Oladimeji Farri

56 papers A* 3B 1Misc 3Journal 17Unranked 30
YearRankTypeTitle / Venue / Authors
2025 J jnl
AI Mag.
Rikhiya Ghosh, Hans-Martin von Stockhausen, Martin Schmitt, Vasile George Marica, Sanjeev Kumar Karn, Oladimeji Farri
2025 J jnl
CoRR
Rikhiya Ghosh, Hans-Martin von Stockhausen, Martin Schmitt, Vasile George Marica, Sanjeev Kumar Karn, Oladimeji Farri
2025 A* conf
AAAI
Rikhiya Ghosh, Hans-Martin von Stockhausen, Martin Schmitt, Vasile George Marica, Sanjeev Kumar Karn, Oladimeji Farri
2025 J jnl
CoRR
Manuela Daniela Danu, George Marica, Constantin Suciu, Lucian Mihai Itu, Oladimeji Farri
2024 J jnl
CoRR
Rikhiya Ghosh, Oladimeji Farri, Hans-Martin von Stockhausen, Martin Schmitt, George Marica
2024 conf
ClinicalNLP@NAACL
Cuong Nhat Ha, Shima Asaadi, Sanjeev Kumar Karn, Oladimeji Farri, Tobias Heimann, Thomas A. Runkler
2024 J jnl
CoRR
Cuong Nhat Ha, Shima Asaadi, Sanjeev Kumar Karn, Oladimeji Farri, Tobias Heimann, Thomas A. Runkler
2024 conf
CLEF (Working Notes)
Manuela Daniela Danu, George Marica, Constantin Suciu, Lucian Mihai Itu, Oladimeji Farri
2023 J jnl
CoRR
Ali H. Dhanaliwala, Rikhiya Ghosh, Sanjeev Kumar Karn, Poikavila Ullaskrishnan, Oladimeji Farri, Dorin Comaniciu, Charles E. Kahn
2023 J jnl
CoRR
Manuela Daniela Danu, Vasile George Marica, Sanjeev Kumar Karn, Bogdan Georgescu, Awais Mansoor, Florin C. Ghesu, Lucian Mihai Itu, Constantin Suciu, Sasa Grbic, Oladimeji Farri, Dorin Comaniciu
2023 conf
ACL (industry)
Rikhiya Ghosh, Oladimeji Farri, Sanjeev Kumar Karn, Manuela Daniela Danu, Ramya Vunikili, Larisa Micu
2023 J jnl
CoRR
Rikhiya Ghosh, Sanjeev Kumar Karn, Manuela Daniela Danu, Larisa Micu, Ramya Vunikili, Oladimeji Farri
2023 conf
BioNLP@ACL
Sanjeev Kumar Karn, Rikhiya Ghosh, Kusuma P, Oladimeji Farri
2023 J jnl
CoRR
Sanjeev Kumar Karn, Rikhiya Ghosh, Kusuma P, Oladimeji Farri
2022 conf
ACL (1)
Sanjeev Kumar Karn, Ning Liu, Hinrich Schütze, Oladimeji Farri
2022 J jnl
CoRR
Sanjeev Kumar Karn, Ning Liu, Hinrich Schütze, Oladimeji Farri
2020 J jnl
CoRR
Rajeev Bhatt Ambati, Ahmed Ada Hanifi, Ramya Vunikili, Puneet Sharma, Oladimeji Farri
2020 conf
IberLEF@SEPLN
Ramya Vunikili, Supriya H. N, Vasile George Marica, Oladimeji Farri
2019 ch.
Data Science for Healthcare
Sadid A. Hasan, Oladimeji Farri
2019 J jnl
Artif. Intell. Medicine
Imon Banerjee, Yuan Ling, Matthew C. Chen, Sadid A. Hasan, Curtis P. Langlotz, Nathaniel Moradzadeh, Brian E. Chapman, Timothy Amrhein, David A. Mong, Daniel L. Rubin, Oladimeji Farri, Matthew P. Lungren
2018 conf
NAACL-HLT
