_OP.LLIL_LSL, LLIL_OP.LLIL_LSR, LLIL_OP.LLIL_ASR,
    LLIL_OP.LLIL_ROL, LLIL_OP.LLIL_RLC, LLIL_OP.LLIL_ROR, LLIL_OP.LLIL_RRC,
}
_TRANSFER = {
    LLIL_OP.LLIL_SET_REG, LLIL_OP.LLIL_SET_REG_SPLIT, LLIL_OP.LLIL_SET_FLAG,
    LLIL_OP.LLIL_GOTO, LLIL_OP.LLIL_IF, LLIL_OP.LLIL_JUMP, LLIL_OP.LLIL_JUMP_TO,
    LLIL_OP.LLIL_RET, LLIL_OP.LLIL_NORET, LLIL_OP.LLIL_PUSH, LLIL_OP.LLIL_POP,
}
_CALL = {
    LLIL_OP.LLIL_CALL, LLIL_OP.LLIL_TAILCALL, LLIL_OP.LLIL_SYSCALL,
}
_COMPARISON = {
    LLIL_OP.LLIL_CMP_E, LLIL_OP.LLIL_CMP_NE,
    LLIL_OP.LLIL_CMP_SLT, LLIL_OP.LLIL_CMP_ULT,
    LLIL_OP.LLIL_CMP_SLE, LLIL_OP.LLIL_CMP_ULE,
    LLIL_OP.LLIL_CMP_SGE, LLIL_OP.LLIL_CMP_UGE,
    LLIL_OP.LLIL_CMP_SGT, LLIL_OP.LLIL_CMP_UGT,
    LLIL_OP.LLIL_TEST_BIT, LLIL_OP.LLIL_FLAG_COND,
}
_MEMORY = {
    LLIL_OP.LLIL_LOAD, LLIL_OP.LLIL_STORE,
}

cfg_features.LLIL_OP_CATEGORIES = {}
for _op in _ARITHMETIC:
    cfg_features.LLIL_OP_CATEGORIES[_op.value] = cfg_features.CAT_ARITHMETIC
for _op in _LOGIC:
    cfg_features.LLIL_OP_CATEGORIES[_op.value] = cfg_features.CAT_LOGIC
for _op in _TRANSFER:
    cfg_features.LLIL_OP_CATEGORIES[_op.value] = cfg_features.CAT_TRANSFER
for _op in _CALL:
    cfg_features.LLIL_OP_CATEGORIES[_op.value] = cfg_features.CAT_CALL
for _op in _COMPARISON:
    cfg_features.LLIL_OP_CATEGORIES[_op.value] = cfg_features.CAT_COMPARISON
for _op in _MEMORY:
    cfg_features.LLIL_OP_CATEGORIES[_op.value] = cfg_features.CAT_MEMORY

# Set of CALL operation values for counting
_CALL_OPS = {op.value for op in _CALL}


# ---------------------------------------------------------------------------
# Task 2.1 + 2.3: Rewritten CFGAnalysis
# ---------------------------------------------------------------------------

class CFGAnalysis:
    def __init__(self, function, llil_function=None):
        self.function = function
        self.llil_function = llil_function

    def extract_function_cfg(self):
        """Extract function-level CFG features as a flat dictionary."""

        if self.function is None:
            return None

        blocks = list(self.function.basic_blocks)
        if not blocks:
            return None

        n = len(blocks)

        # 1. Build index-based adjacency from Binary Ninja blocks
        addr_to_idx = {b.start: i for i, b in enumerate(blocks)}
        successors = [[] for _ in range(n)]
        predecessors = [[] for _ in range(n)]
        for i, block in enumerate(blocks):
            for edge in block.outgoing_edges:
                if edge.target is None:
                    continue
                target_idx = addr_to_idx.get(edge.target.start)
                if target_idx is not None:
                    successors[i].append(target_idx)
                    predecessors[target_idx].append(i)

        # 2. BFS order (reusable across multiple features)
        bfs = cfg_features.bfs_order(successors, n)

        # 3. Collect per-block LLIL operations (for prime product + ACFG features)
        block_llil_ops = self._collect_block_llil_ops(blocks, addr_to_idx, n)
        all_llil_ops = [op for block_ops in block_llil_ops for op in block_ops]

        # 4. Structural counts
        edge_count = sum(len(s) for s in successors)
        total_llil = sum(len(ops) for ops in block_llil_ops)
        call_count = sum(
            1 for ops in block_llil_ops for op in ops
            if op in _CALL_OPS
        )

        # 5. Compute all features
        bb_features = cfg_features.build_block_features(block_llil_ops, successors, n)

        return {
            "cfg_topology_hash": cfg_features.compute_topology_hash(successors, bfs, n),
            "block_count": n,
            "edge_count": edge_count,
            "llil_total_operations": total_llil,
            "call_count": call_count,
            "cyclomatic_complexity": edge_count - n + 2,
            "loop_count": cfg_features.count_back_edges(successors, n),
            "max_depth": cfg_features.bfs_max_depth(successors, n),
            "max_fan_out": max((len(s) for s in successors), default=0),
            "md_index_topdown": cfg_features.compute_md_index_topdown(successors, predecessors, bfs),
            "md_index_bottomup": cfg_features.compute_md_index_bottomup(successors, predecessors, n),
            "prime_product_llil": cfg_features.compute_prime_product(all_llil_ops),
            "cfg_feature_tlsh": cfg_features.compute_cfg_feature_tlsh(bb_features, bfs),
            "wl_minhash": cfg_features.compute_wl_minhash(successors, predecessors, bb_features, n),
            "bb_features": bb_features,
            "cfg_adjacency": cfg_features.pack_adjacency(successors),
        }

    def _collect_block_llil_ops(self, blocks, addr_to_idx, n):
        """
        Collect LLIL operation integers per native basic block.
        Walks the full expression tree of each instruction so that
        nested operations (e.g. ADD inside SET_REG) are captured.
        Returns list of n lists, one per block.
        """
        block_ops = [[] for _ in range(n)]

        if self.llil_function is None:
            return block_ops

        try:
            for llil_block in self.llil_function.basic_blocks:
                # Map LLIL block to native block via source_block
                if llil_block.source_block is not None:
                    native_idx = addr_to_idx.get(llil_block.source_block.start)
                    if native_idx is not None:
                        for instr in llil_block:
                            self._walk_llil_ops(instr, block_ops[native_idx])
        except Exception:
            pass  # Return empty ops — LLIL-dependent fields will be 0/null

        return block_ops

    @staticmethod
    def _walk_llil_ops(expr, ops_list):
        """Collect operation values from an LLIL expression tree iteratively."""
        stack = [expr]
        while stack:
            node = stack.pop()
            if hasattr(node, 'operation'):
                ops_list.append(node.operation.value)
            if hasattr(node, 'operands'):
                for operand in node.operands:
                    if hasattr(operand, 'operation'):
                        stack.append(operand)