Narayanaswamy Srinivasan

34 papers Journal 33Unranked 1
YearRankTypeTitle / Venue / Authors
2022 J jnl
Database J. Biol. Databases Curation
Neha V. Kalmankar, Murugavel Pavalam, Sowmya Indrakumar, Narayanaswamy Srinivasan, Ramanathan Sowdhamini
2022 J jnl
IEEE ACM Trans. Comput. Biol. Bioinform.
Pierrick Craveur, Tarun J. Narwani, Narayanaswamy Srinivasan, Jean-Christophe Gelly, Joseph Rebehmed, Alexandre G. de Brevern
2019 J jnl
Source Code Biol. Medicine
Guilhem Faure, Agnel Praveen Joseph, Pierrick Craveur, Tarun J. Narwani, Narayanaswamy Srinivasan, Jean-Christophe Gelly, Joseph Rebehmed, Alexandre G. de Brevern
2018 J jnl
PLoS Comput. Biol.
Raju Kalaivani, Raju Reema, Narayanaswamy Srinivasan
2018 J jnl
PLoS Comput. Biol.
Sneha Vishwanath, Alexandre G. de Brevern, Narayanaswamy Srinivasan
2015 J jnl
Database J. Biol. Databases Curation
Patricia C. Babbitt, Pantelis G. Bagos, Amos Bairoch, Alex Bateman, Arnaud Chatonnet, Mark Jinan Chen, David J. Craik, Robert D. Finn, David E. Gloriam, Daniel H. Haft, Bernard Henrissat, Gemma L. Holliday, Vignir Ísberg, Quentin Kaas, David Landsman, Nicolas Lenfant, Gerard Manning, Nozomi Nagano, Narayanaswamy Srinivasan, Claire O'Donovan, Kim D. Pruitt, Ramanathan Sowdhamini, Neil D. Rawlings, Milton H. Saier Jr., Joanna L. Sharman, Michael Spedding, Konstantinos D. Tsirigos, Åke Västermark, Gerrit Vriend
2015 J jnl
Nucleic Acids Res.
Richa Mudgal, Sankaran Sandhya, Gayatri Kumar, Ramanathan Sowdhamini, Nagasuma R. Chandra, Narayanaswamy Srinivasan
2015 J jnl
Database J. Biol. Databases Curation
Rahul Metri, Sridhar Hariharaputran, Gayatri Ramakrishnan, Praveen Anand, Upadhyayula S. Raghavender, Bernardo Ochoa-Montaño, Alicia P. Higueruelo, Ramanathan Sowdhamini, Nagasuma R. Chandra, Tom L. Blundell, Narayanaswamy Srinivasan
2014 J jnl
BMC Bioinform.
Mutharasu Gnanavel, Prachi Mehrotra, Ramaswamy Rakshambikai, Juliette Martin, Narayanaswamy Srinivasan, Ramachandra M. Bhaskara
2014 J jnl
J. Bioinform. Comput. Biol.
R. Rakshambikai, Narayanaswamy Srinivasan, Rupali A. Gadkari
2013 J jnl
Database J. Biol. Databases Curation
Swapnil Mahajan, Garima Agarwal, Mohammed Iftekhar, Bernard O. Offmann, Alexandre G. de Brevern, Narayanaswamy Srinivasan
2011 J jnl
BMC Bioinform.
Oruganty Krishnadev, Narayanaswamy Srinivasan
2011 J jnl
Int. J. Knowl. Discov. Bioinform.