Reza Ghaeini, Sadid A. Hasan, Vivek V. Datla, Joey Liu, Kathy Lee, Ashequl Qadir, Yuan Ling, Aaditya Prakash, Xiaoli Z. Fern, Oladimeji Farri
2018 J jnl
CoRR
Reza Ghaeini, Sadid A. Hasan, Vivek V. Datla, Joey Liu, Kathy Lee, Ashequl Qadir, Yuan Ling, Aaditya Prakash, Xiaoli Z. Fern, Oladimeji Farri
2018 conf
CLEF (Working Notes)
Sadid A. Hasan, Yuan Ling, Oladimeji Farri, Joey Liu, Henning Müller, Matthew P. Lungren
2018 conf
CLEF
Bogdan Ionescu, Henning Müller, Mauricio Villegas, Alba Garcia Seco de Herrera, Carsten Eickhoff, Vincent Andrearczyk, Yashin Dicente Cid, Vitali Liauchuk, Vassili Kovalev, Sadid A. Hasan, Yuan Ling, Oladimeji Farri, Joey Liu, Matthew P. Lungren, Duc-Tien Dang-Nguyen, Luca Piras, Michael Riegler, Liting Zhou, Mathias Lux, Cathal Gurrin
2018 ed.
KDH@IJCAI
Kerstin Bach, Razvan C. Bunescu, Oladimeji Farri, Aili Guo, Sadid A. Hasan, Zina M. Ibrahim, Cindy Marling, Jesse Raffa, Jonathan Rubin, Honghan Wu
2018 conf
KDH@IJCAI
Viraj Adduru, Sadid A. Hasan, Joey Liu, Yuan Ling, Vivek V. Datla, Ashequl Qadir, Oladimeji Farri
2017 conf
TREC
Yuan Ling, Sadid A. Hasan, Michele Filannino, Kevin P. Buchan, Kahyun Lee, Joey Liu, William Boag, Di Jin, Özlem Uzuner, Kathy Lee, Vivek V. Datla, Ashequl Qadir, Oladimeji Farri
2017 conf
BIBM
Lucas E. S. Oliveira, Caroline P. Gebeluca, Adalniza Moura Pucca da Silva, Claudia M. C. Moro, Sadid A. Hasan, Oladimeji Farri
2017 A* conf
WWW
Kathy Lee, Ashequl Qadir, Sadid A. Hasan, Vivek V. Datla, Aaditya Prakash, Joey Liu, Oladimeji Farri
2017 conf
CLEF
Sadid A. Hasan, Yuan Ling, Joey Liu, Rithesh Sreenivasan, Shreya Anand, Tilak Raj Arora, Vivek V. Datla, Kathy Lee, Ashequl Qadir, Christine Leon Swisher, Oladimeji Farri
2017 conf
BIBM
Vivek V. Datla, Sadid A. Hasan, Ashequl Qadir, Kathy Lee, Yuan Ling, Joey Liu, Oladimeji Farri
2017 A* conf
AAAI
Aaditya Prakash, Siyuan Zhao, Sadid A. Hasan, Vivek V. Datla, Kathy Lee, Ashequl Qadir, Joey Liu, Oladimeji Farri
2017 conf
MLHC
Yuan Ling, Sadid A. Hasan, Vivek V. Datla, Ashequl Qadir, Kathy Lee, Joey Liu, Oladimeji Farri
2017 conf
TAC
Carson Tao, Kahyun Lee, Michele Filannino, Kevin Buchan, Kathy Lee, Tilak Raj Arora, Joey Liu, Oladimeji Farri, Özlem Uzuner
2017 conf
IJCNLP(1)
Yuan Ling, Sadid A. Hasan, Vivek Varma Datla, Ashequl Qadir, Kathy Lee, Joey Liu, Oladimeji Farri
2017 conf
ICHI
Kathy Lee, Sadid A. Hasan, Oladimeji Farri, Alok N. Choudhary, Ankit Agrawal
2017 conf
TREC
Vivek V. Datla, Tilak Raj Arora, Joey Liu, Viraj Adduru, Sadid A. Hasan, Kathy Lee, Ashequl Qadir, Yuan Ling, Aaditya Prakash, Oladimeji Farri
