Vincent J. Major

19 papers Misc 4Journal 11Unranked 4
YearRankTypeTitle / Venue / Authors
2025 J jnl
J. Am. Medical Informatics Assoc.
Kiran Malhotra, Batia Mishan Wiesenfeld, Vincent J. Major, Himanshu Grover, Yindalon Aphinyanaphongs, Paul A. Testa, Jonathan S. Austrian
2025 J jnl
npj Digit. Medicine
Shaina Mackin, Vincent J. Major, Rumi Chunara, Remle Newton-Dame
2025 J jnl
npj Digit. Medicine
Soumik Mandal, Batia Mishan Wiesenfeld, Adam Szerencsy, William R. Small, Vincent J. Major, Safiya Richardson, Antoinette M. Schoenthaler, Devin M. Mann, Oded Nov
2024 J jnl
J. Am. Medical Informatics Assoc.
Kar-mun C. Woo, Gregory W. Simon, Olumide Akindutire, Yindalon Aphinyanaphongs, Jonathan S. Austrian, Jung G. Kim, Nicholas Genes, Jacob A Goldenring, Vincent J. Major, Chloé S. Pariente, Edwin G. Pineda, Stella K. Kang
2023 conf
ICHI
Vincent J. Major, Walter Wang, Yindalon Aphinyanaphongs
2023 conf
ICHI
Vincent J. Major, Claudia S. Plottel, Yindalon Aphinyanaphongs
2022 J jnl
Appl. Clin. Inform.
Vincent J. Major, Simon Andrew Jones, Narges Razavian, Ashley Bagheri, Felicia Mendoza, Jay Stadelman, Leora I. Horwitz, Jonathan S. Austrian, Yindalon Aphinyanaphongs
2021 Misc conf
FLAIRS
Seda Bilaloglu, Vincent J. Major, Himanshu Grover, Isabel Metzger, Yindalon Aphinyanaphongs
2021 conf
BCB
Garrett Yoon, Vincent J. Major
2020 J jnl
npj Digit. Medicine
Narges Razavian, Vincent J. Major, Mukund Sudarshan, Jesse Burk-Rafel, Peter Stella, Hardev Randhawa, Seda Bilaloglu, Ji Chen, Vuthy Nguy, Walter Wang, Hao Zhang, Ilan Reinstein, David Kudlowitz, Cameron Zenger, Meng Cao, Ruina Zhang, Siddhant Dogra, Keerthi B. Harish, Brian Bosworth, Fritz Francois, Leora I. Horwitz, Rajesh Ranganath, Jonathan S. Austrian, Yindalon Aphinyanaphongs
2020 J jnl
BMC Medical Informatics Decis. Mak.
Vincent J. Major, Yindalon Aphinyanaphongs
2019 J jnl
Comput. Methods Programs Biomed.
Daniel P. Redmond, Yeong Shiong Chiew, Vincent J. Major, J. Geoffrey Chase
2018 Misc conf
AMIA
Vincent J. Major, Alisa Surkis, Yindalon Aphinyanaphongs
2017 Misc conf
AMIA
Vincent J. Major, Alisa Surkis, Yindalon Aphinyanaphongs
2017 J jnl
CoRR
Vincent J. Major, Alisa Surkis, Yindalon Aphinyanaphongs
2016 J jnl
Biomed. Signal Process. Control.
Don Oliver Kannangara, F. Newberry, Sarah L. Howe, Vincent J. Major, Daniel P. Redmond, A. Szlavecs, Yeong Shiong Chiew, Christopher G. Pretty, Balázs Benyó, Geoffrey M. Shaw, J. Geoffrey Chase
2016 J jnl
Biomed. Signal Process. Control.
Vincent J. Major, Simon Corbett, Daniel P. Redmond, Alex Beatson, Daniel Glassenbury, Yeong Shiong Chiew, Christopher G. Pretty, Thomas Desaive, Ákos Szlávecz, Balázs Benyó, Geoffrey M. Shaw, J. Geoffrey Chase
2016 Misc conf
AMIA
Vincent J. Major, Monique S. Tanna, Simon Jones, Yindalon Aphinyanaphongs
2015 conf
EMBC
Yeong Shiong Chiew, Christopher G. Pretty, Alex Beatson, Daniel Glassenbury, Vincent J. Major, Simon Corbett, Daniel P. Redmond, Ákos Szlávecz, Geoffrey M. Shaw, J. Geoffrey Chase
yara/README.md
← Index yara/README.md markdown
# YARA Rules Directory

This folder contains YARA rules for scanning binary samples.

