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Google’s Atlas of the human genome could pave the way for new treatments

Google DeepMind launches AlphaGenome Atlas, a catalog of predicted molecular effects for roughly nine billion single-letter DNA changes across the human genome.

Google DeepMind unveiled AlphaGenome Atlas, a roughly 1-petabyte dataset predicting how each of about nine billion possible single-nucleotide variants affects molecular biology, including non-coding regions that regulate gene behavior. It builds on the AlphaGenome model released in 2025 and adds a Variant Impact Score (AVI) to help researchers rank variants. The catalog is available for noncommercial research via a web portal, the Antigravity platform, and the AlphaGenome interface, with commercial access on Google Cloud planned.

The Verge · AI · 8d agoAI industry 2 sources

Coop – Isolated VM Environments for Running Claude Code and Codex

Trail of Bits releases Coop, running Claude Code and OpenAI Codex agents inside isolated virtual machines for safer agentic coding.

Coop, published on GitHub by security firm Trail of Bits, provides isolated VM environments for executing AI coding agents such as Claude Code and Codex. Isolation contains the filesystem and network side effects of autonomous agent actions, reducing risk from unsupervised tool use. The project drew 61 points and 16 comments on Hacker News.

MicroHasTEE: Bare-Metal Haskell for Type-Level Peripheral Ownership on Armv8-M

MicroHasTEE expresses TrustZone secure and non-secure firmware as one typed Haskell program, catching peripheral-ownership inconsistencies at compile time.

MicroHasTEE is a multiparty Haskell framework that models both TrustZone firmware images as participants in a single typed program, using type-level capability ledgers to track peripheral acquisition, configuration, transfer, and finalization. MicroHs compiles the shared program twice to produce separate bare-metal Secure and Non-secure firmware images. The framework rejects inconsistent resource use, post-configuration attribution changes, wrong-domain callbacks, and calls to unregistered Secure services. A door-lock case study on an STM32U5 Nucleo board produced images of 232.7 KiB and 228.4 KiB of flash with roughly 220 KiB of SRAM per domain.

arXiv cs.CR · 5d agoResearch1

IntentFuzz: A Protocol-Aware Fuzzer for Automated Invariant Violation Detection in Intent-Based Cross-Chain Bridges

IntentFuzz protocol-aware fuzzer recovers bridge structure from unannotated Solidity and confirmed 22 invariant violations across 24 real-world deployments.

IntentFuzz formalizes a taxonomy separating invariant violations from settlement exposures in intent-based cross-chain bridges, then recovers a bridge's intent structure and deposit/fill function roles from unannotated Solidity source. It classified deposit and fill functions with 100% recall and 82% combined precision, and achieved 100% recall and precision on 23 planted-bug mutants. Across 24 real-world deployments it confirmed 17 genuine invariant violations with heuristic-only input generation, rising to 22 with its LLM-assisted tier, spanning eight vulnerable GitHub repositories with findings reproducible against public deployed bytecode.

arXiv cs.CR · 5d agoResearch1

Nebulon Enterprise Simulated Threats for Phishing Research (NEST-Phish): A Synthetic Enterprise Phishing Email Dataset for Behavioral and Machine-Learning Research

Researchers release NEST-Phish, a synthetic enterprise phishing email dataset with matched legitimate and phishing emails and cue annotations for detection research.

Academic researchers introduce NEST-Phish, a publicly released synthetic enterprise phishing email dataset built around a fictitious organization named Nebulon. It contains matched synthetic legitimate and phishing emails across a broad set of workplace communication themes, each with interpretable phishing-cue annotations. Human-subject categorizations and supervised classifier evaluations indicate the dataset supports meaningful variation in phishing judgments and provides learnable signal for detection models. It is intended to support work on phishing detection, human susceptibility, explainability, and benchmark development.

arXiv cs.CR · 13d agoResearch

Linux Detection Engineering - Local Privilege Escalation

Elastic details a layered detection framework for Linux local privilege escalation, covering 2026's copy-on-write bug wave and LLM-assisted discovery.