2017 conf
CLEF (Working Notes)
Sadid A. Hasan, Yuan Ling, Joey Liu, Rithesh Sreenivasan, Shreya Anand, Tilak Raj Arora, Vivek V. Datla, Kathy Lee, Ashequl Qadir, Christine Leon Swisher, Oladimeji Farri
2017 conf
TREC
Kathy Lee, Ashequl Qadir, Yuan Ling, Joey Liu, Sadid A. Hasan, Vivek V. Datla, Aaditya Prakash, Oladimeji Farri
2016 conf
TREC
Kathy Lee, Ashequl Qadir, Vivek V. Datla, Sadid A. Hasan, Joey Liu, Aaditya Prakash, Oladimeji Farri
2016 conf
TREC
Sadid A. Hasan, Siyuan Zhao, Vivek V. Datla, Joey Liu, Kathy Lee, Ashequl Qadir, Aaditya Prakash, Oladimeji Farri
2016 J jnl
CoRR
Aaditya Prakash, Siyuan Zhao, Sadid A. Hasan, Vivek V. Datla, Kathy Lee, Ashequl Qadir, Joey Liu, Oladimeji Farri
2016 Misc conf
AMIA
Gretchen M. Hultman, Jenna L. Marquard, Osadebamwen Ighile, Oladimeji Farri, Elizabeth Lindemann, Elliot G. Arsoniadis, Serguei V. S. Pakhomov, Genevieve B. Melton
2016 conf
ClinicalNLP@COLING 2016
Sadid A. Hasan, Bo Liu, Joey Liu, Ashequl Qadir, Kathy Lee, Vivek V. Datla, Aaditya Prakash, Oladimeji Farri
2016 B conf
COLING
Aaditya Prakash, Sadid A. Hasan, Kathy Lee, Vivek V. Datla, Ashequl Qadir, Joey Liu, Oladimeji Farri
2016 J jnl
CoRR
Aaditya Prakash, Sadid A. Hasan, Kathy Lee, Vivek V. Datla, Ashequl Qadir, Joey Liu, Oladimeji Farri
2016 conf
TREC
Vivek V. Datla, Sadid A. Hasan, Joey Liu, Yassine Benajiba, Kathy Lee, Ashequl Qadir, Aaditya Prakash, Oladimeji Farri
2015 Misc conf
AMIA
Reza Sharifi Sedeh, Xianshu Zhu, Yugang Jia, Joey Liu, Oladimeji Farri, Daniel Elgort
2015 conf
TREC
Sadid A. Hasan, Yuan Ling, Joey Liu, Oladimeji Farri
2015 conf
MedInfo
Sadid A. Hasan, Xianshu Zhu, Joey Liu, Claudia Maria Cabral Moro Barra, Lucas E. S. Oliveira, Oladimeji Farri
2015 conf
TREC
Sadid A. Hasan, Yuan Ling, Joey Liu, Oladimeji Farri
2014 conf
TREC
Sadid A. Hasan, Xianshu Zhu, Yao Dong, Joey Liu, Oladimeji Farri
2013 J jnl
J. Biomed. Informatics
Oladimeji Farri, Karen A. Monsen, Serguei V. S. Pakhomov, David S. Pieczkiewicz, Stuart M. Speedie, Genevieve B. Melton
2012 Misc conf
AMIA
Oladimeji Farri, David S. Pieczkiewicz, Ahmed Rahman, Serguei V. S. Pakhomov, Terrence Adam, Genevieve B. Melton
2012 conf
Nursing Informatics
Karen A. Monsen, Eunice M. Areba, David M. Radosevich, Joan K. Brandt, Amy B. Lytton, Madeleine J. Kerr, Karen E. Johnson, Oladimeji Farri, Karen S. Martin
2012 J jnl
J. Biomed. Informatics
Karen A. Monsen, Claire Neely, Gary Oftedahl, Madeleine J. Kerr, Pam Pietruszewski, Oladimeji Farri
Docker-README.md
← Index Docker-README.md markdown
# REDB Docker Setup

