REVIEW 4 major objections 6 minor 1 cited by
Open Source, Open Threats? Investigating Security Challenges in Open-Source Software
T0 review · 4 major / 6 minor · reviewed 2026-08-07 · deepseek-v4-flash
Pith's one-line read Open-source security is worsening: reported vulnerabilities grow 98% a year, fixes take longer, and NPM and PyPI carry large malicious-package shares.
desk verdict Worth reviewing, but the headline growth numbers are shaky until the authors clarify their counting rules and fix internal inconsistencies. read the letter →
The pith
A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.
The reading
What carries the argument
The instrument carrying the argument is a unified longitudinal dataset built by merging 31,267 deduplicated vulnerability reports from the GitHub Advisory Database and Snyk.io with package-count and version-release metadata from Libraries.io and archived Wayback Machine snapshots. The key derived metric is vulnerability lifespan, defined as the sum, over a package's affected version ranges, of the time from the first vulnerable release to the first patched release; this measure is what supports the claim that vulnerabilities persist longer over time. The second mechanism is CWE classification, especially CWE-506 (Embedded Malicious Code), which separates intentionally malicious packages from accidental flaws and drives the supply-chain attack analysis.
What would settle it
Re-run the vulnerability-lifespan analysis as a survival study: treat every report with no patched release as still open on the data cutoff date, and recompute the average time from first vulnerable release to first patched release. If the 85% rise over 2017-2024 shrinks or disappears once these censored cases are counted, the persistence finding is an artifact of dropping unfixed recent vulnerabilities rather than a real slowdown in fixes.
Extended reading notes
Core claim
The central discovery, stated on the paper's own terms, is that open-source package ecosystems are becoming less secure even as they grow: reported vulnerabilities increased at an average annual rate of 98% during the study period, far outpacing the 25% average growth in the number of packages. Vulnerability lifespans grew from roughly 1,056 to 1,956 days on average, an increase of about 85%, which the paper interprets as evidence that fixes are not keeping pace with discoveries. The paper further finds that a small set of weakness classes drives most reports - on average seven CWEs account for over half of all vulnerabilities across ecosystems - with web-oriented weaknesses such as cross-site scripting (CWE-79) and path traversal (CWE-22) appearing broadly while memory-safety weaknesses such as heap-based buffer overflow (CWE-122) are tied to C/C++ and prototype pollution (CWE-1321) to JavaScript. Finally, it documents a large and growing class of intentionally malicious packages (CWE-506), with 4,456 reports concentrated almost entirely in NPM and PyPI, and attacks executed through typosquatting, dependency confusion, and installation-hook exploitation.
Load-bearing premise
The claim that vulnerabilities persist 85% longer assumes that summing, for each package, the time from the first affected version to the first patched version over all affected ranges gives a fair measure of persistence, with no clear treatment of vulnerabilities that still have no patched release, and version-release metadata exists for only 11,316 of the 14,675 affected packages.
Editorial extensions
If this is right
- If the 98% annual growth in reported vulnerabilities is real, security teams can expect the volume of newly disclosed open-source flaws to roughly quadruple relative to the package base they support, making automated triage necessary.
- If vulnerabilities persist 85% longer on average, prompt upgrading to patched versions becomes more valuable, because the window in which a known flaw remains exploitable is widening.
- Because on average seven CWEs account for over half of all reported vulnerabilities per ecosystem, defenses aimed at those specific weakness classes could plausibly address a majority of reports.
- Because malicious packages account for 48.58% of NPM reports and 13.92% of PyPI reports, registry operators need detection oriented to intentional attacks, such as name-similarity checks, dependency-confusion scanning, and install-script monitoring, alongside classic patching workflows.
Reading between the lines
- Implicit in the data but not tested by the paper: the 98% versus 25% comparison counts reported vulnerabilities, not vulnerability incidence, so rising reporting effort from scanners, researchers, and regulation could explain part of the gap; the true per-package risk increase is likely smaller than fourfold.
- A testable extension of the lifespan analysis would re-run it with survival analysis that treats unpatched vulnerabilities as censored; the reported 85% increase may shrink or vanish once recent, still-unfixed reports are included.
- The CWE-506 shares are computed within advisory databases whose malicious packages were removed after takedown; a registry-wide cohort study of all published NPM and PyPI packages could turn the 49% and 14% figures into true prevalence estimates.
