Osamu Hirose

21 papers Journal 16Unranked 5
YearRankTypeTitle / Venue / Authors
2026 J jnl
CoRR
Osamu Hirose, Emanuele Rodolà
2023 J jnl
IEEE Trans. Pattern Anal. Mach. Intell.
Osamu Hirose
2021 J jnl
IEEE Trans. Pattern Anal. Mach. Intell.
Osamu Hirose
2021 J jnl
IEEE Trans. Pattern Anal. Mach. Intell.
Osamu Hirose
2021 J jnl
IEEE Trans. Pattern Anal. Mach. Intell.
Osamu Hirose
2018 J jnl
IEEE ACM Trans. Comput. Biol. Bioinform.
Osamu Hirose, Shotaro Kawaguchi, Terumasa Tokunaga, Yu Toyoshima, Takayuki Teramoto, Sayuri Kuge, Takeshi Ishihara, Yuichi Iino, Ryo Yoshida
2017 J jnl
CoRR
Osamu Hirose
2016 J jnl
PLoS Comput. Biol.
Yu Toyoshima, Terumasa Tokunaga, Osamu Hirose, Manami Kanamori, Takayuki Teramoto, Moon Sun Jang, Sayuri Kuge, Takeshi Ishihara, Ryo Yoshida, Yuichi Iino
2015 J jnl
CoRR
Osamu Hirose, Shotaro Kawaguchi, Terumasa Tokunaga, Yu Toyoshima, Takayuki Teramoto, Sayuri Kuge, Takeshi Ishihara, Yuichi Iino, Ryo Yoshida
2015 conf
KSE
Xuan Tho Dang, Dang Hung Tran, Osamu Hirose, Kenji Satou
2014 J jnl
Bioinform.
Terumasa Tokunaga, Osamu Hirose, Shotaro Kawaguchi, Yu Toyoshima, Takayuki Teramoto, Hisaki Ikebata, Sayuri Kuge, Takeshi Ishihara, Yuichi Iino, Ryo Yoshida
2014 J jnl
Int. J. Funct. Informatics Pers. Medicine
Thi Tu Kien Le, Osamu Hirose, Thi Lan Anh Nguyen, Thammakorn Saethang, Vu Anh Tran, Xuan Tho Dang, Duc Luu Ngo, Mamoru Kubo, Yoichi Yamada, Kenji Satou
2013 J jnl
Bioinform.
Naoki Nariai, Osamu Hirose, Kaname Kojima, Masao Nagasaki
2012 J jnl
BMC Bioinform.
Thammakorn Saethang, Osamu Hirose, Ingorn Kimkong, Vu Anh Tran, Xuan Tho Dang, Thi Lan Anh Nguyen, Thi Tu Kien Le, Mamoru Kubo, Yoichi Yamada, Kenji Satou
2011 J jnl
Bioinform.
Yoshinori Tamada, Rui Yamaguchi, Seiya Imoto, Osamu Hirose, Ryo Yoshida, Masao Nagasaki, Satoru Miyano
2010 conf
ITBAM
Osamu Hirose, Kentaro Shimizu
2010 J jnl
Adv. Bioinformatics
Seizi Someya, Masanori Kakuta, Mizuki Morita, Kazuya Sumikoshi, Cao Wei, Ge Zhenyi, Osamu Hirose, Shugo Nakamura, Tohru Terada, Kentaro Shimizu
2008 conf
Asia International Conference on Modelling and Simulation
Osamu Hirose, Ryo Yoshida, Rui Yamaguchi, Seiya Imoto, Tomoyuki Higuchi, Satoru Miyano
2008 J jnl
Bioinform.
Osamu Hirose, Ryo Yoshida, Seiya Imoto, Rui Yamaguchi, Tomoyuki Higuchi, Stephen D. Charnock-Jones, Cristin G. Print, Satoru Miyano
2007 conf
ISVC (1)
Osamu Hirose, Tomoharu Nagao
2005 conf
ICCSA (3)
Osamu Hirose, Naoki Nariai, Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Satoru Miyano
redb/extractors/js_extractors/js_patterns.py
← Index redb/extractors/js_extractors/js_patterns.py python
"""Canonical, compiled JavaScript regex patterns shared across JS extractors.

All suspicious-API patterns and the few feature-only patterns live here so each
expression is compiled exactly once per Python process and so any pattern that
was previously duplicated across `js_features.py` and `js_suspicious_apis.py`
now resolves to a single shared compiled object.

