Halil Kilicoglu

96 papers A 1B 2Misc 19Journal 54Unranked 20
YearRankTypeTitle / Venue / Authors
2026 J jnl
CoRR
Neil R. Smalheiser, Joe D. Menke, Arthur W. Holt, Halil Kilicoglu, Jodi Schneider
2025 J jnl
J. Biomed. Informatics
Mingchen Li, Halil Kilicoglu, Hua Xu, Rui Zhang
2025 J jnl
J. Am. Medical Informatics Assoc.
Gibong Hong, Veronica Hindle, Nadine M. Veasley, Hannah D. Holscher, Halil Kilicoglu
2025 J jnl
CoRR
Peter Eckmann, Adrian Barnett, Alexandra Bannach-Brown, Elisa Pilar Bascunan Atria, Guillaume Cabanac, Louise Delwen Owen Franzen, Malgorzata Anna Gazda, Kaitlyn Hair, James Howison, Halil Kilicoglu, Cyril Labbé, Sarah McCann, Vladislav Nachev, Martijn Roelandse, Maia Salholz-Hillel, Robert Schulz, Gerben ter Riet, Colby Vorland, Anita E. Bandrowski, Tracey L. Weissgerber
2024 J jnl
Bioinform.
Maria Janina Sarol, Shufan Ming, Shruthan Radhakrishna, Jodi Schneider, Halil Kilicoglu
2024 J jnl
J. Biomed. Informatics
Mengfei Lan, Mandy Cheng, Linh K. Hoang, Gerben ter Riet, Halil Kilicoglu
2024 J jnl
CoRR
Mingchen Li, Halil Kilicoglu, Hua Xu, Rui Zhang
2024 J jnl
J. Biomed. Semant.
Sarah Mullin, Robert A. McDougal, Kei-Hoi Cheung, Halil Kilicoglu, Amanda Beck, Caroline J. Zeiss
2024 J jnl
J. Am. Medical Informatics Assoc.
Huixue Zhou, Robin Austin, Sheng-Chieh Lu, Greg M. Silverman, Yuqi Zhou, Halil Kilicoglu, Hua Xu, Rui Zhang
2024 J jnl
CoRR
Gibong Hong, Veronica Hindle, Nadine M. Veasley, Hannah D. Holscher, Halil Kilicoglu
2024 J jnl
J. Biomed. Informatics
Shufan Ming, Rui Zhang, Halil Kilicoglu
2024 J jnl
Database J. Biol. Databases Curation
M. Janina Sarol, Gibong Hong, Evan Guerra, Halil Kilicoglu
2024 conf
EMNLP (Findings)
Mengfei Lan, Lecheng Zheng, Shufan Ming, Halil Kilicoglu
2024 J jnl
CoRR
Mengfei Lan, Lecheng Zheng, Shufan Ming, Halil Kilicoglu
2024 J jnl
J. Biomed. Informatics
Halil Kilicoglu, Faezeh Ensan, Bridget T. McInnes, Lucy Lu Wang
2024 conf
BioNLP@ACL
Zhiwen You, Shruthan Radhakrishna, Shufan Ming, Halil Kilicoglu
2023 J jnl
CoRR
Yiren Liu, Halil Kilicoglu
2023 J jnl
J. Biomed. Informatics
Sanya Bathla Taneja, Tiffany J. Callahan, Mary F. Paine, Sandra L. Kane-Gill, Halil Kilicoglu, Marcin P. Joachimiak, Richard D. Boyce
2023 J jnl
CoRR
Sullam Jeoung, Jana Diesner, Halil Kilicoglu
2023 conf
ICHI
Yongkang Xiao, Yu Hou, Huixue Zhou, Gayo Diallo, Marcelo Fiszman, Julian Wolfson, Halil Kilicoglu, You Chen, Hua Xu, William G. Mantyh, Rui Zhang
2022 Misc conf
AMIA
Huixue Zhou, Robin Austin, Halil Kilicoglu, Sheng-Chieh Lu, Rui Zhang
2022 J jnl
J. Biomed. Informatics
Halil Kilicoglu, Faezeh Ensan, Bridget T. McInnes, Lucy Lu Wang
2022 J jnl
CoRR
Sanya Bathla Taneja, Tiffany J. Callahan, Mary F. Paine, Sandra L. Kane-Gill, Halil Kilicoglu, Marcin P. Joachimiak, Richard D. Boyce
2022 J jnl
J. Biomed. Informatics
Dalton Schutte, Jake Vasilakes, Anusha Bompelli, Yuqi Zhou, Marcelo Fiszman, Hua Xu, Halil Kilicoglu, Jeffrey R. Bishop, Terrence Adam, Rui Zhang
2022 Misc conf
AMIA
Linh K. Hoang, Yingjun Guan, Halil Kilicoglu
2022 conf
WWW (Companion Volume)
Faezeh Ensan, Halil Kilicoglu, Bridget T. McInnes, Lucy Lu Wang
2021 J jnl
ACM Trans. Comput. Heal.