## Setting Up YARA-Forge Rules

To use the YARA-Forge rules from [https://github.com/YARAHQ/yara-forge](https://github.com/YARAHQ/yara-forge):

```bash
# Download the latest release
cd /path/to/redb/yara
# wget https://github.com/YARAHQ/yara-forge/releases/latest/download/yara-forge-rules-core.zip
wget https://github.com/YARAHQ/yara-forge/releases/latest/download/yara-forge-rules-extended.zip

# Extract rules
# unzip yara-forge-rules-core.zip
unzip yara-forge-rules-extended.zip
```

Available packages:
- `yara-forge-rules-core.zip` - Core rules (~5,000 rules)
- `yara-forge-rules-extended.zip` - Extended rules (~10,000 rules)
- `yara-forge-rules-full.zip` - Full rules (~11,000+ rules)

## Pre-compiling Rules (Recommended for Production)

For large rulesets like YARA-Forge, pre-compiling rules significantly improves startup time:

```bash
# Pre-compile all rules into a single .yarac file
python -m redb.extractors.yara --compile

# Or specify custom paths
python -m redb.extractors.yara --compile --rules-path /path/to/rules --output /path/to/output.yarac
```

This creates `yara/compiled_rules.yarac` which is loaded automatically on subsequent runs.

### Performance Comparison

| Method | First Scan Startup | Subsequent Scans |
|--------|-------------------|------------------|
| Source files (.yar) | ~10-30 seconds (11k rules) | Instant (cached) |
| Pre-compiled (.yarac) | ~1-2 seconds | Instant (cached) |

## Directory Structure

```
yara/
├── README.md
├── .gitkeep
├── compiled_rules.yarac    # (optional) Pre-compiled rules
├── packages/               # YARA-Forge packages
│   └── core/
│       └── *.yar
└── custom/                 # Your custom rules
    └── my_rules.yar
```

Rules are loaded in this priority:
1. `compiled_rules.yarac` (if exists) - fastest
2. All `.yar` and `.yara` files recursively - compiles on first run

## Usage

### Scan with YARA only

```bash
# Scan local files
python start.py --path /path/to/samples -y --repo my_repo --index_prefix redb

# Scan S3 samples
python start.py --s3 --repo bazaar -y --index_prefix redb

# Dry-run (print results instead of storing in ClickHouse)
python start.py --path /path/to/samples -y --dry-run --repo test --index_prefix redb
```

### Scan already-analyzed samples

Run YARA on samples that were previously analyzed (already in `basic_properties`).
Deduplication is handled by the `yara_matches` table — samples already scanned are
automatically excluded before processing begins:

```bash
# Scan all analyzed macho samples with YARA
python start.py --analyzed --magika macho -y --index_prefix redb

# Scan all analyzed PE samples with YARA
python start.py --analyzed --magika pe -y --index_prefix redb

# Scan all analyzed samples (no filetype filter)
python start.py --analyzed -y --index_prefix redb
```

### Partition large YARA runs by date

Combine `--analyzed` with `--range` to partition millions of samples into
manageable batches. Only samples in `basic_properties` AND within the date
range (by `first_seen` in `catalog_samples`) are processed:

```bash
# Scan analyzed PE samples from Feb 2025
python start.py --range 2025-02-01 2025-02-28 --analyzed --magika pebin -y --index_prefix redb

# Scan analyzed PE samples from first week of March 2025
python start.py --range 2025-03-01 2025-03-08 --analyzed --magika pebin -y --index_prefix redb
```

YARA dedup still applies — re-running a range safely skips already-scanned samples.