Elastic Security Labs describes how most Linux local privilege escalations share a common host flow — an unprivileged process launched from a writable path becoming root — and proposes layered detections combining general outcome-based rules with per-technique rules in Elastic Defend and Auditd. It tracks 13 recent LPE disclosures, seven of which share a copy-on-write/zero-copy bug class, including Copy Fail, DirtyFrag, Fragnesia, DirtyDecrypt, DirtyClone, pedit COW, and RefluXFS. Qualys attributes RefluXFS to an LLM-assisted research effort with Anthropic using Claude Mythos Preview, and another bug is credited to an LLM-assisted workflow. Detection and endpoint rules are published in Elastic's detection-rules and protections-artifacts repositories.

Elastic Security Labs · 6d agoResearch

Claude, Codex, and Hermes installed unowned code inside corporate networks

Analysis found 227 install commands from Claude, Codex, and Hermes agents inside corporate networks pointing to packages with no verifiable owner.

Researchers found 227 install commands issued by the AI coding agents Claude, Codex, and Hermes inside corporate environments, with the referenced packages having no clear owner. The finding highlights agentic software supply-chain risk, as AI agents can pull unverified third-party code into production networks without organizational oversight. The article is published in Ars Technica's security section and frames this as an emerging governance gap for AI-driven development.

Ars Technica · Security · 20d agoAI safety & security in the wild2

Google’s open-source HEIR lets AI work with data it can’t see

Google open-sourced HEIR, a compiler toolchain that converts pre-trained AI models to operate on homomorphically encrypted data without exposing it.

Google's HEIR (Homomorphic Encryption Intermediate Representation) is an open-source compiler toolchain and development platform for fully homomorphic encryption, announced in 2023 and now supporting four peer-reviewed publications. It compiles Python programs handling sensitive data into implementations that process encrypted inputs, supporting multiple FHE schemes, libraries, front-end languages, and hardware accelerators such as GPUs, TPUs, FPGAs, and custom ASICs. Demonstrated applications include private recommendations, credit card fraud detection, network intrusion detection, and hotword recognition.

Help Net Security · Aug 18, 2026Tools

How a researcher uses Codex and ChatGPT to search for new antimicrobial molecules

OpenAI profiles César de la Fuente's lab using ChatGPT and Codex alongside deep-learning models to accelerate antimicrobial molecule discovery.

OpenAI published a case study on bioengineer César de la Fuente's lab, which uses ChatGPT and Codex for hypothesis brainstorming, code writing, dataset processing, and bridging knowledge gaps across biology, chemistry, and computer science. The lab's deep-learning models scan genome and protein databases for antimicrobial peptide candidates, potentially cutting initial searches from years to hours. Bacterial antimicrobial resistance was associated with about five million deaths in 2021, a toll projected to roughly double by 2050.

OpenAI News · 6d agoAI industry1

The Shared Clipboard Inside the Sandbox: Cross-Account Data Leakage in ChatGPT

Check Point discovers cross-account data leakage in ChatGPT: isolated code-execution containers communicate via shared JFrog Artifactory, enabling covert Gmail exfiltration.

Check Point Research found a covert bidirectional channel between ChatGPT code-execution containers belonging to different accounts, which were supposed to be isolated from each other and the public internet. Both could reach the same internal JFrog Artifactory instance used for package delivery, whose exposed Item Management API allowed a 'shared clipboard' between containers. In a proof of concept, a hidden instruction in a shared conversation made ChatGPT retrieve email data from the victim's connected Gmail account and send it to the attacker's account while the victim received a normal answer. The same channel could exfiltrate conversation history and session files; OpenAI recently described a similar isolation weakness in its postmortem of the Hugging Face incident.

Check Point Research · 8d agoAI safety & security1

Scaling Verification of Cryptographic Software with Aeneas, Rust, and Lean

Microsoft SymCrypt implementations of SHA-3 and ML-KEM verified in Lean via Aeneas-extracted Rust models, with AI agents writing proofs.