Tung Tran, Ramakanth Kavuluru, Halil Kilicoglu
2021 J jnl
CoRR
Dalton Schutte, Jake Vasilakes, Anusha Bompelli, Yuqi Zhou, Marcelo Fiszman, Hua Xu, Halil Kilicoglu, Jeffrey R. Bishop, Terrence Adam, Rui Zhang
2021 J jnl
J. Biomed. Informatics
Rui Zhang, Dimitar Hristovski, Dalton Schutte, Andrej Kastrin, Marcelo Fiszman, Halil Kilicoglu
2021 J jnl
J. Biomed. Informatics
Halil Kilicoglu, Graciela Rosemblat, Linh K. Hoang, Sahil Wadhwa, Zeshan Peng, Mario Malicki, Jodi Schneider, Gerben ter Riet
2021 conf
SemEval@ACL/IJCNLP
Haoyang Liu, Maria Janina Sarol, Halil Kilicoglu
2021 J jnl
CoRR
Haoyang Liu, Maria Janina Sarol, Halil Kilicoglu
2020 J jnl
BMC Bioinform.
Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, Dongwook Shin
2020 J jnl
CoRR
Rui Zhang, Dimitar Hristovski, Dalton Schutte, Andrej Kastrin, Marcelo Fiszman, Halil Kilicoglu
2020 Misc conf
AMIA
Halil Kilicoglu, Linh K. Hoang, Sahil Wadhwa
2019 J jnl
CoRR
Tung Tran, Ramakanth Kavuluru, Halil Kilicoglu
2019 J jnl
CoRR
Tung Tran, Ramakanth Kavuluru, Halil Kilicoglu
2019 J jnl
J. Biomed. Informatics
Halil Kilicoglu, Zeshan Peng, Shabnam Tafreshi, Tung Tran, Graciela Rosemblat, Jodi Schneider
2019 J jnl
Int. J. Medical Informatics
Lou Ann Scarton, Liqin Wang, Halil Kilicoglu, Margaret Jahries, Guilherme Del Fiol
2019 Misc conf
AMIA
Mehmet G. Bakal, Halil Kilicoglu, Ramakanth Kavuluru
2019 Misc conf
AMIA
Dimitar Hristovski, Andrej Kastrin, Halil Kilicoglu
2019 J jnl
J. Biomed. Informatics
Graciela Rosemblat, Marcelo Fiszman, Dongwook Shin, Halil Kilicoglu
2018 conf
TAC
Tung Tran, Ramakanth Kavuluru, Halil Kilicoglu
2018 J jnl
J. Am. Medical Informatics Assoc.
Halil Kilicoglu, Graciela Rosemblat, Mario Malicki, Gerben ter Riet
2018 J jnl
Briefings Bioinform.
Halil Kilicoglu
2018 Misc conf
AMIA
Graciela Rosemblat, Dongwook Shin, Halil Kilicoglu
2018 J jnl
J. Biomed. Semant.
Thomas C. Rindflesch, Catherine Blake, Michael J. Cairelli, Marcelo Fiszman, Caroline J. Zeiss, Halil Kilicoglu
2018 Misc conf
AMIA
Dongwook Shin, Halil Kilicoglu
2018 Misc conf
AMIA
Halil Kilicoglu, Aurélie Névéol, Timothy Clark, Hua Xu, Neil R. Smalheiser
2018 J jnl
BMC Bioinform.
Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Sonya E. Shooshan, Laritza Rodriguez, Kate Masterton, Dina Demner-Fushman
2017 J jnl
J. Assoc. Inf. Sci. Technol.
Ariel Deardorff, Kate Masterton, Kirk Roberts, Halil Kilicoglu, Dina Demner-Fushman
2017 conf
ACL (1)
Yassine Mrabet, Halil Kilicoglu, Dina Demner-Fushman
2016 conf
WebNLG
Yassine Mrabet, Pavlos Vougiouklis, Halil Kilicoglu, Claire Gardent, Dina Demner-Fushman, Jonathon S. Hare, Elena Simperl
2016 B conf
LREC
Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Kirk Roberts, Laritza Rodriguez, Sonya E. Shooshan, Dina Demner-Fushman
2016 Misc conf
AMIA
Yassine Mrabet, Halil Kilicoglu, Kirk Roberts, Dina Demner-Fushman
2016 conf
BioNLP@ACL
Halil Kilicoglu
2016 J jnl
BMC Bioinform.
Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, Thomas C. Rindflesch
2016 A conf
ECAI
Yassine Mrabet, Halil Kilicoglu, Dina Demner-Fushman
2015 Misc conf
AMIA
Halil Kilicoglu, Marcelo Fiszman, Kirk Roberts, Dina Demner-Fushman
2015 J jnl
J. Biomed. Informatics
Kirk Roberts, Sonya E. Shooshan, Laritza Rodriguez, Swapna Abhyankar, Halil Kilicoglu, Dina Demner-Fushman
2014 B conf
LREC
Kirk Roberts, Kate Masterton, Marcelo Fiszman, Halil Kilicoglu, Dina Demner-Fushman
2014 J jnl
PLoS Comput. Biol.
Guocai Chen, Michael J. Cairelli, Halil Kilicoglu, Dongwook Shin, Thomas C. Rindflesch
2014 Misc conf
AMIA
Kirk Roberts, Halil Kilicoglu, Marcelo Fiszman, Dina Demner-Fushman
2014 conf
BioNLP@ACL
Halil Kilicoglu, Dina Demner-Fushman
2014 conf
BioNLP@ACL
Kirk Roberts, Halil Kilicoglu, Marcelo Fiszman, Dina Demner-Fushman
2014 J jnl
J. Biomed. Informatics
Rui Zhang, Michael J. Cairelli, Marcelo Fiszman, Graciela Rosemblat, Halil Kilicoglu, Thomas C. Rindflesch, Serguei V. S. Pakhomov, Genevieve B. Melton
2013 J jnl
J. Biomed. Informatics
Graciela Rosemblat, Dongwook Shin, Halil Kilicoglu, Charles Sneiderman, Thomas C. Rindflesch
2013 Misc conf
AMIA
Rashmi Mishra, Guilherme Del Fiol, Halil Kilicoglu, Siddhartha Jonnalagadda, Marcelo Fiszman
2013 conf
BioNLP@ACL
Halil Kilicoglu, Marcelo Fiszman, Dina Demner-Fushman
2012 J jnl
BMC Bioinform.
Halil Kilicoglu, Sabine Bergler
2012 conf
CLEF (Online Working Notes/Labs/Workshop)
Sabine Rosenberg, Halil Kilicoglu, Sabine Bergler
2012 J jnl
Bioinform.
Halil Kilicoglu, Dongwook Shin, Marcelo Fiszman, Graciela Rosemblat, Thomas C. Rindflesch
2011 conf
BioNLP@ACL (Shared Task)
Halil Kilicoglu, Sabine Bergler
2011 J jnl
BMC Bioinform.
Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, Thomas C. Rindflesch
2011 J jnl
Comput. Intell.
Halil Kilicoglu, Sabine Bergler
2011 J jnl
Inf. Serv. Use
Thomas C. Rindflesch, Halil Kilicoglu, Marcelo Fiszman, Graciela Rosemblat, Dongwook Shin
2011 J jnl
BMC Bioinform.
Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E. Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana L. Neves, Alberto D. Pascual-Montano, Arzucan Özgür, Dragomir R. Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
2010 conf
CoNLL Shared Task
Halil Kilicoglu, Sabine Bergler
2010 J jnl
J. Assoc. Inf. Sci. Technol.
Alla Keselman, Graciela Rosemblat, Halil Kilicoglu, Marcelo Fiszman, Honglan Jin, Dongwook Shin, Thomas C. Rindflesch
2010 conf
BioNLP@ACL
Halil Kilicoglu, Marcelo Fiszman, Graciela Rosemblat, Sean Marimpietri, Thomas C. Rindflesch
2010 conf
MedInfo
Marcelo Fiszman, Bruce E. Bray, Dongwook Shin, Halil Kilicoglu, Glen C. Bennett, Olivier Bodenreider, Thomas C. Rindflesch
2009 J jnl
J. Biomed. Informatics
Marcelo Fiszman, Dina Demner-Fushman, Halil Kilicoglu, Thomas C. Rindflesch
2009 conf
BioNLP@HLT-NAACL (Shared Task)
Halil Kilicoglu, Sabine Bergler
2009 J jnl
J. Am. Medical Informatics Assoc.
Halil Kilicoglu, Dina Demner-Fushman, Thomas C. Rindflesch, Nancy L. Wilczynski, R. Brian Haynes
2008 conf
BioNLP
Halil Kilicoglu, Sabine Bergler
2008 J jnl
BMC Bioinform.
Halil Kilicoglu, Sabine Bergler
2008 Misc conf
AMIA
Halil Kilicoglu, Dina Demner-Fushman, Thomas C. Rindflesch, Nancy L. Wilczynski, R. Brian Haynes
2007 Misc conf
AMIA
Caroline B. Ahlers, Dimitar Hristovski, Halil Kilicoglu, Thomas C. Rindflesch
2006 J jnl
BMC Bioinform.
Marco Masseroli, Halil Kilicoglu, François-Michel Lang, Thomas C. Rindflesch
2006 Misc conf
AMIA
Marcelo Fiszman, Thomas C. Rindflesch, Halil Kilicoglu
2006 J jnl
J. Assoc. Inf. Sci. Technol.
Susanne M. Humphrey, Willie J. Rogers, Halil Kilicoglu, Dina Demner-Fushman, Thomas C. Rindflesch
2005 Misc conf
AMIA
Thomas C. Rindflesch, Serguei Pakhomov, Marcelo Fiszman, Halil Kilicoglu, Vincent R. Sánchez
2004 conf
MedInfo
Marcelo Fiszman, Thomas C. Rindflesch, Halil Kilicoglu
2003 Misc conf
AMIA
Marcelo Fiszman, Thomas C. Rindflesch, Halil Kilicoglu
2003 Misc conf
AMIA
Marcelo Fiszman, Thomas C. Rindflesch, Halil Kilicoglu
2003 Misc conf
AMIA
Thomas C. Rindflesch, Bisharah Libbus, Dimitar Hristovski, Alan R. Aronson, Halil Kilicoglu
sql/redb_js_tables.sql
← Index sql/redb_js_tables.sql sql
-- JavaScript malware analysis tables
-- Engine: ReplacingMergeTree(analysis_date) — latest analysis wins on re-processing
--
-- File order:
--   1. redb_js_features
--   2. redb_js_suspicious_apis
--   3. redb_js_deobfuscation
--   4. code_text_content              (generic text-content table; JS today,
--                                      PowerShell / Python / email / extracted
--                                      PDF / Office text in the future)
--   5. redb_iocs source_type ALTER    (extends Enum8 with text_raw/text_normalized
--                                      so JS — and any future text-based pipeline —
--                                      can distinguish IOCs found in the raw vs
--                                      normalised surface)
--   6. redb_iocs ioc_type ALTER       (adds registry_key=42 so HKLM/HKCU/HKEY_*
--                                      keys are extracted alongside file paths)
--
-- Decoded strings from JS still go into the shared code_binja_strings_raw
-- table (same schema used by DecompileBinja and DecompileAPK). JS
-- string_encoding values: hex, unicode, charcode, base64, concat. Plain long
-- literals are not extracted here — they're already in code_text_content and
-- scraped by the IOC pipeline over text_raw/text_normalized.
