Karen Eilbeck

37 papers A 2C 1Misc 7Journal 18Unranked 9
YearRankTypeTitle / Venue / Authors
2026 J jnl
J. Am. Medical Informatics Assoc.
Guilherme Del Fiol, Emerson P. Borsato, Richard L. Bradshaw, Jiantao Bian, Alana Woodbury, Courtney Gauchel, Karen Eilbeck, Whitney Maxwell, Kelsey Ellis, Anne C. Madeo, Chelsey R. Schlechter, Polina V. Kukhareva, Caitlin G. Allen, Michael Kean, Elena B. Elkin, Ravi Sharaf, Muhammad D. Ahsan, Melissa Frey, Lauren Davis-Rivera, Wendy Kohlmann, David W. Wetter, Kimberly A. Kaphingst, Kensaku Kawamoto
2025 conf
MedInfo
Evan Christensen, Courtney Gauchel, Lourdes Valdez, Chinmayee Rayguru, Kseniia Sholokhova, Umashankar Upadhyay, Sari Rahmawati Kusuma Dewi, Marco Aigner, Monica Phariss, Minke C. Holleboom, Cynthia Groenevelt, Karen Eilbeck, Shabbir Syed Abdul
2024 J jnl
J. Am. Medical Informatics Assoc.
Robert F. Lario, Richard Soley, Stephen White, John Butler, Guilherme Del Fiol, Karen Eilbeck, Stanley M. Huff, Kensaku Kawamoto
2023 J jnl
J. Biomed. Informatics
Robert F. Lario, Kensaku Kawamoto, Davide Sottara, Karen Eilbeck, Stanley M. Huff, Guilherme Del Fiol, Richard Soley, Blackford Middleton
2023 conf
MIE
Thomas Engelsma, Carolin Anders, Susan J. Oudbier, Karen Eilbeck, Petra Knaup, Linda W. Peute, Matthias Ganzinger
2022 Misc conf
AMIA
Michael T. Watkins, Wendy Kohlmann, Therese Berry, Neetha Sama, Cathryn Koptiuch, Shawn Rynearson, Karen Eilbeck
2020 J jnl
Bioinform.
Thomas Desvignes, Phillipe Loher, Karen Eilbeck, Jeffery Ma, Gianvito Urgese, Bastian Fromm, Jason Sydes, Ernesto Aparicio-Puerta, Víctor Barrera, Roderic Espín, Florian Thibord, Xavier Bofill-De Ros, Eric Londin, Aristeidis G. Telonis, Elisa Ficarra, Marc R. Friedländer, John H. Postlethwait, Isidore Rigoutsos, Michael Hackenberg, Ioannis S. Vlachos, Marc K. Halushka, Lorena Pantano
2020 Misc conf
AMIA
Robert F. Lario, Steve Hasely, Stephen White, Karen Eilbeck, Richard Soley, Stan Huff, Kensaku Kawamoto
2019 Misc conf
AMIA
Amber Kiser, Devin Horton, Karen Eilbeck, Samir E. AbdelRahman
2019 Misc conf
AMIA
Michael T. Watkins, Shawn Rynearson, Alex Henrie, Karen Eilbeck
2018 J jnl
BMC Bioinform.
Steven Flygare, Edgar Javier Hernandez, Lon Phan, Barry Moore, Man Li, Anthony P. Fejes, Hao Hu, Karen Eilbeck, Chad D. Huff, Lynn Jorde, Martin G. Reese, Mark Yandell
2017 conf
ICCABS
Jingshan Huang, Dejing Dou, Ming Tan, Glen M. Borchert, Karen Eilbeck, Alan Ruttenberg, Ping Yang
2016 J jnl
J. Biomed. Semant.
Jingshan Huang, Fernando Gutierrez, Harrison J. Strachan, Dejing Dou, Weili Huang, Barry Smith, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Yu Lin, Bin Wu, Nisansa de Silva, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan, Alan Ruttenberg
2016 J jnl
J. Biomed. Semant.
Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan
2016 J jnl
Int. J. Data Min. Bioinform.
Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Nisansa de Silva, Mohan Vamsi Kasukurthi, Vikash Kumar Jha, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan
2016 J jnl
J. Biomed. Informatics
Ayesha Aziz, Kensaku Kawamoto, Karen Eilbeck, Marc S. Williams, Robert R. Freimuth, Mark A. Hoffman, Luke V. Rasmussen, Casey Lynnette Overby, Brian H. Shirts, James M. Hoffman, Brandon M. Welch
2015 conf
BIBM
Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg, Barry Smith, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Yongqun He, Shaojie Zhang, Xiaowei Wang, He Zhang, Zixing Liu, Ming Tan
2015 conf
BIBM
Jingshan Huang, Fernando Gutierrez, Dejing Dou, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Barry Smith, Yu Lin, Xiaowei Wang, Zixing Liu, Ming Tan, Alan Ruttenberg
2015 J jnl
J. Am. Medical Informatics Assoc.
Jeffrey Duncan, Scott P. Narus, Stephen Clyde, Karen Eilbeck, Sidney N. Thornton, Catherine J. Staes
2015 J jnl
J. Biomed. Semant.
Fiona Cunningham, Barry Moore, Nicole Ruiz-Schultz, Graham R. S. Ritchie, Karen Eilbeck
2014 Misc conf
AMIA
Brandon M. Welch, Salvador Loya, Karen Eilbeck, Kensaku Kawamoto
2014 Misc conf
AMIA
Karen Eilbeck, Julie Lipstein, Sunanda R. McGarvey, Catherine J. Staes
2014 J jnl
J. Biomed. Informatics
Brandon M. Welch, Karen Eilbeck, Guilherme Del Fiol, Laurence J. Meyer, Kensaku Kawamoto
2013 conf
ICBO
Karen Eilbeck, Jason R. Jacobs, Sunanda R. McGarvey, Cynthia Vinion, Catherine J. Staes
2013 conf
HICSS
Karen Eilbeck, Jason R. Jacobs, Catherine J. Staes
2013 Misc conf
AMIA
Jeffrey Duncan, Karen Eilbeck, Catherine J. Staes, Scott P. Narus, Stephen Clyde
2012 conf
ICBO
Michael Bada, Karen Eilbeck
2012 conf
AIMM
Barry Moore, Shawn Rynearson, Fiona Cunningham, Graham R. S. Ritchie, Karen Eilbeck
2011 J jnl
J. Biomed. Informatics
Christopher J. Mungall, Colin R. Batchelor, Karen Eilbeck
2011 J jnl
Appl. Ontology
Robert Hoehndorf, Colin R. Batchelor, Thomas Bittner, Michel Dumontier, Karen Eilbeck, Rob Knight, Chris Mungall, Jane S. Richardson, Jesse Stombaugh, Eric Westhof, Craig L. Zirbel, Neocles Leontis
2010 J jnl
Nucleic Acids Res.
Barry Moore, Guozhen Fan, Karen Eilbeck
2009 J jnl
BMC Bioinform.
Karen Eilbeck, Barry Moore, Carson Holt, Mark Yandell
2008 J jnl
Bioinform.
Gabrielle A. Reeves, Karen Eilbeck, Michele Magrane, Claire O'Donovan, Luisa Montecchi-Palazzi, Midori A. Harris, Sandra E. Orchard, Rafael C. Jiménez, Andreas Prlic, Tim J. P. Hubbard, Henning Hermjakob, Janet M. Thornton
2001 C conf
BIBE
Mike Cornell, Norman W. Paton, Shengli Wu, Carole A. Goble, Crispin J. Miller, Paul Kirby, Karen Eilbeck, Andy Brass, Andrew Hayes, Stephen G. Oliver
2000 J jnl
Bioinform.
Norman W. Paton, Shakeel A. Khan, Andrew Hayes, Fouzia Moussouni, Andy Brass, Karen Eilbeck, Carole A. Goble, Simon J. Hubbard, Stephen G. Oliver
1999 A conf
ISMB
Karen Eilbeck, Andy Brass, Norman W. Paton, Charlie Hodgman
1999 A conf
GD
Wojciech Basalaj, Karen Eilbeck
docs/CODE_ANALYSIS_APPROACH.md
← Index docs/CODE_ANALYSIS_APPROACH.md markdown
# Code Analysis Approach