Editorial analysis
A structured set of objections, weighed in public.
Referee Report
Summary. This paper presents a longitudinal observational study of 31,267 vulnerability reports collected from the GitHub Advisory Database and Snyk.io, covering 14,675 packages across 10 programming languages and 8 package managers from 2017 to January 2025. The authors report three main findings: (i) the annual growth rate of vulnerable packages (98% in the abstract, 91% in Section 5.1) far exceeds the 25% growth of total packages; (ii) the average vulnerability lifespan increased by 85% (1,056 to 1,956 days); and (iii) on average, seven CWEs account for over 50% of reported vulnerabilities across ecosystems. The paper also analyzes CWE-506 (embedded malicious code), reporting that it constitutes 48.58% of NPM and 13.92% of PyPI vulnerability reports, and discusses attack vectors such as typosquatting, dependency confusion, and installation-hook abuse. The authors release the dataset and analysis scripts.
Significance. If the reported trends are robust, this work would provide the most comprehensive cross-ecosystem longitudinal view of OSS vulnerabilities to date, extending prior studies to C/C++ and to a substantially larger report corpus, and would offer a useful baseline for policy discussions and for the design of automated vulnerability detection. The public release of the dataset and scripts is a concrete strength. However, the central quantitative claims (the 98%/91% vs 25% growth comparison and the 85% lifespan increase) are sensitive to counting definitions, data filtering, and censoring, and the paper does not currently provide the sensitivity analyses needed to establish that these results are not artifacts of those choices.
major comments (4)
- [Section 5.1 / Figure 3 / Abstract] The definition of the 'vulnerable packages' count used for growth-rate calculation is not specified. The text defines growth rate as year-over-year percentage change, but it does not state whether the vulnerable-package count is the number of packages newly reported as vulnerable in each year, the cumulative number of distinct vulnerable packages, or the count of affected package-version records. The total-package counts, taken from Libraries.io snapshots via the Wayback Machine (Section 4.2), are point-in-time registry sizes; comparing them to an unspecified vulnerable-package count may not be apples-to-apples. Moreover, the abstract and conclusion report a 98% annual increase while Section 5.1 reports 91%, and this discrepancy is never reconciled. No confidence intervals or significance tests are reported for either growth rate. Since this comparison is the central RQ1 claim, please clarify the counting unit and provide the underlying time series and uncertainty estimates.
- [Section 5.2 / Appendix A] The lifespan analysis sums, for each package, the durations of all affected version ranges from the first vulnerable release to the first patched release (Appendix A). The paper does not state how vulnerabilities with no patched release are treated, and Section 4.2 reports that version metadata is available for only 11,316 of the 14,675 affected packages. If vulnerabilities lacking a patched release are excluded, the reported increase in average lifespan from 1,056 to 1,956 days (an 85% increase) could be an artifact of right-censoring: recent vulnerabilities are less likely to have a patched release yet. Please report the proportion of observations with a patched release, and provide a sensitivity analysis that treats unfixed cases as censored (e.g., a survival-based estimator or a lower-bound analysis).
- [Section 4.3] The filtering decisions in dataset generation are not tested for their effect on the headline results. Removing 6,770 reports with discouraged or prohibited CWEs (including CWE-400 and CWE-200) can remove a large share of early NVD-sourced reports, mechanically increasing year-over-year growth rates. Similarly, using only GitHub-reviewed advisories and excluding 242,000+ unreviewed advisories changes the denominator and the vulnerability mix. The paper should quantify how the RQ1 growth rates, the 'seven CWEs account for over 50%' finding, and the CWE-506 percentages change when these exclusions are relaxed or when unreviewed advisories are included as a robustness check.
- [Abstract / Introduction / Section 7] The headline numbers are inconsistent across the paper: the abstract and conclusion state a 98% annual increase in vulnerable packages, while Section 5.1 states 91%; the introduction states that lifespan increased by 95% from 2017 to 2024, while the abstract, RQ2, and Section 5.2 state 85%. These discrepancies are not explained and directly affect the paper's central claims. Please reconcile them or clarify that different time windows or metrics produce the different values.
minor comments (6)
- [Table 3 / Section 5.4] The reported percentages for CWE-506 (48.58% for NPM and 13.92% for PyPI) do not match the totals in Table 2 (3,893/8,237 = 47.3% and 518/3,907 = 13.3%). Please recompute these values or clarify the denominator used.