-- string_offset is the line number in the source file.
--
-- redb_js_features.script_type values (file format / container, first match):
--   jse, wsf, hta, embedded_html, wscript, esm, node_module, standalone, unknown
-- redb_js_features.detected_environment values (runtime by API surface, first
-- match):
--   wscript, browser_extension, service_worker, deno, node, browser, unknown

-- 1. Core features & obfuscation metrics (1 row per sample)
CREATE TABLE IF NOT EXISTS redb_js_features (
    sha256 FixedString(64),
    line_count UInt32,
    char_count UInt64,
    text_entropy Float64,
    max_line_length UInt32,
    avg_line_length Float64,
    is_minified UInt8,
    is_likely_obfuscated UInt8,
    obfuscator_name LowCardinality(String),
    obfuscation_score UInt8,
    obfuscation_techniques Array(String),
    eval_count UInt32,
    function_constructor_count UInt32,
    settimeout_setinterval_count UInt32,
    document_write_count UInt32,
    innerhtml_count UInt32,
    unescape_count UInt32,
    fromcharcode_count UInt32,
    atob_count UInt32,
    decodeuri_count UInt32,
    total_function_count UInt32,
    total_variable_count UInt32,
    max_nesting_depth UInt16,
    avg_identifier_length Float64,
    hex_string_count UInt32,
    unicode_escape_count UInt32,
    long_string_count UInt32,
    base64_string_count UInt32,
    comment_ratio Float64,
    script_type LowCardinality(String),
    detected_environment LowCardinality(String),
    analysis_date DateTime64(3, 'UTC')
) ENGINE = ReplacingMergeTree(analysis_date)
ORDER BY sha256;

-- 2. Suspicious API calls (multi-row per sample)
--
-- `revealed_by_deobf` is 1 when the API only appears after the deobfuscation
-- pass (i.e. the call site is hidden in the raw artefact and surfaces only in
-- text_normalized). Useful for filtering "what did normalisation actually
-- buy us" without re-running the diff.
CREATE TABLE IF NOT EXISTS redb_js_suspicious_apis (
    sha256 FixedString(64),
    api_name String,
    api_category LowCardinality(String),
    call_count UInt32,
    line_numbers Array(UInt32),
    context_snippet String,
    revealed_by_deobf UInt8,
    analysis_date DateTime64(3, 'UTC')
) ENGINE = ReplacingMergeTree(analysis_date)
ORDER BY (sha256, api_name);

-- 3. Deobfuscation results (1 row per sample)
CREATE TABLE IF NOT EXISTS redb_js_deobfuscation (
    sha256 FixedString(64),
    deobfuscator_used LowCardinality(String),
    deobfuscation_successful UInt8,
    original_size UInt64,
    deobfuscated_size UInt64,
    size_change_ratio Float64,
    original_entropy Float64,
    deobfuscated_entropy Float64,
    new_strings_found UInt32,
    new_apis_found UInt32,
    deobfuscated_sha256 FixedString(64),
    analysis_date DateTime64(3, 'UTC')
) ENGINE = ReplacingMergeTree(analysis_date)
ORDER BY sha256;

-- 4. Generic text-content table for any text-based artefact (JS today;
--    PowerShell, Python, plain text, email bodies, extracted PDF/Office text
--    in the future). One row per sha256. content_type carries the magika
--    label so callers can filter without joining other tables.
CREATE TABLE IF NOT EXISTS code_text_content (
    sha256 FixedString(64),
    content_type LowCardinality(String),
    text_raw String CODEC(ZSTD(3)),
    text_normalized Nullable(String) CODEC(ZSTD(3)),
    normalizer_used Nullable(String),
    analysis_date DateTime64(3, 'UTC')
) ENGINE = ReplacingMergeTree(analysis_date)
ORDER BY sha256;

-- 5. Extend redb_iocs.source_type Enum8 with two universal text-content
--    surfaces: text_raw (the artefact's original text) and text_normalized
--    (a deobfuscated/canonicalised form). Used by the JS IOC extraction
--    pipeline today; any future text-based pipeline (PowerShell, PDF, etc.)