Narayanaswamy Srinivasan, Garima Agarwal, Ramachandra M. Bhaskara, Rupali A. Gadkari, Oruganty Krishnadev, B. Lakshmi, Swapnil Mahajan, Smita Mohanty, Richa Mudgal, R. Rakshambikai, Sankaran Sandhya, G. Sudha, L. S. Swapna, N. Tyagi
2011 J jnl
Nucleic Acids Res.
Jean-Christophe Gelly, Agnel Praveen Joseph, Narayanaswamy Srinivasan, Alexandre G. de Brevern
2010 J jnl
Int. J. Knowl. Discov. Bioinform.
Oruganty Krishnadev, Shveta Bisht, Narayanaswamy Srinivasan
2009 conf
GENSiPS
Smita Mohanty, Narayanaswamy Srinivasan
2009 J jnl
Silico Biol.
Ambrish Roy, Narayanaswamy Srinivasan, Venkatraman S. Gowri
2008 J jnl
Silico Biol.
Oruganty Krishnadev, Narayanaswamy Srinivasan
2007 J jnl
Nucleic Acids Res.
K. G. Tina, Rana Bhadra, Narayanaswamy Srinivasan
2006 J jnl
Nucleic Acids Res.
Rana Bhadra, Sankaran Sandhya, K. R. Abhinandan, Saikat Chakrabarti, Ramanathan Sowdhamini, Narayanaswamy Srinivasan
2006 J jnl
Nucleic Acids Res.
Ganesan Pugalenthi, Khader Shameer, Narayanaswamy Srinivasan, Ramanathan Sowdhamini
2006 J jnl
Nucleic Acids Res.
V. S. Gowri, Oruganty Krishnadev, C. S. Swamy, Narayanaswamy Srinivasan
2006 J jnl
Nucleic Acids Res.
Manoj Tyagi, P. Sharma, C. S. Swamy, F. Cadet, Narayanaswamy Srinivasan, Alexandre G. de Brevern, Bernard O. Offmann
2005 J jnl
Silico Biol.
Rana Bhadra, Narayanaswamy Srinivasan, Shashi B. Pandit
2005 J jnl
Nucleic Acids Res.
Oruganty Krishnadev, N. Rekha, Shashi B. Pandit, S. Abhiman, Smita Mohanty, L. S. Swapna, Swanand P. Gore, Narayanaswamy Srinivasan
2005 J jnl
Bioinform.
B. Anand, V. S. Gowri, Narayanaswamy Srinivasan
2004 J jnl
Silico Biol.
Shashi B. Pandit, Narayanaswamy Srinivasan
2004 J jnl
Nucleic Acids Res.
A. Krupa, K. R. Abhinandan, Narayanaswamy Srinivasan
2004 J jnl
Silico Biol.
Seema Namboori, Narayanaswamy Srinivasan, Shashi B. Pandit
2004 J jnl
BMC Bioinform.
Shashi B. Pandit, Rana Bhadra, V. S. Gowri, S. Balaji, B. Anand, Narayanaswamy Srinivasan
2003 J jnl
Nucleic Acids Res.
V. S. Gowri, Shashi B. Pandit, P. S. Karthik, Narayanaswamy Srinivasan, S. Balaji
2002 J jnl
Nucleic Acids Res.
Shashi B. Pandit, Dilip Gosar, S. Abhiman, S. Sujatha, Sayali S. Dixit, Natasha S. Mhatre, Ramanathan Sowdhamini, Narayanaswamy Srinivasan
2001 J jnl
Nucleic Acids Res.
S. Balaji, S. Sujatha, S. Sai Chetan Kumar, Narayanaswamy Srinivasan
2001 J jnl
Bioinform.
S. Sujatha, S. Balaji, Narayanaswamy Srinivasan
docs/apk-code-schema.md
← Index docs/apk-code-schema.md markdown
# APK Code Analysis — ClickHouse Schema