This document explains the code analysis methodologies used in the REDB malware analysis framework.

## Disassembly Normalization

The framework implements a sophisticated three-level normalization strategy for disassembled code that provides different levels of abstraction for similarity detection and feature extraction.

### Overall Normalization Strategy

The framework implements a **hierarchical abstraction approach** where each instruction is normalized at three different levels simultaneously:

1. **Level 0 (fully_normalized)**: Maximum abstraction - reduces operands to broad categories
2. **Level 1 (api_normalized)**: Medium abstraction - preserves semantic meaning while normalizing details  
3. **Level 2 (category_normalized)**: Minimum abstraction - maintains architectural specificity

This multi-level approach allows analysts to perform similarity analysis at different granularities depending on their specific detection goals.

### Implementation Architecture

The normalization process follows this workflow:

1. **Token Parsing**: Each instruction is parsed from Binary Ninja's instruction tokens to extract the mnemonic and operands
2. **Multi-Level Processing**: Each operand is processed through all three normalization functions
3. **Instruction Reconstruction**: Normalized instructions are rebuilt with the mnemonic plus normalized operands
4. **Control Flow Tagging**: Control flow instructions get a `<TARGET>` suffix for easier pattern matching

### Level 0: Fully Normalized (Maximum Abstraction)

**Purpose**: Creates the most abstract representation for broad pattern detection across different malware families.

**Transformations**:
- **Registers**: All registers normalized to semantic categories via `normalize_register()`:
  - General purpose registers (EAX, EBX, R8, etc.) → `GPR`
  - Stack/Base pointers (ESP, EBP, RSP) → `PTR` 
  - SIMD registers (XMM0, XMM1) → `XMM`
  - FPU registers (ST0, ST1) → `FPU`
- **Memory Operations**: All memory references → `MEM`
- **Constants**: All immediate values → `CONST`  
- **Data References**: All symbols/data references → `DATA_REF`

**Example**:
```
mov eax, [ebp+8]     → MOV GPR MEM
call CreateFileW     → CALL DATA_REF <TARGET>
add ecx, 0x10        → ADD GPR CONST
```

### Level 1: API Normalized (Medium Abstraction)

**Purpose**: Preserves semantic distinctions while normalizing architectural details. Focuses on behavioral patterns and API usage.