JavaScript is case-sensitive at runtime, but every suspicious-API pattern matches
either a literal-case identifier (`\\beval\\s*\\(`, `String\\.fromCharCode`, etc.)
or a string-quoted token (`"powershell"`). Compiling them with `re.IGNORECASE`
matches the historical behaviour of `JSSuspiciousAPIsExtractor` and is safe for
the patterns that historically came from `JSFeaturesExtractor` — those literals
are spelled in real-world JS exactly as written.

`scan_source()` is the entry point used by extractors: it walks the source once
per pattern using the pre-compiled regexes and returns a flat
`{name: {"count": N, "lines": [unique_line_numbers_sorted]}}` dict. Both
`JSFeaturesExtractor` and `JSSuspiciousAPIsExtractor` consume the same dict so
the per-pattern × per-line loops they used to run independently collapse to a
single shared scan.
"""

import bisect
import re
from typing import Dict, Iterable, List, Mapping

_FLAGS = re.IGNORECASE

# Canonical compiled patterns, keyed by their human-readable name. The name is
# also the value emitted into `redb_js_suspicious_apis.api_name`.
PATTERNS = {
    # ---- code execution ----
    "eval": re.compile(r"\beval\s*\(", _FLAGS),
    "Function constructor": re.compile(r"\bnew\s+Function\s*\(", _FLAGS),
    "execScript": re.compile(r"\bexecScript\s*\(", _FLAGS),
    "document.write": re.compile(r"\bdocument\.write(?:ln)?\s*\(", _FLAGS),
    "innerHTML assignment": re.compile(r"\.innerHTML\s*=", _FLAGS),
    "outerHTML assignment": re.compile(r"\.outerHTML\s*=", _FLAGS),
    "insertAdjacentHTML": re.compile(r"\.insertAdjacentHTML\s*\(", _FLAGS),
    # ---- network ----
    "XMLHttpRequest": re.compile(r"\bnew\s+XMLHttpRequest\b", _FLAGS),
    "fetch": re.compile(r"\bfetch\s*\(", _FLAGS),
    "WebSocket": re.compile(r"\bnew\s+WebSocket\s*\(", _FLAGS),
    "navigator.sendBeacon": re.compile(r"\bnavigator\.sendBeacon\s*\(", _FLAGS),
    "ActiveXObject XMLHTTP": re.compile(
        r"ActiveXObject\s*\(\s*[\"\'](?:MSXML2\.XMLHTTP|Microsoft\.XMLHTTP)", _FLAGS
    ),
    "require network module": re.compile(
        r"require\s*\(\s*[\"\'](?:http|https|net|dgram)[\"\']", _FLAGS
    ),
    "axios": re.compile(r"\baxios\b", _FLAGS),
    # ---- filesystem ----
    "require fs": re.compile(r"require\s*\(\s*[\"\']fs[\"\']", _FLAGS),
    "require path": re.compile(r"require\s*\(\s*[\"\']path[\"\']", _FLAGS),
    "FileSystemObject": re.compile(r"Scripting\.FileSystemObject", _FLAGS),
    "ADODB.Stream": re.compile(r"ADODB\.Stream", _FLAGS),
    "Shell.Application": re.compile(r"Shell\.Application", _FLAGS),
    "WScript.CreateObject": re.compile(r"WScript\.CreateObject", _FLAGS),
    # ---- process ----
    "require child_process": re.compile(r"require\s*\(\s*[\"\']child_process[\"\']", _FLAGS),
    "child_process exec": re.compile(r"child_process\.(?:exec|spawn|execFile|fork)\s*\(", _FLAGS),
    "WScript.Shell": re.compile(r"WScript\.Shell", _FLAGS),
    "WScript.Shell.Run": re.compile(r"\.Run\s*\(", _FLAGS),
    "WScript.Shell.Exec": re.compile(r"\.Exec\s*\(", _FLAGS),
    "ShellExecute": re.compile(r"\bShellExecute\b", _FLAGS),
    "PowerShell reference": re.compile(r"[\"\']powershell[\"\']", _FLAGS),
    "cmd.exe reference": re.compile(r"[\"\']cmd\.exe[\"\']", _FLAGS),
    "require os": re.compile(r"require\s*\(\s*[\"\']os[\"\']", _FLAGS),
    # ---- registry ----
    "RegRead": re.compile(r"\.RegRead\s*\(", _FLAGS),
    "RegWrite": re.compile(r"\.RegWrite\s*\(", _FLAGS),
    "RegDelete": re.compile(r"\.RegDelete\s*\(", _FLAGS),
    "StdRegProv": re.compile(r"StdRegProv", _FLAGS),
    # ---- crypto / encoding ----
    "atob": re.compile(r"\batob\s*\(", _FLAGS),
    "btoa": re.compile(r"\bbtoa\s*\(", _FLAGS),
    "String.fromCharCode": re.compile(r"String\.fromCharCode\s*\(", _FLAGS),
    "unescape": re.compile(r"\bunescape\s*\(", _FLAGS),
    "decodeURIComponent": re.compile(r"\bdecodeURIComponent\s*\(", _FLAGS),
    "Buffer.from": re.compile(r"Buffer\.from\s*\(", _FLAGS),
    "crypto module": re.compile(r"crypto\.create(?:Cipher|Decipher|Hash|Hmac)", _FLAGS),
    # ---- DOM manipulation ----
    "document.forms": re.compile(r"document\.forms", _FLAGS),
    "document.cookie": re.compile(r"document\.cookie", _FLAGS),
    "querySelector sensitive input": re.compile(
        r"document\.querySelector\s*\([^)]*(?:password|credit|card|cvv|ssn)", _FLAGS
    ),
    "submit event listener": re.compile(r"addEventListener\s*\(\s*[\"\']submit", _FLAGS),
    "createElement script/iframe": re.compile(
        r"\.createElement\s*\(\s*[\"\'](?:script|iframe)", _FLAGS
    ),
    "dynamic script src": re.compile(r"\.src\s*=\s*[\"\'](?:https?://|//)", _FLAGS),
}