This document describes the Docker containerization for the REDB malware analysis framework.

## Overview

REDB has been containerized as a single unified image that supports both feature extraction and decompilation analysis. The container is stateless, processes files from S3 or local mounts, and exports results to ClickHouse database or via API callbacks.

## Architecture

- **Single Unified Container**: One image handles both feature extraction and decompilation
- **Runtime Tool Installation**: Tools (CAPA, DIE, Binary Ninja) installed at runtime from host snapshots
- **Stateless Processing**: No persistent storage required between runs
- **Multiple Invocation Modes**: Supports `--nomad-job`, `--s3`, `--s3-solo`, and `--path` modes
- **External Dependencies**: Connects to external ClickHouse and S3 services

## Files Structure

```
├── Dockerfile                 # Single unified container definition
├── docker-build.sh            # Build script with Docker Desktop bug workaround
├── docker-push.sh             # Push script to registry
├── test-docker.sh             # Container testing script
├── test-nomad.sh              # Nomad job mode testing
├── .dockerignore              # Build context exclusions
└── scripts/
    └── setup-and-run.sh       # Runtime tool setup entrypoint
```

## Tool Installation Strategy

The container uses a **runtime installation** approach:

1. **Base Image**: Contains Python dependencies and REDB code
2. **Runtime Setup**: `scripts/setup-and-run.sh` configures tools at container start
3. **Host Snapshots**: Binary Ninja installed from `/opt/binaryninja` if available
4. **System Tools**: CAPA and DIE expected at `/usr/bin/capa` and `/usr/bin/nfdc`

## Build and Run

### 1. Build Container

```bash
# Build unified image
./docker-build.sh

# Manual build
docker build --platform linux/amd64 -f Dockerfile -t redb:latest .
```

### 2. Run Modes

#### Nomad Job Mode (Primary)
```bash
# Feature extraction
docker run --rm \
  -e JOB_ID="analysis_001" \
  -e S3_KEY="samples/malware.exe" \
  -e S3_BUCKET="malware-bucket" \
  -e WORKER_TYPE="feature_extraction" \
  -e CALLBACK_URL="https://api.example.com/callbacks" \
  -e ANALYSIS_MODULES="BasicPropertiesExtractor,PEFeaturesExtractor" \
  -e CLICKHOUSE_HOST="clickhouse.example.com" \
  -e S3_ENDPOINT="s3.example.com" \
  -e S3_ACCESS_KEY="your-key" \
  -e S3_SECRET_KEY="your-secret" \
  redb:latest python3 start.py --nomad-job

# Decompilation (same container, different flags)
docker run --rm \
  -e JOB_ID="analysis_002" \
  -e S3_KEY="samples/malware.exe" \
  -e S3_BUCKET="malware-bucket" \
  -e WORKER_TYPE="decompilation" \
  -e CALLBACK_URL="https://api.example.com/callbacks" \
  -e ANALYSIS_MODULES="all" \
  -v /opt/binaryninja:/opt/binaryninja:ro \
  redb:latest python3 start.py --nomad-job --decompile
```

#### S3 Solo Mode
```bash
# Process single sample by S3 key (standard sharded path)
docker run --rm \
  -e S3_BUCKET="samples-bucket" \
  -e CLICKHOUSE_HOST="clickhouse.example.com" \
  -e S3_ENDPOINT="s3.example.com" \
  -e INDEX_PREFIX="redb" \
  -e REPO="test-analysis" \
  redb:latest python3 start.py --s3-solo "09/f7/09f7d02a3c2382199458c98a62b045145ee54ab6aba86166aecf3d10c3c1444c.zip"

# Process private sample (with prepath)
docker run --rm \
  -e S3_BUCKET="samples-bucket" \
  -e CLICKHOUSE_HOST="clickhouse.example.com" \
  -e S3_ENDPOINT="s3.example.com" \
  -e INDEX_PREFIX="redb" \
  -e REPO="test-analysis" \
  redb:latest python3 start.py --s3-solo "private/ab/cd/abcd1234567890abcdef1234567890abcdef1234567890abcdef123456.zip"
```

#### Local Files Mode
```bash
# Mount local samples
docker run --rm \
  -v /path/to/samples:/samples:ro \
  -v ./logs:/app/logs \
  -e CLICKHOUSE_HOST="clickhouse.example.com" \
  redb:latest python3 start.py --path /samples --repo local_test --index_prefix redb
```

