Robot Updated at:2 Feb 2025 21:09:45 GMT

Author: yiliuyan161

docs/awesome/awesome-agi-cocosci.md

@@ -1369,6 +1369,8 @@ English-language description for use by biologists.
 
 * [A human-machine interface for automatic exploration of chemical reaction networks](https://www.nature.com/articles/s41467-024-47997-9) - ***Nature Communications***, 2024. [[All Versions](https://scholar.google.com/scholar?cluster=13306522324804014261)]. Autonomous reaction network exploration algorithms offer a systematic approach to explore mechanisms of complex chemical processes. However, the resulting reaction networks are so vast that an exploration of all potentially accessible intermediates is computationally too demanding. This paper introduces a STEERING WHEEL to guide an otherwise unbiased automated exploration. The STEERING WHEEL algorithm is intuitive, generally applicable, and enables one to focus on specific regions of an emerging network. It also allows for guiding automated data generation in the context of mechanism exploration, catalyst design, and other chemical optimization challenges.
 
+* [PatCID: an open-access dataset of chemical structures in patent documents](https://www.nature.com/articles/s41467-024-50779-y) - ***Nature Communications***, 2024. [[All Versions](https://scholar.google.com/scholar?cluster=329287456191953845)]. The automatic analysis of patent publications has potential to accelerate research across various domains, including drug discovery and material science. Within patent documents, crucial information often resides in visual depictions of molecule structures. PatCID (Patent-extracted Chemical-structure Images database for Discovery) allows to access such information at scale. It enables users to search which molecules are displayed in which documents. PatCID contains 81M chemical-structure images and 14M unique chemical structures. This work compares PatCID with state-of-the-art chemical patent-databases. On a random set, PatCID retrieves 56.0% of molecules, which is higher than automatically-created databases, Google Patents (41.5%) and SureChEMBL (23.5%), as well as manually-created databases, Reaxys (53.5%) and SciFinder (49.5%). Leveraging state-of-the-art methods of document understanding, PatCID high-quality data outperforms currently available automatically-generated patent-databases. PatCID even competes with proprietary manually-created patent-databases. This enables promising applications for automatic literature review and learning-based molecular generation methods. 
+
 * [ChipNeMo: Domain-Adapted LLMs for Chip Design](https://arxiv.org/abs/2311.00176) - 2023. [[All Versions](https://scholar.google.com/scholar?cluster=5962372610489019326)].
 
 * [Single-atom alloy catalysts designed by first-principles calculations and artificial intelligence](https://www.nature.com/articles/s41467-021-22048-9) - ***Nature Communications***, 2021. [[All Versions](hhttps://scholar.google.com/scholar?cluster=6593978922251447907)]. This paper addresses the problem of new Single-atom-alloy catalysts (SAACs) discovery by applying a compressed-sensing data-analytics approach parameterized with density-functional inputs.

docs/awesome/awesome-annual-security-reports.md

@@ -43,6 +43,7 @@ Reports will be classified by a header that describes their primary content or e
 
