Veerabhadran Baladandayuthapani

32 papers A* 1A 1Misc 2Journal 18Unranked 10
YearRankTypeTitle / Venue / Authors
2025 J jnl
J. Comput. Graph. Stat.
Neel Desai, Veerabhadran Baladandayuthapani, Russell T. Shinohara, Jeffrey S. Morris
2023 J jnl
Patterns
Maria Masotti, Nathaniel Osher, Joel Eliason, Arvind Rao, Veerabhadran Baladandayuthapani
2023 J jnl
Medical Image Anal.
Shariq Mohammed, Sebastian Kurtek, Karthik Bharath, Arvind Rao, Veerabhadran Baladandayuthapani
2022 J jnl
J. Mach. Learn. Res.
Yang Ni, Francesco C. Stingo, Veerabhadran Baladandayuthapani
2022 J jnl
Bioinform.
Satwik Acharyya, Xiang Zhou, Veerabhadran Baladandayuthapani
2020 conf
Computer-Aided Diagnosis
Evan D. H. Gates, Jonathan S. Lin, Jeffrey S. Weinberg, Sujit S. Prabhu, Jackson Hamilton, John D. Hazle, Gregory N. Fuller, Veerabhadran Baladandayuthapani, David T. Fuentes, Dawid Schellingerhout
2020 J jnl
Bioinform.
Priyam Das, Christine B. Peterson, Kim-Anh Do, Rehan Akbani, Veerabhadran Baladandayuthapani
2020 Misc conf
PSB
Qingzhi Liu, Min Jin Ha, Rupam Bhattacharyya, Lana X. Garmire, Veerabhadran Baladandayuthapani
2020 J jnl
J. Mach. Learn. Res.
Nilabja Guha, Veerabhadran Baladandayuthapani, Bani K. Mallick
2019 J jnl
Comput. Stat. Data Anal.
Sayantan Banerjee, Rehan Akbani, Veerabhadran Baladandayuthapani
2018 Misc conf
PSB
Katherine Shoemaker, Brian P. Hobbs, Karthik Bharath, Chaan S. Ng, Veerabhadran Baladandayuthapani
2018 J jnl
Bioinform.
Caleb A. Class, Min Jin Ha, Veerabhadran Baladandayuthapani, Kim-Anh Do
2016 conf
ISBI
Shabnam Azadeh, Brian P. Hobbs, Liangsuo Ma, David A. Nielsen, F. Gerard Moeller, Veerabhadran Baladandayuthapani
2016 J jnl
NeuroImage
Shabnam Azadeh, Brian P. Hobbs, Liangsuo Ma, David A. Nielsen, F. Gerard Moeller, Veerabhadran Baladandayuthapani
2015 J jnl
Bioinform.
Min Jin Ha, Veerabhadran Baladandayuthapani, Kim-Anh Do
2014 J jnl
ACM Trans. Knowl. Discov. Data
Carlos Ordonez, Carlos Garcia-Alvarado, Veerabhadran Baladandayuthapani
2014 J jnl
IEEE ACM Trans. Comput. Biol. Bioinform.
Karl B. Gregory, Amin A. Momin, Kevin R. Coombes, Veerabhadran Baladandayuthapani
2013 A conf
CIKM
David Sergio Matusevich, Carlos Ordonez, Veerabhadran Baladandayuthapani
2013 J jnl
EURASIP J. Bioinform. Syst. Biol.
Elizabeth M. Jennings, Jeffrey S. Morris, Raymond J. Carroll, Ganiraju Manyam, Veerabhadran Baladandayuthapani
2013 conf
DTMBIO
Wellington Cabrera, Carlos Ordonez, David Sergio Matusevich, Veerabhadran Baladandayuthapani
2013 conf
SIGMOD Conference
Carlos Ordonez, Javier García-García, Carlos Garcia-Alvarado, Wellington Cabrera, Veerabhadran Baladandayuthapani, Mohammed S. Quraishi
2013 J jnl
EURASIP J. Bioinform. Syst. Biol.
Sanvesh Srivastava, Wenyi Wang, Ganiraju Manyam, Carlos Ordonez, Veerabhadran Baladandayuthapani
2013 conf
GENSiPS
Rolando J. Olivares, Arvind U. K. Rao, Ganesh Rao, Jeffrey S. Morris, Veerabhadran Baladandayuthapani
2013 J jnl
BMC Bioinform.
Wenting Wang, Veerabhadran Baladandayuthapani, Chris C. Holmes, Kim-Anh Do
2013 conf
GENSiPS
Anindya Bhadra, Veerabhadran Baladandayuthapani
2013 J jnl
Bioinform.
Wenting Wang, Veerabhadran Baladandayuthapani, Jeffrey S. Morris, Bradley M. Broom, Ganiraju Manyam, Kim-Anh Do
2012 conf
GENSiPS
Elizabeth M. Jennings, Jeffrey S. Morris, Raymond J. Carroll, Ganiraju Manyam, Veerabhadran Baladandayuthapani
2012 conf
GENSiPS
Sanvesh Srivastava, Wenyi Wang, Pascal O. Zinn, Rivka R. Colen, Veerabhadran Baladandayuthapani
2012 conf
GENSiPS
Karl B. Gregory, Kevin R. Coombes, Amin A. Momin, Luc Girard, Lauren A. Byers, Steven Lin, Michael Peyton, John V. Heymach, John D. Minna, Veerabhadran Baladandayuthapani
2012 conf
PIKM
Carlos Garcia-Alvarado, Carlos Ordonez, Veerabhadran Baladandayuthapani
2011 J jnl
Bioinform.
Vinícius Bonato, Veerabhadran Baladandayuthapani, Bradley M. Broom, Erik P. Sulman, Kenneth D. Aldape, Kim-Anh Do
2010 A* conf
ICDM
Mario Navas, Carlos Ordonez, Veerabhadran Baladandayuthapani
tests/unit/test_cfg_features.py
← Index tests/unit/test_cfg_features.py python
"""
Unit tests for cfg_features.py — all new CFG feature computations.