**Transformations**:
- **Registers**: Categorized by functional role:
  - Data registers → `GPR_DATA`
  - Index registers (ESI, EDI) → `GPR_INDEX`  
  - Stack registers (ESP, EBP) → `GPR_STACK`
  - SIMD registers → `XMM_REG`
- **Memory Operations**: Classified by access pattern:
  - Stack access → `MEM_STACK`
  - String operations → `MEM_STRING` 
  - General access → `MEM_GENERAL`
- **Constants**: Categorized by range:
  - Small constants (-16 to 16) → `CONST_{value}`
  - Large constants → `CONST_LARGE`
- **API Calls**: Resolved to specific API names:
  - `CreateFileW` → `API_CreateFileW`
  - Other symbols → `DATA_SYM`

**Example**:
```
mov eax, [ebp+8]     → MOV GPR_DATA MEM_STACK
call CreateFileW     → CALL API_CreateFileW <TARGET>
add ecx, 0x10        → ADD GPR_DATA CONST_LARGE
```

### Level 2: Category Normalized (Minimum Abstraction)

**Purpose**: Maintains architectural specificity while normalizing specific values. Best for detecting variants with similar implementation details.

**Transformations**:
- **Registers**: Architecture-specific categories:
  - 64-bit registers → `REG_64`, with special cases for `REG_64_SP`, `REG_64_BP`
  - 32-bit registers → `REG_32`
  - 16/8-bit registers → `REG_16_8`
- **Memory Operations**: Detailed addressing mode classification:
  - Complex addressing → `MEM_SCALED_INDEX`
  - Base + offset → `MEM_BASE_OFFSET`
  - Direct addressing → `MEM_DIRECT`
- **Constants**: Type-specific classification:
  - Hexadecimal → `CONST_HEX`
  - Decimal → `CONST_DEC`
- **API Calls**: Categorized by functional group:
  - File operations → `API_FILE_OP`
  - Memory operations → `API_MEMORY_OP`
  - Network operations → `API_NETWORK_OP`

**Example**:
```
mov eax, [ebp+8]     → MOV REG_32 MEM_BASE_OFFSET
call CreateFileW     → CALL API_FILE_OP <TARGET>
add ecx, 0x10        → ADD REG_32 CONST_HEX
```

### Key Features and Benefits

#### 1. Multi-Granularity Similarity Detection
- **Level 0**: Detects broad behavioral patterns across malware families
- **Level 1**: Identifies API usage patterns and semantic similarities
- **Level 2**: Finds variants with similar implementation approaches

#### 2. Robust Pattern Matching
- Control flow instructions tagged with `<TARGET>` for easier CFG analysis
- Handles edge cases with fallback mechanisms
- Consistent uppercase normalization prevents case sensitivity issues

#### 3. API-Aware Analysis
The framework includes sophisticated API recognition through the `ApiCategory` enum and resolution methods:
- **File Operations**: CreateFile, ReadFile, WriteFile, etc.
- **Memory Operations**: VirtualAlloc, HeapAlloc, VirtualProtect, etc.  
- **Registry Operations**: RegOpenKey, RegSetValue, etc.
- **Network Operations**: WSASocket, send, recv, etc.
- **Process Operations**: CreateProcess, OpenProcess, etc.

#### 4. Scalable Feature Extraction
Each level produces different hash values for the same function:
- `fully_normalized_disassembly_hash`
- `api_normalized_disassembly_hash`  
- `category_normalized_disassembly_hash`

This enables efficient similarity searches at different abstraction levels in the ClickHouse database.

### Practical Applications for Malware Analysis

#### Threat Hunting Scenarios:

1. **Family Detection** (Level 0): Find samples using similar algorithmic approaches regardless of specific implementation
2. **Variant Analysis** (Level 1): Identify samples with similar API usage patterns and behavioral semantics
3. **Code Reuse Detection** (Level 2): Discover samples sharing specific implementation techniques or code fragments

#### Similarity Metrics Integration:
- Each normalization level can be used with different fuzzy hashing algorithms (ssdeep, TLSH, etc.)
- Level 0 works well with structural similarity metrics
- Level 1 optimal for behavioral similarity analysis  
- Level 2 suitable for implementation-specific pattern matching

This three-tiered approach provides malware analysts with flexible tools for detecting similarities across the threat landscape while maintaining the precision needed for detailed variant analysis.



---

*More code analysis approaches will be documented in additional sections as they are implemented.*