 ## Threat Intelligence
 - [ASD](https://www.cyber.gov.au/about-us/view-all-content/reports-and-statistics/annual-cyber-threat-report-2023-2024) - [Cyber Threat Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2024/ASD-Cyber-Threat-Report-2024.pdf) (2024) - Insights into Australia’s evolving cyber threat landscape, attack trends, and defense strategies.
+- [ArticWolfLabs](https://arcticwolf.com/arctic-wolf-labs-2025-cybersecurity-predictions/) - [Cybersecurity Predictions](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2025/ArticWolfLabs-Cybersecurity-Predictions-2025.pdf) (2025) -  Aims to prepare security teams for the challenges ahead by offering insights and advice to mitigate threat actor risks in an evolving threat landscape.
 - [BD](https://news.bd.com/2024-06-13-BD-Issues-Annual-Product-Security-Report,-Highlighting-Transparency-and-Collaboration) - [Product Security Annual Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2023/BD-Product-Security-Annual-Report-2023.pdf) (2023) - Highlights cybersecurity threats in healthcare, addressing the growing sophistication and frequency of cyberattacks through transparency, collaboration, and adherence to high security standards.
 - [Blackpoint](https://blackpointcyber.com/resources/cybersecurity-annual-threat-report-2024/) - [Annual Threat Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2024/Blackpoint-Cyber-Annual-Threat-Report-2024.pdf) (2024) - Analyzes current cyber threats, attack techniques, and emerging trends, providing actionable intelligence for organizations to enhance their security posture.
 - [CheckPoint](https://www.checkpoint.com/security-report/) - [Cybersecurity Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2025/CheckPoint-Cybersecurity-Report-2025.pdf) (2025) - Provides practical insights to help strengthen your defenses, adapt to an ever-changing threat landscape, stay ahead of attackers, and secure your organization effectively.
@@ -86,7 +87,10 @@ Reports will be classified by a header that describes their primary content or e
 - [BlackDuck](https://www.blackduck.com/resources/analyst-reports/software-vulnerability-trends.html) - [Software Vulnerability Snapshot Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2024/BlackDuck-Software-Vulnerability-Snapshot-Report-2024.pdf) (2024) - A snapshot of software vulnerabilities, highlighting key findings, potential business impacts, and recommendations.
 - [Escape](https://escape.tech/the-api-secret-sprawl-2024) - [State of API Exposure](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2024/Escape-State-of-API-Exposure-2024.pdf) (2024)  
   Analyzes API security across Fortune 1000 and CAC 40 companies, uncovering 30,000 exposed APIs and 100,000 API issues, emphasizing risks in large organizations.
+- [Grip](https://www.grip.security/saas-security-risks-report-2025) - [SaaS Security Risks Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2025/Grip-SaaS-Security-Risks-Report-2025.pdf) (2025) - Outlines key security risks associated with the growing adoption of SaaS applications, including trends in usage across industries and specific SaaS app statistics.
+- [Kodem](https://www.kodemsecurity.com/lp/report/appsec/workflows) - [State of AppSec Workflow](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2025/Kodem-State-of-AppSec-Workflow-2025.pdf) (2025) - Outlines the current state of application security workflows, providing an overview of the processes and challenges involved in securing applications.
 - [RunZero](https://www.runzero.com/research-report/) - [RunZero Research Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2024/RunZero-Research-Report-Vol1-2024.pdf) (2024) - Examines a broad range of organizational and network security issues through an innovative asset-centric approach, with a focus on "dark matter" in networks, segmentation issues, and unusual asset detection.
+- [LegitSecurity](https://www.legitsecurity.com/blog/announcing-2025-state-of-application-risk-report) - [State of Application Risk Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2025/LegitSecurity-State-of-Application-Risk-Report-2025.pdf) (2025) - Examines the current and future landscape of application security risks, including their extent and adherence to AppSec practices.
 - [Sonatype](https://www.sonatype.com/resources/whitepapers/2024-open-source-malware-threat-report) - [2024 in Open Source Malware Threat Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2024/Sonatype-2024-in-Open-Source-Malware-Report-2024.pdf) (2024)  
   Reports a 156% year-over-year increase in malicious open source packages, highlighting the growing threat of intentionally crafted malware in software supply chain attacks.
 - [Synopsys](https://www.synopsys.com/software-integrity/resources/analyst-reports/open-source-security-risk-analysis.html) - [Open Source Risk Analysis Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2024/Synopsys-Open-Source-Risk-Analysis-Report-2024.pdf) (2024) - Examines security risks associated with open-source software components, offering insights into vulnerability trends and mitigation strategies.
@@ -153,9 +157,10 @@ Reports will be classified by a header that describes their primary content or e
   Examines application security challenges and strategies from the perspectives of CISOs, AppSec Directors, and DevSecOps managers across the UK, US, and Germany.
 - [Synopsys](https://www.synopsys.com/software-integrity/resources/analyst-reports/sans-devsecops-survey.html) - [SANS 2023 DevSecOps Survey](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2023/SANS-DevSecOps-Survey-2023.pdf) (2023) - Examines the current state of DevSecOps practices across various industries.
 - [Snyk](https://snyk.io/lp/state-of-open-source-2024) - [State of Open Source Security](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2024/Snyk-State-of-Open-Source-Security-2024.pdf) (2024) - Examines the current state of open source security, including trends and challenges across various industries.
+- [Traceable](https://www.traceable.ai/2025-state-of-api-security) - [Global State of API Security](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2025/Traceable-Global-State-of-API-Security-2025.pdf) (2025) - Annual survey gathering insights from 1,548 respondents across 100+ countries on the state of API security.
 