# Pattern name -> category (one of code_execution / network / filesystem /
# process / registry / crypto_encoding / dom_manipulation).
CATEGORIES = {
    "eval": "code_execution",
    "Function constructor": "code_execution",
    "execScript": "code_execution",
    "document.write": "code_execution",
    "innerHTML assignment": "code_execution",
    "outerHTML assignment": "code_execution",
    "insertAdjacentHTML": "code_execution",
    "XMLHttpRequest": "network",
    "fetch": "network",
    "WebSocket": "network",
    "navigator.sendBeacon": "network",
    "ActiveXObject XMLHTTP": "network",
    "require network module": "network",
    "axios": "network",
    "require fs": "filesystem",
    "require path": "filesystem",
    "FileSystemObject": "filesystem",
    "ADODB.Stream": "filesystem",
    "Shell.Application": "filesystem",
    "WScript.CreateObject": "filesystem",
    "require child_process": "process",
    "child_process exec": "process",
    "WScript.Shell": "process",
    "WScript.Shell.Run": "process",
    "WScript.Shell.Exec": "process",
    "ShellExecute": "process",
    "PowerShell reference": "process",
    "cmd.exe reference": "process",
    "require os": "process",
    "RegRead": "registry",
    "RegWrite": "registry",
    "RegDelete": "registry",
    "StdRegProv": "registry",
    "atob": "crypto_encoding",
    "btoa": "crypto_encoding",
    "String.fromCharCode": "crypto_encoding",
    "unescape": "crypto_encoding",
    "decodeURIComponent": "crypto_encoding",
    "Buffer.from": "crypto_encoding",
    "crypto module": "crypto_encoding",
    "document.forms": "dom_manipulation",
    "document.cookie": "dom_manipulation",
    "querySelector sensitive input": "dom_manipulation",
    "submit event listener": "dom_manipulation",
    "createElement script/iframe": "dom_manipulation",
    "dynamic script src": "dom_manipulation",
}