### Combined Features + YARA

Run feature extraction and YARA scanning together on the same samples:

```bash
# Local files with features + YARA
python start.py --path /path/to/samples --with-yara --repo my_repo --index_prefix redb

# S3 samples with features + YARA
python start.py --s3 --repo bazaar --with-yara --index_prefix redb
```

### Pre-compile Rules

```bash
# Compile and save to default location (yara/compiled_rules.yarac)
python -m redb.extractors.yara --compile

# Compile with custom paths
python -m redb.extractors.yara --compile --rules-path ./my_rules --output ./compiled.yarac
```

### Sync Rules to Database

Before batch scanning, sync rules to ensure all rule metadata is stored:

```bash
# Sync rules to database
python -m redb.extractors.yara --sync-rules

# Sync with custom source collection name
python -m redb.extractors.yara --sync-rules --source-collection yara-forge-core

# Compile and sync in one command
python -m redb.extractors.yara --compile --sync-rules
```

## ClickHouse Table Schema

YARA data uses a **normalized schema** with two tables for efficient storage.

### Matches Table: `yara_matches`

Stores one row per sample-rule match (optimized with binary sha256 and rule_id):

| Column | Type | Description |
|--------|------|-------------|
| sha256 | FixedString(32) | Binary SHA256 (32 bytes, use `hex(sha256)` to display) |
| rule_id | UInt64 | Unique rule identifier (xxHash64 of canonical rule content) |
| rule_name | LowCardinality(String) | YARA rule name (denormalized for convenience) |
| scan_date | DateTime64(3, 'UTC') | Scan timestamp |
| match_strings | Array(String) | Matched string identifiers |

### Rules Table: `yara_rules`

Stores rule metadata once per unique rule (deduplicated by rule_id):

| Column | Type | Description |
|--------|------|-------------|
| rule_id | UInt64 | Unique rule identifier (xxHash64 of canonical rule content) |
| rule_name | String | YARA rule name |
| source_collection | LowCardinality(String) | Source collection (e.g., 'yara-forge-core', 'malpedia') |
| ingested_at | DateTime64(3, 'UTC') | When this rule was ingested |
| rule_text | String | Full rule source code |
| rule_meta | JSON | Rule metadata (author, description, reference, etc.) |
| rule_tags | Array(LowCardinality(String)) | Rule tags |

### Schema Benefits

- **Binary SHA256**: 32 bytes vs 64 bytes (50% storage savings on hash columns)
- **UInt64 rule_id**: Fast joins and lookups via integer key
- **Content-based rule_id**: xxHash64 of canonical rule content (excluding metadata) for deduplication
- **Denormalized rule_name**: Allows queries without joins for common use cases

### Example Queries

```sql
-- Get matches with hex sha256
SELECT
    hex(m.sha256) as sha256,
    m.rule_name,
    m.match_strings
FROM yara_matches m
WHERE m.sha256 = unhex('abc123...')

-- Join with rules for full metadata
SELECT
    hex(m.sha256) as sha256,
    m.rule_name,
    m.match_strings,
    r.rule_meta,
    r.source_collection
FROM yara_matches m
JOIN yara_rules r ON m.rule_id = r.rule_id
WHERE m.sha256 = unhex('abc123...')

-- Find all samples matching a specific rule
SELECT hex(sha256), scan_date
FROM yara_matches
WHERE rule_name = 'APT_Lazarus_Loader'
ORDER BY scan_date DESC
```

## Environment Variables

| Variable | Description | Default |
|----------|-------------|---------|
| `YARA_RULES_PATH` | Override the YARA rules directory | `yara/` |
| `YARA_COMPILED_RULES` | Compiled rules filename | `compiled_rules.yarac` |
| `YARA_SOURCE_COLLECTION` | Default source collection name | `default` |