All tables follow the `ReplacingMergeTree(analysis_date)` pattern from
`docs/new-code-binja-schema.md`, except `code_apk_analysis_errors` which
uses `MergeTree()`.

**Companion PDD:** `APK_CODE_ANALYSIS_PDD-Tech_Annex.md` §7

---

## Table overview

| # | Table | Analog (Binja) | Engine | Key |
|---|-------|----------------|--------|-----|
| 1 | `code_apk_decompiled_methods_content` | `code_binja_decompiled_functions_content` | ReplacingMergeTree | `decompiled_method_hash` |
| 2 | `code_apk_decompiled_methods_references` | `code_binja_decompiled_functions_references` | ReplacingMergeTree | `(sha256, decompiled_method_hash)` |
| 3 | `code_apk_smali_methods_content` | `code_binja_disassembled_functions_content` | ReplacingMergeTree | `smali_method_hash` |
| 4 | `code_apk_smali_methods_references` | `code_binja_disassembled_functions_references` | ReplacingMergeTree | `(sha256, smali_method_hash)` |
| 5 | `code_apk_method_similarity_metrics` | `code_binja_function_similarity_metrics` | ReplacingMergeTree | `smali_method_hash` |
| 6 | `code_apk_cfg_methods` | `code_binja_cfg_functions` | ReplacingMergeTree | `smali_method_hash` |
| 7 | `code_binja_strings_raw` *(shared)* | — | Null (→ MV) | — |
| 8 | `code_apk_analysis_errors` | `function_analysis_errors_binja` | MergeTree | `(sha256, error_location, error_hash)` |

---

## Table 1: `code_apk_decompiled_methods_content`

**Analog:** `code_binja_decompiled_functions_content`

```sql
CREATE TABLE IF NOT EXISTS code_apk_decompiled_methods_content (
    decompiled_method_hash FixedString(64),          -- SHA-256 of normalized Java source
    decompiled_method String CODEC(ZSTD(3)),          -- Full Java method source
    decompiled_method_type Enum8('USER'=1, 'LIBRARY'=2, 'UNKNOWN'=5) DEFAULT 'UNKNOWN',
    decompiled_has_string_encryption UInt8 DEFAULT 0,
    decompiled_has_reflection_calls UInt8 DEFAULT 0,
    decompiled_excessive_goto_count UInt8 DEFAULT 0,
    analysis_date DateTime64(3, 'UTC'),

    INDEX idx_method_content_token lower(decompiled_method) TYPE tokenbf_v1(32768, 3, 0) GRANULARITY 1
) ENGINE = ReplacingMergeTree(analysis_date)
ORDER BY decompiled_method_hash;
```

## Table 2: `code_apk_decompiled_methods_references`

**Analog:** `code_binja_decompiled_functions_references`

```sql
CREATE TABLE IF NOT EXISTS code_apk_decompiled_methods_references (
    sha256 FixedString(64),
    decompiled_method_hash FixedString(64),
    smali_method_hash Nullable(FixedString(64)),
    decompiled_class_name LowCardinality(String),
    decompiled_method_name LowCardinality(String),
    decompiled_method_signature String,               -- Dalvik descriptor: (Landroid/os/Bundle;)V
    decompiled_method_prototype String,               -- Java-style: void onCreate(Bundle)
    functions_caller Array(String),
    functions_call Array(String),
    analysis_date DateTime64(3, 'UTC'),

    INDEX idx_decompiled_class_name decompiled_class_name TYPE tokenbf_v1(32768, 3, 0) GRANULARITY 1,
    INDEX idx_decompiled_method_name decompiled_method_name TYPE tokenbf_v1(32768, 3, 0) GRANULARITY 1,
    INDEX idx_functions_caller functions_caller TYPE tokenbf_v1(32768, 3, 0) GRANULARITY 1,
    INDEX idx_functions_call functions_call TYPE tokenbf_v1(32768, 3, 0) GRANULARITY 1
) ENGINE = ReplacingMergeTree(analysis_date)
ORDER BY (sha256, decompiled_method_hash);
```