These tests use plain Python data structures (index-based adjacency lists)
and require no Binary Ninja dependency.
"""
import pytest

from redb.extractors.decompiler.bninja.analysis.cfg_features import (
    bfs_order,
    bfs_max_depth,
    count_back_edges,
    compute_topology_hash,
    compute_md_index_topdown,
    compute_md_index_bottomup,
    compute_prime_product,
    build_block_features,
    compute_cfg_feature_tlsh,
    compute_wl_minhash,
    pack_adjacency,
    LLIL_OP_CATEGORIES,
    CAT_ARITHMETIC,
    CAT_LOGIC,
    CAT_CALL,
    CAT_MEMORY,
    NUM_WL_MINHASH_PERMS,
)


# ===================================================================
# Helper: common graph topologies
# ===================================================================

def _linear_chain(n):
    """0 -> 1 -> 2 -> ... -> (n-1)"""
    return [[i + 1] if i < n - 1 else [] for i in range(n)]


def _diamond():
    """
    0 -> 1, 0 -> 2, 1 -> 3, 2 -> 3
    (classic if/else diamond)
    """
    return [[1, 2], [3], [3], []]


def _predecessors_from_successors(successors, n):
    preds = [[] for _ in range(n)]
    for src, targets in enumerate(successors):
        for tgt in targets:
            preds[tgt].append(src)
    return preds