- [Section 5.2] The sentence 'The data suggests that RubyGems and NPM have the highest number of published versions of different packages per day, with an average of 0.06 versions while we saw that it has the largest vulnerability lifespan' is confusingly worded; please rephrase to indicate which ecosystem has the largest lifespan and how version publication frequency is computed.
- [Section 5.4] The analysis of attack vectors names typosquatting, dependency confusion, and installation-hook exploitation as the three dominant vectors, but the paper does not report how many of the 4,456 CWE-506 packages fall into each category. Providing these counts would strengthen the claim.
- [Section 4.2] For the historical package counts collected from the Wayback Machine, please state the exact snapshot dates and how missing snapshots are handled; this affects the reproducibility of the 25% growth figure.
- [Figure 5] The 'Overall Average' series in Figure 5 is not defined; please specify whether it is an unweighted average over ecosystems or a vulnerability-weighted average.
- [General] There are several minor typos, e.g., 'detail analysis' in the contribution list and 'Pashchenko et al. [29] study' in Section 2.3; proofreading is needed.
Circularity Check
No significant circularity: the paper is an observational study of external advisory databases whose reported trends are direct aggregations of the data, not outputs of a fitted model or of a self-citation chain.
full rationale
This paper does not derive its conclusions from its own assumptions in a circular way. The central claims—vulnerability growth outpacing package growth, increasing vulnerability lifespan, CWE concentration, and the prevalence of CWE-506 packages—are all computed directly from external vulnerability advisories (GitHub Advisory Database and Snyk.io) and package metadata. No parameter is fitted to the data and then renamed as a prediction, and no result is defined in terms of the quantity it claims to explain. The growth rates are year-over-year percentage changes in reported counts, which are straightforward summaries of the collected dataset. The paper makes no self-citations that carry a load-bearing argument, and it does not invoke any uniqueness theorem or prior-authority result to force its interpretation. The identified methodological concerns, such as the unreported handling of vulnerabilities without patched versions in the lifespan calculation and the discrepancy between the 98% and 91% growth figures, are empirical or reporting issues that could affect validity, but they are not circularity: the conclusions are not equivalent to the inputs by construction. Overall, the derivation chain is self-contained relative to the external data sources, and the paper's findings remain independently checkable against those sources. Therefore, the circularity score is 0.
Assumptions & free parameters
assumptions (4)
- domain assumption GitHub-reviewed advisories and Snyk provide a representative sample of OSS vulnerabilities
- domain assumption Vulnerability lifespan is accurately measured as the summed durations of affected version ranges
- domain assumption Removing MITRE-discouraged CWEs removes noise rather than signal
- domain assumption Wayback Machine snapshots of Libraries.io provide accurate historical package counts
Cite this review
Pith. "Pith review of Open Source, Open Threats? Investigating Security Challenges in Open-Source Software." pith.science (2026). https://pith.science/paper/5KPGZMSG
@misc{pith2026250612995,
author = {Pith},
title = {Pith review of: Open Source, Open Threats? Investigating Security Challenges in Open-Source Software},
year = {2026},
howpublished = {\url{https://pith.science/paper/5KPGZMSG}},
note = {Machine review of arXiv:2506.12995}
}
read the original abstract
Open-source software (OSS) has become increasingly more popular across different domains. However, this rapid development and widespread adoption come with a security cost. The growing complexity and openness of OSS ecosystems have led to increased exposure to vulnerabilities and attack surfaces. This paper investigates the trends and patterns of reported vulnerabilities within OSS platforms, focusing on the implications of these findings for security practices. To understand the dynamics of OSS vulnerabilities, we analyze a comprehensive dataset comprising 31,267 unique vulnerability reports from GitHub's advisory database and Snyk.io, belonging to 14,675 packages across 10 programming languages. Our analysis reveals a significant surge in reported vulnerabilities, increasing at an annual rate of 98%, far outpacing the 25% average annual growth in the number of open-source software (OSS) packages. Additionally, we observe an 85% increase in the average lifespan of vulnerabilities across ecosystems during the studied period, indicating a potential decline in security. We identify the most prevalent Common Weakness Enumerations (CWEs) across programming languages and find that, on average, just seven CWEs are responsible for over 50% of all reported vulnerabilities. We further examine these commonly observed CWEs and highlight ecosystem-specific trends. Notably, we find that vulnerabilities associated with intentionally malicious packages comprise 49% of reports in the NPM ecosystem and 14% in PyPI, an alarming indication of targeted attacks within package repositories. We conclude with an in-depth discussion of the characteristics and attack vectors associated with these malicious packages.