## Table 3: `code_apk_smali_methods_content`

**Analog:** `code_binja_disassembled_functions_content`

```sql
CREATE TABLE IF NOT EXISTS code_apk_smali_methods_content (
    smali_method_hash FixedString(64),                -- SHA-256 of normalized smali body
    smali_method String CODEC(ZSTD(3)),               -- Full smali method body
    smali_method_type Enum8('USER'=1, 'LIBRARY'=2, 'UNKNOWN'=5) DEFAULT 'UNKNOWN',
    smali_instructions_count UInt32,
    smali_register_count UInt16,
    smali_has_string_encryption UInt8 DEFAULT 0,
    smali_has_reflection_calls UInt8 DEFAULT 0,
    smali_excessive_goto_count UInt8 DEFAULT 0,
    smali_flattened_score Float64 DEFAULT 0.0,       -- Control flow flattening score (0.01.0)
    smali_mba_score Float64 DEFAULT 0.0,             -- Mixed boolean-arithmetic score (0.01.0)
    analysis_date DateTime64(3, 'UTC'),

    INDEX idx_smali_ngram smali_method TYPE ngrambf_v1(3, 32768, 3, 0) GRANULARITY 1,
    INDEX idx_smali_method_type smali_method_type TYPE set(3) GRANULARITY 1,
    INDEX idx_smali_instr_count smali_instructions_count TYPE minmax GRANULARITY 4,
    INDEX idx_smali_reg_count smali_register_count TYPE minmax GRANULARITY 4,
    INDEX idx_smali_flattened smali_flattened_score TYPE minmax GRANULARITY 4,
    INDEX idx_smali_mba smali_mba_score TYPE minmax GRANULARITY 4
) ENGINE = ReplacingMergeTree(analysis_date)
ORDER BY smali_method_hash;
```

## Table 4: `code_apk_smali_methods_references`

**Analog:** `code_binja_disassembled_functions_references`

```sql
CREATE TABLE IF NOT EXISTS code_apk_smali_methods_references (
    sha256 FixedString(64),
    smali_method_hash FixedString(64),
    decompiled_method_hash Nullable(FixedString(64)),
    smali_class_name LowCardinality(String),
    smali_method_name LowCardinality(String),
    smali_method_signature String,
    analysis_date DateTime64(3, 'UTC'),

    INDEX idx_smali_class_name smali_class_name TYPE tokenbf_v1(32768, 3, 0) GRANULARITY 1,
    INDEX idx_smali_method_name smali_method_name TYPE tokenbf_v1(32768, 3, 0) GRANULARITY 1
) ENGINE = ReplacingMergeTree(analysis_date)
ORDER BY (sha256, smali_method_hash);
```

## Table 5: `code_apk_method_similarity_metrics`

**Analog:** `code_binja_function_similarity_metrics`

Content-based fuzzy matching table. Structural/CFG scalars (block_count, edge_count, etc.)
are in `code_apk_cfg_methods` (Table 6) — this table holds only fuzzy hashes and MinHash.

```sql
CREATE TABLE IF NOT EXISTS code_apk_method_similarity_metrics (
    smali_method_hash FixedString(64),
    -- Raw smali fuzzy hashes (analog: ssdeep_disassembly / tlsh_disassembly)
    ssdeep_smali Nullable(String),
    tlsh_smali Nullable(FixedString(72)),
    -- Semantically normalized smali fuzzy hashes (analog: ssdeep_llil / tlsh_llil)
    ssdeep_smali_normalized Nullable(String),
    tlsh_smali_normalized Nullable(FixedString(72)),
    minhash Array(UInt8),
    analysis_date DateTime64(3, 'UTC'),

    INDEX idx_ssdeep ssdeep_smali TYPE bloom_filter GRANULARITY 1,
    INDEX idx_tlsh tlsh_smali TYPE bloom_filter GRANULARITY 1,
    INDEX idx_ssdeep_norm ssdeep_smali_normalized TYPE bloom_filter GRANULARITY 1,
    INDEX idx_tlsh_norm tlsh_smali_normalized TYPE bloom_filter GRANULARITY 1
) ENGINE = ReplacingMergeTree(analysis_date)
ORDER BY smali_method_hash;
```