--    plugs into the same two values.
--
-- Existing rows keep their stored integer values; only newly-inserted rows
-- can use 4/5. The MODIFY COLUMN must list the full final enum, including
-- the existing values (1/2/3) — ClickHouse rejects partial alters.
ALTER TABLE redb_iocs
    MODIFY COLUMN source_type
    Enum8('decompiled_function'=1, 'disassembled_function'=2, 'string'=3,
          'text_raw'=4, 'text_normalized'=5);

-- 6. Extend redb_iocs.ioc_type Enum8 with registry_key=42. Windows registry
--    paths (HKLM\..., HKCU\..., HKEY_LOCAL_MACHINE\...) are a distinct class
--    of IOC from filesystem paths and were previously extracted by nothing.
--    Same MODIFY COLUMN constraint as the source_type alter — the full final
--    enum must be listed.
ALTER TABLE redb_iocs
    MODIFY COLUMN ioc_type
    Enum8('ipv4'=1, 'ipv6'=2, 'fqdn'=3, 'url'=4, 'email'=5, 'server'=6,
          'hash_md5'=10, 'hash_sha1'=11, 'hash_sha256'=12,
          'cve'=20, 'cwe'=21, 'cpe'=22,
          'crypto_btc'=30, 'crypto_eth'=31, 'crypto_xrp'=32, 'crypto_bch'=33,
          'crypto_ada'=34, 'crypto_substrate'=35,
          'path_linux'=40, 'path_windows'=41, 'registry_key'=42,
          'onion'=50);

-- 7. Migrate redb_js_features to the two-tier obfuscation verdict.
--    `is_obfuscated` (binary heuristic at score >=40) is renamed to
--    `is_likely_obfuscated` (heuristic at >=60 + ≥1 strong signal, OR
--    js-x-ray flagged the obfuscator family). `obfuscator_name` is the
--    family name reported by @nodesecure/js-x-ray (jsfuck, obfuscator.io,
--    morse, jjencode, freejsobfuscator, ...) or empty when not detected.
--
--    Run once against an existing deployment. The CREATE TABLE above
--    already reflects the post-migration shape, so fresh installs skip this.
ALTER TABLE redb_js_features
    RENAME COLUMN is_obfuscated TO is_likely_obfuscated;
ALTER TABLE redb_js_features
    ADD COLUMN IF NOT EXISTS obfuscator_name LowCardinality(String) AFTER is_likely_obfuscated;

-- 8. Harmonise code_text_content column names with redb_iocs.source_type
--    enum values. The enum already uses `text_raw` / `text_normalized` for
--    the surface labels; the table previously stored the same data under
--    `content_raw` / `content_normalized`, forcing every join across the two
--    to translate names. Renaming the columns produces a self-documenting
--    schema where `redb_iocs.source_type='text_raw'` points directly at
--    `code_text_content.text_raw`.
--
--    Run once against an existing deployment. The CREATE TABLE above
--    already reflects the post-migration shape, so fresh installs skip this.
ALTER TABLE code_text_content
    RENAME COLUMN content_raw TO text_raw;
ALTER TABLE code_text_content
    RENAME COLUMN content_normalized TO text_normalized;

-- 9. Add revealed_by_deobf flag to redb_js_suspicious_apis. The strings/APIs
--    extractors now scan both the raw source and the deobfuscated text so APIs
--    hidden behind one obfuscation layer (Vjw0rm-style array.join + eval,
--    Dean-Edwards packers, ...) surface in the table. The flag is 1 only when
--    the API was *not* found in the raw source — querying for it isolates
--    "deobf-only" findings without joining redb_js_deobfuscation.
--
--    Run once against an existing deployment. The CREATE TABLE above
--    already reflects the post-migration shape, so fresh installs skip this.
ALTER TABLE redb_js_suspicious_apis
    ADD COLUMN IF NOT EXISTS revealed_by_deobf UInt8 AFTER context_snippet;