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npm, “rc - npm package,” 2024. Accessed: 2024-10-14
2024
-
[64]
coa - npm package,
npm, “coa - npm package,” 2024. Accessed: 2024-10-14
2024
-
[65]
ua-parser-js - npm package,
npm, “ua-parser-js - npm package,” 2024. Accessed: 2024-10- 14
2024
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[66]
CWE - CWE-79: Improper Neutralization of Input During Web Page Generation (’Cross Site Scripting’),
“CWE - CWE-79: Improper Neutralization of Input During Web Page Generation (’Cross Site Scripting’),” 2024. Accessed: 2024-10-14
2024
-
[67]
CWE - CWE-22: Improper limitation of a pathname to a restricted directory (’path traversal’),
“CWE - CWE-22: Improper limitation of a pathname to a restricted directory (’path traversal’),” 2024. Accessed: 2024- 10-14
2024
-
[68]
CWE - CWE-94: Improper control of generation of code (’code injection’),
“CWE - CWE-94: Improper control of generation of code (’code injection’),” 2024. Accessed: 2024-10-14
2024
-
[69]
CWE - CWE-1321: Improper Handling of Prototype Pollu- tion,
“CWE - CWE-1321: Improper Handling of Prototype Pollu- tion,” 2024. Accessed: 2024-10-14
2024
-
[70]
CWE - CWE-122: Heap-based Buffer Overflow,
“CWE - CWE-122: Heap-based Buffer Overflow,” 2024. Ac- cessed: 2024-10-14
2024
-
[71]
CWE - CWE-416: Use After Free,
“CWE - CWE-416: Use After Free,” 2024. Accessed: 2024-10- 14
2024
-
[72]
CWE - CWE-787: Out-of-Bounds Write,
“CWE - CWE-787: Out-of-Bounds Write,” 2024. Accessed: 2024-10-14
2024
-
[73]
Range operator
Microsoft, “Range operator.” Microsoft Docs, 2024. Accessed: 2024-10-14
2024
-
[74]
CWE - CWE-362: Concurrent Execution using Shared Re- source with Improper Synchronization (’Race Condition’),
“CWE - CWE-362: Concurrent Execution using Shared Re- source with Improper Synchronization (’Race Condition’),”
-
[77]
Below, we provide the formulas and definitions for each term used in our study to ensure clarity and precision
Terminology Definitions. Below, we provide the formulas and definitions for each term used in our study to ensure clarity and precision. Vulnerability LifespanThe vulnerability lifespan mea- sures the duration a vulnerability persists in a package before being patched. Since a...
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[78]
These CWEs have either become more prominent or less frequent due to improvements in ecosystem security practices
Rise and Fall of Top CWEs Figure 9 illustrates different ecosystem’s top five most reported CWEs over time. These CWEs have either become more prominent or less frequent due to improvements in ecosystem security practices. 20182019202020212022202320242025 0 1000 2000 3000 4000...
2000
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[79]
Discouraged and Prohibited CWEs Table 4 includes the CWEs that are marked as discouraged or prohibited to use by MITRE
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[80]
14 TABLE 4
Common and Ecosystem-Specific CWEs Table 5 includes examples for common and ecosystem-specific CWEs. 14 TABLE 4. DISCOURAGED ANDPROHIBITEDCOMMONWEAKNESSENUMERATION(CWE)ANDTHEIRDESCRIPTION CWE ID Description CWE ID Description CWE-19 Data Processing Errors CWE-200 Exposure of S...
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[2023]
Accessed: 2024-10-14
2024
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[2024]
Appendix
Accessed: 2024-10-14. Appendix
2024
Reviewed August 7, 2026 · model on record in the stance chip above.
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