## Environment Variables

### Required for Nomad Job Mode
- `JOB_ID` - Unique job identifier
- `S3_KEY` - S3 object key for sample
- `S3_BUCKET` - S3 bucket name
- `WORKER_TYPE` - "feature_extraction" or "decompilation"
- `CALLBACK_URL` - API endpoint for results
- `ANALYSIS_MODULES` - Comma-separated extractor list or "all"

### Database Configuration
- `CLICKHOUSE_HOST` - ClickHouse server hostname
- `CLICKHOUSE_PORT` - Port (default: 8123)
- `CLICKHOUSE_USER` - Database user (default: default)
- `CLICKHOUSE_PASSWORD` - Database password
- `CLICKHOUSE_DATABASE` - Database name (default: default)

### S3 Configuration
- `S3_ENDPOINT` - S3 endpoint URL
- `S3_ACCESS_KEY` - S3 access key
- `S3_SECRET_KEY` - S3 secret key
- `S3_SECURE` - "true" or "false" for HTTPS

### Processing Configuration
- `INDEX_PREFIX` - Database table prefix (default: redb)
- `REPO` - Repository identifier for this analysis batch
- `BATCH_SIZE` - Processing batch size (default: 10)
- `REDB_TIMEOUT` - Analysis timeout in seconds (default: 300)

### Tool Timeouts
- `CAPA_TIMEOUT` - CAPA analysis timeout (default: 300)
- `DIE_TIMEOUT` - DIE analysis timeout (default: 180)
- `BINJA_TIMEOUT` - Binary Ninja timeout (default: 1200)
- `DECOMPILE_EXTRACTOR_TIMEOUT` - Decompilation timeout (default: 2580)

## Binary Ninja Setup

For decompilation capabilities, mount Binary Ninja from host:

```bash
# Mount Binary Ninja installation
-v /opt/binaryninja:/opt/binaryninja:ro

# Mount license file
-v /path/to/license.dat:/home/analyzer/.binaryninja/license.dat:ro
```

The container will automatically detect and configure Binary Ninja at runtime.

## Registry Deployment

### Push to Registry
```bash
# Tag and push
./docker-push.sh

# Or manually
docker tag redb:latest your-registry/redb:latest
docker push your-registry/redb:latest
```

### Pull and Run
```bash
docker pull your-registry/redb:latest
docker run your-registry/redb:latest python3 start.py --nomad-job
```

## Testing

### Container Functionality Test
```bash
# Test with S3 key (standard sharded path)
./test-docker.sh "09/f7/09f7d02a3c2382199458c98a62b045145ee54ab6aba86166aecf3d10c3c1444c.zip"

# Test with private sample S3 key
./test-docker.sh "private/ab/cd/abcd1234567890abcdef1234567890abcdef1234567890abcdef123456.zip"
```

### Nomad Job Architecture Test
```bash
# Test Nomad job mode
./test-nomad.sh
```

## Development

### Interactive Container
```bash
# Debug container interactively
docker run -it --entrypoint /bin/bash redb:latest

# Check tool availability
docker run --rm redb:latest which python3
docker run --rm redb:latest ls -la /usr/bin/capa
```

### Build Troubleshooting

The build script includes workarounds for Docker Desktop bugs:

```bash
# If build hangs at "exporting to image", press Ctrl+C
# The image will still be created and tagged automatically
./docker-build.sh
```

### Container Logs
```bash
# View logs from mounted directory
docker run -v ./logs:/app/logs redb:latest python3 start.py --path /samples
tail -f logs/*.txt
```

## Production Notes

### Resource Requirements
- **Memory**: 2-4GB recommended (8GB for decompilation)
- **CPU**: 2+ cores recommended
- **Disk**: Minimal (stateless container)
- **Network**: Access to ClickHouse and S3 services

### Security
- Container runs as non-root user `analyzer` (UID 1000)
- Sample files should be mounted read-only
- No persistent state between container runs
- Isolated processing environment for malware analysis

### Deployment Architecture

This container is designed for:
- **Nomad job dispatch**: Single-use containers processing one sample each
- **Kubernetes jobs**: Batch processing with external orchestration
- **CI/CD pipelines**: Automated analysis in build systems
- **Development**: Local testing and debugging

The unified container approach means the same image handles both feature extraction and decompilation - the difference is only in the command-line flags used when starting the container.