 ## Cloud Security
-- [Fortinet](https://www.fortinet.com/blog/industry-trends/key-findings-cloud-security-report-2024) - [Cloud Security Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2024/Fortinet-Cloud-Security-Report-2024.pdf) (2024) - Examines the state of cloud security, highlighting key challenges, trends, and best practices for organizations across various industries.
+- [Fortinet](https://www.fortinet.com/resources/reports/cloud-security) - [Cloud Security Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2025/Fortinet-Cloud-Security-Report-2025.pdf) (2025) - Examines the state of cloud security, highlighting key challenges, trends, and best practices for organizations across various industries.
 - [ISC2](https://cloud.connect.isc2.org/cloud-security-report) - [Cloud Security Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2024/ISC2-Cloud-Security-Report-2024.pdf) (2024) - Provides insights into cloud security challenges, trends, and strategies across different sectors.
 - [Mend](https://www.mend.io/resources/research-reports/the-state-of-supply-chain-threats/) - [State of Supply Chain Threats](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2023/Mend-State-of-Supply-Chain-Threats.pdf) (2023) - Examines the current state of supply chain threats and vulnerabilities across different sectors.
 - [PaloAlto](https://www.paloaltonetworks.com/state-of-cloud-native-security) - [State of Cloud Native Security Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2024/PaloAlto-State-of-Cloud-Native-Security-2024.pdf) (2024) - Examines the current state of cloud-native security, including trends, challenges, and best practices across different sectors.
@@ -186,6 +191,7 @@ Reports will be classified by a header that describes their primary content or e
   Highlights insider threat risks and trends based on insights from over 700 security professionals.
 - [Immuta](https://www.immuta.com/resources/2024-trendbook/) - [State of Data Security Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2024/Immuta-State-of-Data-Security-Report-2024.pdf) (2024) - Examines the current state of data security, including challenges, trends, and best practices across various industries.
 - [ISACA](https://www.isaca.org/resources/reports/state-of-privacy-2025) - [State of Privacy](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2025/ISACA-State-of-Privacy-2025.pdf) (2025) - Outlines key trends in global privacy practices, including staffing needs, budget constraints, and the increasing integration of AI in privacy operations.
+- [Kiteworks](https://www.kiteworks.com/report-2025-forecast-for-managing-private-content-exposure-risk/) - [Forecast for Managing Private Content Exposure Risk](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2025/Kiteworks-Forecast-for-Managing-Private-Content-Exposure-Risk-2025.pdf) (2025) - Outlines 12 predictions for managing private content exposure risk, based on cybercrime, cybersecurity, and compliance trends focusing on sensitive content communications.
 - [Proofpoint](https://www.proofpoint.com/us/resources/threat-reports/data-loss-landscape) - [Data Loss Landscape](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2024/Proofpoint-Data-Loss-Landscape-2024.pdf) (2024) - Provides an overview of the data loss landscape, including trends and challenges faced by organizations across various industries.
 - [Proofpoint](https://go.proofpoint.com/2024-Frost-Radar-for-Email-Security.html) - [Global Email Security Market Report](https://github.com/jacobdjwilson/awesome-annual-security-reports/blob/master/Annual%20Security%20Reports/2024/Proofpoint-Global-Email-Security-Market-Report-2024.pdf) (2024) - Benchmarks 21 top email security vendors, highlighting growth opportunities and market trends.
 