# Patterns consumed only by JSFeaturesExtractor (no category, never surfaced as
# a suspicious-API row). Kept here so every JS regex is compiled in one place.
FEATURE_PATTERNS = {
    "hex_escape": re.compile(r"\\x[0-9a-fA-F]{2}"),
    "unicode_escape": re.compile(r"\\u[0-9a-fA-F]{4}"),
    "base64_string": re.compile(r"[A-Za-z0-9+/]{40,}={0,2}"),
    # decodeURI matches BOTH decodeURI and decodeURIComponent. The latter is also
    # a suspicious-API pattern in PATTERNS; this broader form is what the
    # `decodeuri_count` feature column has historically counted.
    "decodeURI": re.compile(r"\b(?:decodeURI|decodeURIComponent)\s*\(", _FLAGS),
    "settimeout_setinterval": re.compile(r"\b(?:setTimeout|setInterval)\s*\(", _FLAGS),
    "function_decl": re.compile(r"\bfunction\s+\w+\s*\(|\bfunction\s*\("),
    "var_decl": re.compile(r"\b(?:var|let|const)\s+"),
    "string_concat": re.compile(r"[\"\'][\s]*\+[\s]*[\"\']"),
    "comment": re.compile(r"//.*?$|/\*[\s\S]*?\*/", re.MULTILINE),
    "long_string": re.compile(r"[\"\']([^\"\']{256,})[\"\']"),
    "array_function_call": re.compile(r"\[(?:0x[0-9a-f]+|[\d]+)\]\s*\(", _FLAGS),
}

# Patterns consumed only by JSStringsExtractor for encoded-string discovery.
# Scoped to *hidden* strings only — patterns whose decoded form is not visible
# to a substring search over the raw text. Plain long literals are not
# extracted here because they're already preserved in code_text_content and
# scraped by the IOC pipeline over text_raw / text_normalized.
#
# Distinct from FEATURE_PATTERNS even where the names rhyme:
#   FEATURE_PATTERNS["hex_escape"] / ["unicode_escape"]   -> single escape
#   STRING_PATTERNS["hex_escape_seq"] / ["unicode_escape_seq"] -> 4+ / 3+ in a row
#   FEATURE_PATTERNS["base64_string"]                     -> bare base64 token
#   STRING_PATTERNS["base64_quoted"]                      -> base64 inside JS quotes
# These do not share match objects with the suspicious-API or feature scans, so
# they are not folded into JSContext.scan; the strings extractor walks them
# itself (one finditer per pattern, with shared line-offset bisect in #4b).
STRING_PATTERNS = {
    "hex_escape_seq": re.compile(r"(?:\\x[0-9a-fA-F]{2}){4,}"),
    "unicode_escape_seq": re.compile(r"(?:\\u[0-9a-fA-F]{4}){3,}"),
    "charcode_call": re.compile(r"String\.fromCharCode\s*\(\s*([\d,\s]+)\s*\)"),
    "base64_quoted": re.compile(r"[\"\']([A-Za-z0-9+/]{40,}={0,2})[\"\']"),
    "concat_chain": re.compile(r"(?:[\"\'][^\"\']+[\"\']\s*\+\s*){3,}[\"\'][^\"\']+[\"\']"),
}


def line_offsets(source: str) -> List[int]:
    """Sorted list of byte offsets for every newline in `source`, plus a final
    sentinel of len(source). Used to translate match offsets into 1-indexed
    line numbers via bisect.
    """
    offsets = [-1]  # so that bisect_right of offset 0 returns line 1
    push = offsets.append
    idx = source.find("\n")
    while idx != -1:
        push(idx)
        idx = source.find("\n", idx + 1)
    return offsets


def _scan_one(
    pattern: "re.Pattern[str]", source: str, offsets: List[int]
) -> Dict[str, object]:
    """Run a single compiled pattern over `source` and return count + unique lines."""
    count = 0
    seen_lines: "set[int]" = set()
    for m in pattern.finditer(source):
        count += 1
        seen_lines.add(bisect.bisect_right(offsets, m.start()))
    if not count:
        return None  # type: ignore[return-value]
    return {"count": count, "lines": sorted(seen_lines)}


def scan_source(
    source: str,
    patterns: Iterable[Mapping[str, "re.Pattern[str]"]] = (PATTERNS, FEATURE_PATTERNS),
) -> Dict[str, Dict[str, object]]:
    """Scan `source` against every compiled pattern in `patterns`.

    Returns a dict keyed by pattern name. Each entry has:
        "count": total number of matches in the source
        "lines": sorted list of unique 1-indexed line numbers where the pattern
                 matched (deduplicated — multiple matches on the same line
                 collapse to one entry, preserving the historical
                 line-set semantics of JSSuspiciousAPIsExtractor)
    Patterns with zero matches are absent from the dict; callers should default
    to {"count": 0, "lines": []}.
    """
    if not source:
        return {}
    offsets = line_offsets(source)
    results: Dict[str, Dict[str, object]] = {}
    for table in patterns:
        for name, pat in table.items():
            entry = _scan_one(pat, source, offsets)
            if entry is not None:
                results[name] = entry
    return results