# ===================================================================
# TestBfsOrder
# ===================================================================

class TestBfsOrder:
    def test_empty_graph(self):
        assert bfs_order([], 0) == []

    def test_single_node(self):
        assert bfs_order([[]], 1) == [0]

    def test_linear_chain(self):
        succs = _linear_chain(4)
        assert bfs_order(succs, 4) == [0, 1, 2, 3]

    def test_diamond(self):
        succs = _diamond()
        order = bfs_order(succs, 4)
        assert order[0] == 0
        assert order[-1] == 3
        assert set(order) == {0, 1, 2, 3}

    def test_unreachable_nodes(self):
        # 0 -> 1, node 2 is unreachable
        succs = [[1], [], []]
        order = bfs_order(succs, 3)
        assert order[:2] == [0, 1]
        assert 2 in order  # unreachable appended

    def test_all_nodes_visited(self):
        succs = _diamond()
        order = bfs_order(succs, 4)
        assert len(order) == 4


# ===================================================================
# TestBfsMaxDepth
# ===================================================================

class TestBfsMaxDepth:
    def test_empty_graph(self):
        assert bfs_max_depth([], 0) == 0

    def test_single_block(self):
        assert bfs_max_depth([[]], 1) == 0

    def test_linear_chain(self):
        succs = _linear_chain(5)
        assert bfs_max_depth(succs, 5) == 4

    def test_diamond(self):
        succs = _diamond()
        assert bfs_max_depth(succs, 4) == 2

    def test_wide_graph(self):
        # 0 -> 1, 0 -> 2, 0 -> 3 (all at depth 1)
        succs = [[1, 2, 3], [], [], []]
        assert bfs_max_depth(succs, 4) == 1


# ===================================================================
# TestCountBackEdges
# ===================================================================

class TestCountBackEdges:
    def test_empty_graph(self):
        assert count_back_edges([], 0) == 0

    def test_no_loops(self):
        succs = _linear_chain(3)
        assert count_back_edges(succs, 3) == 0

    def test_single_loop(self):
        # 0 -> 1 -> 2 -> 0 (one back edge: 2->0)
        succs = [[1], [2], [0]]
        assert count_back_edges(succs, 3) == 1

    def test_nested_loops(self):
        # 0 -> 1 -> 2 -> 1 (inner), 2 -> 3 -> 0 (outer)
        succs = [[1], [2], [1, 3], [0]]
        assert count_back_edges(succs, 4) == 2

    def test_self_loop(self):
        # 0 -> 0 (self-loop)
        succs = [[0]]
        assert count_back_edges(succs, 1) == 1

    def test_diamond_no_loops(self):
        succs = _diamond()
        assert count_back_edges(succs, 4) == 0

    def test_single_node_no_loop(self):
        succs = [[]]
        assert count_back_edges(succs, 1) == 0


# ===================================================================
# TestTopologyHash
# ===================================================================

class TestTopologyHash:
    def test_same_graph_same_hash(self):
        succs = _diamond()
        bfs = bfs_order(succs, 4)
        h1 = compute_topology_hash(succs, bfs, 4)
        h2 = compute_topology_hash(succs, bfs, 4)
        assert h1 == h2

    def test_different_graphs_different_hash(self):
        succs1 = _linear_chain(3)
        bfs1 = bfs_order(succs1, 3)
        h1 = compute_topology_hash(succs1, bfs1, 3)

        succs2 = _diamond()
        bfs2 = bfs_order(succs2, 4)
        h2 = compute_topology_hash(succs2, bfs2, 4)

        assert h1 != h2

    def test_returns_16_bytes(self):
        succs = _diamond()
        bfs = bfs_order(succs, 4)
        h = compute_topology_hash(succs, bfs, 4)
        assert isinstance(h, bytes)
        assert len(h) == 16

    def test_isomorphic_graphs_same_hash(self):
        # Graph A: 0->1, 0->2, 1->3, 2->3 (diamond with successors [1,2])
        succs_a = [[1, 2], [3], [3], []]
        # Graph B: same structure but successors listed as [2,1]
        # BFS from 0 will visit them in different order, but after remapping
        # the canonical form should be identical for isomorphic graphs
        succs_b = [[2, 1], [3], [3], []]

        bfs_a = bfs_order(succs_a, 4)
        bfs_b = bfs_order(succs_b, 4)

        h_a = compute_topology_hash(succs_a, bfs_a, 4)
        h_b = compute_topology_hash(succs_b, bfs_b, 4)
        assert h_a == h_b

    def test_empty_graph(self):
        h = compute_topology_hash([], [], 0)
        assert h == b'\x00' * 16

    def test_single_node(self):
        succs = [[]]
        bfs = bfs_order(succs, 1)
        h = compute_topology_hash(succs, bfs, 1)
        assert isinstance(h, bytes)
        assert len(h) == 16