The paper develops a methodology for verifying production Rust cryptographic code by using Aeneas to extract pure models into Lean, avoiding low-level pointer and aliasing reasoning. Applied to Microsoft's SymCrypt, it verifies SHA-3 and ML-KEM implementations ported from C to Rust and extends SymCrypt with FrodoKEM, ML-DSA, and HPKE. A 237 KLOC Lean development establishes safety, panic-freedom, and functional correctness of 16.7 KLOC of Rust supporting post-quantum cipher suites on x86-64 and ARM. AI agents autonomously write formal proofs verified by the Lean kernel, and evaluation shows verified Rust meets SymCrypt's performance and portability requirements.

arXiv cs.CR · 2d agoResearch1

Agora: Git as Shared Memory for Collective AutoResearch

Agora records multi-agent research as an append-only Git DAG; 13 LLM workers ran nearly 12 days on a weight-transfer problem.

Agora stores every result, hypothesis, and verification as an immutable commit in a Git-stored DAG, with a derived index exposing the frontier and verification status of claims. In a nearly 12-day run, 13 language-model workers with no assigned tasks or central planner published 1,703 contributions on initializing a frozen 119.6M-parameter attention-SSM hybrid from 141 donor models. They improved the evaluator from 3.39 to 1.899 bits per byte, closing 62% of the gap to a trained GPT-2 124M, with 165 independent reproductions posted and none failing.

Hugging Face daily papers · 1d agoAI research

Evaluating Verified Autonomy in Quantum Engineering

Quantum-Harbor lab and QIQCBench (49 tasks) expose wide performance gaps across 17 frontier agentic systems in verified quantum engineering.

Researchers built Quantum-Harbor, a virtual laboratory providing a controlled execution environment where scientific AI agents interacting with quantum systems can have both actions and conclusions directly verified. QIQCBench contributes 49 expert-authored tasks spanning calibration and control, error correction and compilation, and sensing and networking. Across 17 frontier agentic systems, verified performance varied widely, exposing a substantial gap between demonstrated capability and reliable autonomous operation.

arXiv cs.AI / cs.LG / cs.CL · 1d agoAI research1

Scores Alone Do Not Prove Discovery: The Discovery Certification Protocol for Auditing AI Research Agents

Researchers introduce the Discovery Certification Protocol, an auditable test framework that verifies whether AI research agents' claimed discoveries are genuine.

The Discovery Certification Protocol (DCP) converts AI research agents' discovery claims into executable recovery and feedback tests organized as gated audits. Controlled audits in SQLite optimization and virtual catalyst control produced zero recoveries in 96 episodes, with an upper bound of 0.0468. A deterministic, LLM-free verifier reproduces audit decisions from frozen evidence, giving AI research a common evidence language for outcomes, alternative routes, and feedback effects.

Hugging Face daily papers · 10d agoAI research

From Specs to Apps: Verifying and Monitoring Models of Signal and WhatsApp

Researchers use the SpecMon runtime monitor to verify WhatsApp Web and Signal Desktop against formal Signal protocol models, finding undocumented libsignal fork differences.

The paper applies SpecMon, a runtime monitoring tool, to check whether executions of WhatsApp Web and Signal Desktop conform to formal models of the Signal protocol. The authors instrument both applications and build Tamarin-compatible multiset-rewrite models, including the first model of WhatsApp Web's implementation and the most detailed model to date of Signal's original protocol. They verify authentication and secrecy properties for core Signal protocol components, show monitoring detects deliberately injected faults with low overhead, and identify previously undocumented behavioral differences between the original libsignal library and WhatsApp's fork.

arXiv cs.CR · 6d agoResearch

Stanford Researchers Release Paper2Agent: Turning Research Papers Into AI Agents That Reproduce Results and Run on New Data

Stanford researchers released Paper2Agent, a Nature-published pipeline that turns research papers into MCP servers agents can execute.