docs/awesome/awesome-for-beginners.md

@@ -294,6 +294,7 @@ If you would like to be guided through how to contribute to a repository on GitH
 - [Oppia](https://github.com/oppia/oppia) _(label: good first issue)_ <br> Oppia is an open-source project whose aim is to empower learners across the globe by providing access to high-quality, engaging education. We envision a society in which access to high-quality education is a human right rather than a privilege.
 - [opsdroid](https://github.com/opsdroid/opsdroid) _(label: good first issue)_ <br> An open source chat-ops bot framework.
 - [pandas](https://github.com/pandas-dev/pandas) _(label: good first issue)_ <br> Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
+- [PyMC](https://github.com/pymc-devs/pymc) _(label: beginner friendly)_ <br> A Python library for Bayesian statistical modeling and probabilistic machine learning. Beginner-friendly with 'good first issue' labels.
 - [Pytest](https://github.com/pytest-dev/pytest) _(label: status:-easy)_ <br> The pytest framework makes it easy to write small tests, yet scales to support complex functional testing.
 - [Python Babel](https://github.com/python-babel/babel) _(label: difficulty/low)_ <br> The Python Internationalization Library.
 - [pythonping](https://github.com/alessandromaggio/pythonping) _(label: good first issue)_ <br> PythonPing is a simple library to execute ICMP pings natively in Python without resorting to spawning a shell.

docs/awesome/awesome-go.md

@@ -550,6 +550,7 @@ _Data stores with expiring records, in-memory distributed data stores, or in-mem
 - [nscache](https://github.com/no-src/nscache) - A Go caching framework that supports multiple data source drivers.
 - [otter](https://github.com/maypok86/otter) - A high performance lockless cache for Go. Many times faster than Ristretto and friends.
 - [pocache](https://github.com/naughtygopher/pocache) - Pocache is a minimal cache package which focuses on a preemptive optimistic caching strategy.
+- [ristretto](https://github.com/dgraph-io/ristretto) -  A high performance memory-bound Go cache.
 - [sturdyc](https://github.com/viccon/sturdyc) - A caching library with advanced concurrency features designed to make I/O heavy applications robust and highly performant.
 - [theine](https://github.com/Yiling-J/theine-go) - High performance, near optimal in-memory cache with proactive TTL expiration and generics.
 - [timedmap](https://github.com/zekroTJA/timedmap) - Map with expiring key-value pairs.

docs/awesome/awesome-selfhosted.md

@@ -1414,6 +1414,7 @@ A [pastebin](https://en.wikipedia.org/wiki/Pastebin) is a type of online content
 - [FlashPaper](https://github.com/AndrewPaglusch/FlashPaper) - A one-time encrypted zero-knowledge password/secret sharing application focused on simplicity and security. No database or complicated set-up required. ([Demo](https://flashpaper.io)) `MIT` `Docker/PHP`
 - [Hemmelig](https://hemmelig.app) - Share encrypted secrets cross organizations, or as private persons. ([Source Code](https://github.com/HemmeligOrg/Hemmelig.app)) `MIT` `Docker/Nodejs`
 - [lesma](https://lesma.eu) - Simple paste app friendly with browser and command line. ([Demo](https://lesma.eu), [Source Code](https://gitlab.com/ogarcia/lesma)) `GPL-3.0` `Rust/Docker`
+- [not-th.re](https://not-th.re) - Simple paste sharing platform, with client side encryption, featuring the monaco browser-based code editor. ([Demo](https://not-th.re), [Source Code](https://github.com/not-three/main)) `AGPL-3.0` `Nodejs/Docker`
 - [Opengist](https://github.com/thomiceli/opengist) - Self-hosted pastebin powered by Git. ([Demo](https://demo.opengist.io)) `AGPL-3.0` `Docker/Go/Nodejs`
 - [paaster](https://paaster.io) - Paaster is a secure by default end-to-end encrypted pastebin built with the objective of simplicity. ([Source Code](https://github.com/WardPearce/paaster)) `GPL-3.0` `Docker`
 - [Password Pusher](https://pwpush.com) - A dead-simple application to securely communicate passwords (or text) over the web. Passwords automatically expire after a certain number of views and/or time has passed. ([Source Code](https://github.com/pglombardo/PasswordPusher)) `GPL-3.0` `Docker/K8S/Ruby`