# ===================================================================
# TestMdIndex
# ===================================================================

class TestMdIndex:
    def test_single_block_topdown(self):
        succs = [[]]
        preds = [[]]
        bfs = [0]
        result = compute_md_index_topdown(succs, preds, bfs)
        assert isinstance(result, int)
        assert result > 0

    def test_single_block_bottomup(self):
        succs = [[]]
        preds = [[]]
        result = compute_md_index_bottomup(succs, preds, 1)
        assert isinstance(result, int)
        assert result > 0

    def test_linear_chain_topdown_vs_bottomup(self):
        succs = _linear_chain(4)
        preds = _predecessors_from_successors(succs, 4)
        bfs = bfs_order(succs, 4)
        td = compute_md_index_topdown(succs, preds, bfs)
        bu = compute_md_index_bottomup(succs, preds, 4)
        # Top-down and bottom-up should be different for a linear chain
        # (entry has in_deg=0, exit has out_deg=0, so the sequences differ)
        assert td != bu

    def test_deterministic(self):
        succs = _diamond()
        preds = _predecessors_from_successors(succs, 4)
        bfs = bfs_order(succs, 4)
        td1 = compute_md_index_topdown(succs, preds, bfs)
        td2 = compute_md_index_topdown(succs, preds, bfs)
        assert td1 == td2

    def test_different_graphs_different_index(self):
        succs1 = _linear_chain(3)
        preds1 = _predecessors_from_successors(succs1, 3)
        bfs1 = bfs_order(succs1, 3)
        td1 = compute_md_index_topdown(succs1, preds1, bfs1)

        succs2 = _diamond()
        preds2 = _predecessors_from_successors(succs2, 4)
        bfs2 = bfs_order(succs2, 4)
        td2 = compute_md_index_topdown(succs2, preds2, bfs2)

        assert td1 != td2

    def test_topdown_empty(self):
        assert compute_md_index_topdown([], [], []) == 0

    def test_bottomup_empty(self):
        assert compute_md_index_bottomup([], [], 0) == 0


# ===================================================================
# TestPrimeProduct
# ===================================================================

class TestPrimeProduct:
    def test_empty(self):
        assert compute_prime_product([]) == 0

    def test_known_sequence(self):
        # Use actual LLIL enum values from conftest_binja_stubs:
        # LLIL_NOP=0 -> prime 1, LLIL_LOAD=4 -> prime 5
        from redb.extractors.decompiler.bninja.analysis.cfg_features import LLIL_OP_PRIMES
        nop_val = 0   # LLIL_NOP
        load_val = 4  # LLIL_LOAD
        expected = LLIL_OP_PRIMES.get(nop_val, 1) * LLIL_OP_PRIMES.get(load_val, 1)
        result = compute_prime_product([nop_val, load_val])
        assert result == expected

    def test_order_independence(self):
        # LLIL_LOAD=4, LLIL_STORE=5, LLIL_ADD=13
        ops_a = [4, 5, 13]
        ops_b = [13, 4, 5]
        assert compute_prime_product(ops_a) == compute_prime_product(ops_b)

    def test_unknown_ops_map_to_1(self):
        # Unknown ops get prime 1, so they don't change the product
        result_known = compute_prime_product([4])  # LLIL_LOAD -> 5
        result_with_unknown = compute_prime_product([4, 9999])  # LOAD * unknown(1)
        assert result_known == result_with_unknown

    def test_mod_2_64(self):
        # Product should be mod 2^64
        result = compute_prime_product([4] * 1000)  # LLIL_LOAD
        assert 0 <= result < 2**64

    def test_single_op(self):
        # LLIL_STORE=5 -> prime 7
        assert compute_prime_product([5]) == 7