## Table 6: `code_apk_cfg_methods`

**Analog:** `code_binja_cfg_functions` (see `db_migration/cfg_functions_ddl.sql`)

Structural and topological features computed from smali CFG. All fields mirror
the Binja table with APK-appropriate naming.

```sql
CREATE TABLE IF NOT EXISTS code_apk_cfg_methods (
    -- Identity
    smali_method_hash FixedString(64),

    -- Tier 0: Exact structural match
    cfg_topology_hash FixedString(16),

    -- Tier 1: Structural pre-filtering
    block_count UInt16,
    edge_count UInt16,
    cfg_instructions_count UInt32,            -- Dalvik instruction count (analog: llil_total_operations)
    call_count UInt16,
    cyclomatic_complexity UInt16,
    loop_count UInt16,
    max_depth UInt16,
    max_fan_out UInt16,
    md_index_topdown UInt64,
    md_index_bottomup UInt64,
    prime_product_smali UInt64,              -- Dalvik semantic primes (analog: prime_product_llil)

    -- Tier 2: Fuzzy matching
    cfg_feature_tlsh Nullable(FixedString(72)),
    wl_minhash Array(UInt8),

    -- Embedding-ready storage
    bb_features Array(Array(UInt16)),        -- ACFG block feature vectors
    cfg_adjacency Array(UInt32),             -- Packed (src << 16 | tgt)

    analysis_date DateTime64(3, 'UTC'),

    -- Indexes
    INDEX idx_topology cfg_topology_hash TYPE bloom_filter GRANULARITY 1,
    INDEX idx_complexity cyclomatic_complexity TYPE minmax GRANULARITY 4,
    INDEX idx_block_count block_count TYPE minmax GRANULARITY 4,
    INDEX idx_edge_count edge_count TYPE minmax GRANULARITY 4,
    INDEX idx_call_count call_count TYPE minmax GRANULARITY 4,
    INDEX idx_cfg_instr_count cfg_instructions_count TYPE minmax GRANULARITY 4,
    INDEX idx_loop_count loop_count TYPE minmax GRANULARITY 4,
    INDEX idx_max_depth max_depth TYPE minmax GRANULARITY 4,
    INDEX idx_max_fan_out max_fan_out TYPE minmax GRANULARITY 4,
    INDEX idx_md_topdown md_index_topdown TYPE minmax GRANULARITY 4,
    INDEX idx_md_bottomup md_index_bottomup TYPE minmax GRANULARITY 4,
    INDEX idx_prime prime_product_smali TYPE bloom_filter GRANULARITY 1,
    INDEX idx_cfg_tlsh cfg_feature_tlsh TYPE bloom_filter GRANULARITY 1
) ENGINE = ReplacingMergeTree(analysis_date)
ORDER BY smali_method_hash;
```

**Column mapping (APK → Binja):**

| APK column | Binja column | Notes |
|------------|-------------|-------|
| `smali_method_hash` | `disassembled_function_hash` | Both SHA-256 of normalized code |
| `cfg_instructions_count` | `llil_total_operations` | Dalvik instructions vs LLIL operations |
| `prime_product_smali` | `prime_product_llil` | Same prime algorithm, Dalvik semantic categories |
| All others | Same name | Identical algorithms from shared `cfg_features.py` |

## Table 7: `code_binja_strings_raw` (shared)

APK strings are inserted into the existing `code_binja_strings_raw` Null-engine table,
which feeds materialized views (`code_binja_strings_by_binary`, `mv_string_popularity_public`).
This enables cross-format string correlation between PE/ELF/Mach-O/APK samples.

No new table creation needed — see `docs/new-code-binja-schema.md` for the existing DDL.

## Table 8: `code_apk_analysis_errors`

**Analog:** `function_analysis_errors_binja`

```sql
CREATE TABLE IF NOT EXISTS code_apk_analysis_errors (
    sha256 FixedString(64),
    class_name Nullable(String) CODEC(ZSTD(3)),
    method_name Nullable(String) CODEC(ZSTD(3)),
    error_location LowCardinality(String) CODEC(ZSTD(3)),   -- 'jadx', 'apktool', 'androguard', 'analysis'
    error_message Nullable(String) CODEC(ZSTD(3)),
    error_type Nullable(String) CODEC(ZSTD(3)),
    error_hash FixedString(32),                               -- MD5 for dedup
    status Enum8('new' = 1, 'investigating' = 2, 'fixed' = 3, 'wontfix' = 4) DEFAULT 'new',
    analysis_date DateTime64(3, 'UTC')
) ENGINE = MergeTree()
ORDER BY (sha256, error_location, error_hash);
```