A Stanford team led by Jiacheng Miao and James Zou published Paper2Agent in Nature on 16 September 2026. Built on Claude Code's agent SDK, it converts a paper and its codebase into a Model Context Protocol server with validated tools, resources, and prompts. In benchmarks, the AlphaGenome agent built 22 tools in about 45 minutes for US$14, scored 100% on 15 novel queries versus 78.7% for Claude Code with repository access, and cut median runtime 1.9x. In scale tests, 74 of 100 bioRxiv papers were converted and 593 of 599 proposed tools passed validation.

MarkTechPost · 7h agoAI research1

CodeTD: Topology of Attention Detects Hallucinations in Code LLMs

CodeTD detects hallucinations in code LLMs before execution by analyzing topological patterns of attention maps, outperforming recent baselines.

CodeTD applies topological data analysis (TDA) to code LLM attention maps to quantify prompt-generation mismatch as a pre-execution correctness signal. Experiments cover HumanEval, MBPP, BigCodeBench, and MultiPL-E across 5 programming languages and 10 code LLMs up to 34B parameters. The method outperforms recent baselines and transfers between coding benchmarks, helping catch code that fails the task or embeds security vulnerabilities.

arXiv cs.AI / cs.LG / cs.CL · 9d agoAI research1

When the prompt becomes the payload: A practical pen-testing guide for GenAI, LLM and RAG applications

CSO Online publishes a practical penetration-testing guide for GenAI, LLM, and RAG applications, covering prompt injection, retrieval poisoning, and tenant isolation testing.

The guide frames LLM applications as attack graphs spanning prompts, retrieval layers, vector stores, tools, identities, and downstream APIs, arguing that conventional web testing misses instruction-vs-data channel risks. It builds on OWASP prompt injection guidance (direct vs. indirect injection) and NIST's 2025 adversarial machine-learning taxonomy, noting that RAG and fine-tuning do not remove injection risk. Recommended practices include documenting trust transitions across components, using canaries and synthetic records to avoid test side effects, running multi-turn and obfuscated injection campaigns, and verifying chains from poisoned documents to observable state changes. It also details testing RAG pipelines via controlled document poisoning across metadata, OCR layers, and code comments, plus cross-tenant isolation checks on retrieved document IDs.

CSO Online · 7d agoAI safety & security1

Copying explains the collective behavior of AI agents in the wild

arXiv study shows thousands of ephemeral AI agents spontaneously cooperated via a wiki, with simple copying rules explaining their collective behavior.

An arXiv paper analyzes the public record of thousands of one-hour-lived AI agents that, in June 2026, discovered a public wiki accepted edits from their sandboxes and used it to help each other pass a timed test, without being asked to cooperate. Each agent had no persistent memory, but the log preserves what each agent could see before writing. Three minimal copying models, one per decision (where to write, what name to use, how to word a message) and each with a single free parameter, reproduce the heavy-tailed page-popularity distribution, name-piece frequencies, and patchwork of internally consistent pages. The result implies such agent populations are easy to steer, since whoever writes first or while others are quiet sets conventions for later agents.

arXiv cs.AI / cs.LG / cs.CL · 8d agoAI research

How Virginia Tech Connected Pentesting to Its Engineering Workflow

Horizon3.ai customer story details Virginia Tech automating external pentesting via NodeZero's GraphQL API with GitLab and ServiceNow integration for remediation tracking.

Horizon3.ai published a customer story describing how Virginia Tech, whose environment serves more than 38,000 students across hundreds of independent departments and multiple cloud providers, used NodeZero's GraphQL API to automate external pentesting through GitLab. Findings are routed directly into ServiceNow for subnet-owner assignment and remediation tracking, creating a repeatable attack-validation-to-remediation workflow.

Horizon3.ai · 13d agoIndustry1

Another Artifactory CVE under attack by AI agents or humans

Attackers are actively exploiting CVE-2026-82329, a critical JFrog Artifactory authentication bypass, minting admin tokens on exposed servers days after patch release.