# ===================================================================
# TestBuildBlockFeatures
# ===================================================================

class TestBuildBlockFeatures:
    def test_empty_llil(self):
        succs = [[1], []]
        features = build_block_features([[], []], succs, 2)
        assert len(features) == 2
        # All zeros except successor_count
        assert features[0] == [0, 0, 0, 0, 0, 0, 0, 1]  # 1 successor
        assert features[1] == [0, 0, 0, 0, 0, 0, 0, 0]  # 0 successors

    def test_correct_categorization(self):
        # Set up categories for testing
        import redb.extractors.decompiler.bninja.analysis.cfg_features as cf
        old_cats = cf.LLIL_OP_CATEGORIES.copy()
        cf.LLIL_OP_CATEGORIES.update({
            100: CAT_ARITHMETIC,
            101: CAT_ARITHMETIC,
            200: CAT_LOGIC,
            300: CAT_CALL,
            400: CAT_MEMORY,
        })
        try:
            block_ops = [[100, 101, 200, 300, 400]]
            succs = [[]]
            features = build_block_features(block_ops, succs, 1)
            assert features[0][0] == 5   # instr_count
            assert features[0][1] == 2   # arithmetic
            assert features[0][2] == 1   # logic
            assert features[0][4] == 1   # call
            assert features[0][6] == 1   # memory
        finally:
            cf.LLIL_OP_CATEGORIES.clear()
            cf.LLIL_OP_CATEGORIES.update(old_cats)

    def test_cap_at_65535(self):
        # More than 65535 ops in one block
        huge_ops = [0] * 70000  # NOP x 70000
        succs = [[]]
        features = build_block_features([huge_ops], succs, 1)
        assert features[0][0] == 65535  # capped

    def test_missing_block_ops(self):
        # block_llil_ops shorter than n
        succs = [[1], [2], []]
        features = build_block_features([[1, 2]], succs, 3)
        assert len(features) == 3
        # Block 1 and 2 get empty ops since block_llil_ops only has 1 entry
        assert features[1] == [0, 0, 0, 0, 0, 0, 0, 1]
        assert features[2] == [0, 0, 0, 0, 0, 0, 0, 0]


# ===================================================================
# TestCfgFeatureTlsh
# ===================================================================

class TestCfgFeatureTlsh:
    def test_too_few_blocks_returns_none(self):
        # 5 blocks = 5 * 9 bytes = 45 < 50
        bb_features = [[10, 1, 0, 2, 0, 1, 1, 2]] * 5
        bfs = list(range(5))
        result = compute_cfg_feature_tlsh(bb_features, bfs)
        assert result is None

    def test_uniform_data_returns_none(self):
        # 7 identical blocks — TLSH returns TNULL for low-entropy input
        bb_features = [[10, 1, 0, 2, 0, 1, 1, 2]] * 7
        bfs = list(range(7))
        result = compute_cfg_feature_tlsh(bb_features, bfs)
        assert result is None

    def test_varied_data_returns_string(self):
        # 20 blocks with varied features — enough entropy for TLSH
        bb_features = [
            [i * 7 + 3, (i * 13) % 50, (i * 17) % 30, (i * 23) % 40,
             (i * 11) % 20, (i * 7) % 25, (i * 19) % 35, (i * 3) % 10]
            for i in range(20)
        ]
        bfs = list(range(20))
        result = compute_cfg_feature_tlsh(bb_features, bfs)
        assert isinstance(result, str)
        assert len(result) > 0
        assert result.startswith("T1")


# ===================================================================
# TestWlMinhash
# ===================================================================

class TestWlMinhash:
    def test_empty_function(self):
        result = compute_wl_minhash([], [], [], 0)
        assert result == [255] * NUM_WL_MINHASH_PERMS

    def test_returns_128_elements(self):
        succs = _diamond()
        preds = _predecessors_from_successors(succs, 4)
        bb_feats = [[5, 1, 0, 2, 0, 1, 1, 2]] * 4
        result = compute_wl_minhash(succs, preds, bb_feats, 4)
        assert len(result) == 128

    def test_all_uint8(self):
        succs = _linear_chain(3)
        preds = _predecessors_from_successors(succs, 3)
        bb_feats = [[3, 1, 0, 1, 0, 0, 1, 1]] * 3
        result = compute_wl_minhash(succs, preds, bb_feats, 3)
        assert all(0 <= v <= 255 for v in result)

    def test_identical_graphs_same_signature(self):
        succs = _diamond()
        preds = _predecessors_from_successors(succs, 4)
        bb_feats = [[5, 1, 0, 2, 0, 1, 1, 2]] * 4
        sig1 = compute_wl_minhash(succs, preds, bb_feats, 4)
        sig2 = compute_wl_minhash(succs, preds, bb_feats, 4)
        assert sig1 == sig2

    def test_different_graphs_different_signatures(self):
        # Graph 1: linear chain
        succs1 = _linear_chain(4)
        preds1 = _predecessors_from_successors(succs1, 4)
        bb_feats1 = [[5, 1, 0, 2, 0, 1, 1, i] for i in range(4)]
        sig1 = compute_wl_minhash(succs1, preds1, bb_feats1, 4)

        # Graph 2: diamond
        succs2 = _diamond()
        preds2 = _predecessors_from_successors(succs2, 4)
        bb_feats2 = [[10, 3, 2, 1, 0, 0, 0, i] for i in range(4)]
        sig2 = compute_wl_minhash(succs2, preds2, bb_feats2, 4)

        assert sig1 != sig2

    def test_single_node(self):
        succs = [[]]
        preds = [[]]
        bb_feats = [[1, 0, 0, 0, 0, 0, 0, 0]]
        result = compute_wl_minhash(succs, preds, bb_feats, 1)
        assert len(result) == 128


# ===================================================================
# TestPackAdjacency
# ===================================================================

class TestPackAdjacency:
    def test_empty(self):
        assert pack_adjacency([]) == []

    def test_single_edge(self):
        succs = [[1], []]
        edges = pack_adjacency(succs)
        assert len(edges) == 1
        assert edges[0] == (0 << 16) | 1

    def test_correct_packing(self):
        succs = _diamond()
        edges = pack_adjacency(succs)
        assert len(edges) == 4
        # 0->1, 0->2, 1->3, 2->3
        expected = {
            (0 << 16) | 1,
            (0 << 16) | 2,
            (1 << 16) | 3,
            (2 << 16) | 3,
        }
        assert set(edges) == expected

    def test_roundtrip(self):
        """Unpack edges and verify source/target pairs."""
        succs = [[1, 2], [3], [3], []]
        edges = pack_adjacency(succs)
        unpacked = [(e >> 16, e & 0xFFFF) for e in edges]
        expected = [(0, 1), (0, 2), (1, 3), (2, 3)]
        assert sorted(unpacked) == sorted(expected)

    def test_large_index_filtered(self):
        # Create a successor list where index >= 65536
        succs = [[] for _ in range(65537)]
        succs[0] = [65536]  # target is exactly 65536 — should be filtered
        edges = pack_adjacency(succs)
        assert len(edges) == 0

    def test_max_valid_index(self):
        # Index 65535 is the maximum valid
        succs = [[] for _ in range(65536)]
        succs[0] = [65535]
        edges = pack_adjacency(succs)
        assert len(edges) == 1
        assert edges[0] == (0 << 16) | 65535