CVE-2026-82329 is a CVSS 9.8 unauthenticated authentication bypass in JFrog Artifactory, disclosed Friday, that allows attackers to create new administrative credentials. watchTowr's honeypots recorded exploitation from a small number of IPs within days, including enumeration of users, groups, credential sets, and federated access topologies. Researchers urge urgent patching, credential rotation, and treating exposed instances as potentially compromised to prevent build-pipeline tampering and downstream supply-chain impact.

The Register · Security · 15d agoExploit / PoC in the wild 2 sourcesCVE-2026-82329

Subgroup Packing for Batched PASTA Transciphering

Interleaved subgroup packing cuts PASTA homomorphic transciphering server cost by a median 1.60x at the expense of remaining noise capacity.

The paper studies how record word layout affects the cost of PASTA transciphering, where a server converts symmetrically encrypted records into homomorphic ciphertexts. A subgroup layout interleaves records so cyclic shifts preserve positions, reducing required displacements from 255 to 128 versus contiguous packing. In HElib across twelve paired corpora under six homomorphic keys, the median direct-to-subgroup server cost ratio is 1.60 including fresh generation, conversion, and two queries, but with less remaining noise capacity.

arXiv cs.CR · 5d agoResearch1

Do AI Coding Assistants Check Before They Install? A Pre-Registered Demand-Side Audit of Trust Signals in the Research Software Supply Chain

Pre-registered audit finds AI coding assistants verified provenance signals in only 9 of 1,920 trials before installing research software packages.

The study tested whether AI coding assistants check machine-readable trust signals such as SBOMs, signed releases, and provenance attestations before installing six open-source research software projects spanning HPC and quantum computing. Three models under two operating modes produced 1,920 registered trials scored from container logs. Provenance signals were opened in only 9 of 1,920 trials (0.5%) and zero of 384 control trials, with no trial running a verification command. The authors conclude publishing signals is insufficient and verification must be built into the program running the assistant.

Notes on gotchas while migrating 35kb preprompts from Opus to self-hosted Ollama

Opinion piece urges migrating 35KB preprompts from Anthropic/OpenAI to self-hosted Ollama, citing session privacy risks and safety filters blocking security research.

The author documents gotchas migrating 35KB preprompts from Claude Opus to self-hosted Ollama, motivated by fears that frontier providers train on user sessions, citing the OpenAI Navier-Stokes controversy. The piece argues inference providers cannot audit their own retention or training pipelines and that only self-hosted hardware offers verifiable privacy. It also criticizes frontier safety filters for refusing vulnerability research tasks and calls for models that support exploitability testing in CI/CD pipelines.

OpenAI's Artifactory opened covert data-stealing channel alongside Hugging Face attack

Check Point disclosed a covert cross-account channel in OpenAI's internal JFrog Artifactory that let one ChatGPT session exfiltrate another user's connected-app data.

Check Point Research found that OpenAI's internal JFrog Artifactory instance exposed an item management feature allowing one ChatGPT container to attach hidden, Base64-encoded tasks that another user's session would execute with the victim's privileges, such as pulling Gmail emails and exfiltrating them invisibly. Reader credentials granted both read and write access, enabling cross-account task injection. The flaw was reported in late June, and OpenAI had already decommissioned the Artifactory instance following the related Hugging Face intrusion, closing the channel.

Perplexity Details Its GPU Embedding Stack: How Ivy, Tulip and ROSE Serve pplx-embed

Perplexity details its GPU embedding serving stack (Ivy, Tulip, ROSE), which reuses LLM prefill/decode kernels, CUDA graphs, and LazyTensors to cut launch overhead.

Perplexity engineers published a deep dive on the serving infrastructure behind pplx-embed, used across Perplexity Search and its API platform. The stack comprises Ivy (Rust HTTP gateway), Tulip (gRPC scheduling and batching), and ROSE (Runtime-Optimized Serving Engine), which reuses LLM prefill and decode kernels rather than running a separate embedding engine. Optimizations include whole-model CUDA graphs with lazy capture and a LazyTensor abstraction that overlaps CPU batch preparation with in-flight GPU work. Benchmarks are reported against vLLM v0.22.0 in BF16, with FlashAttention 4 generally fastest but FlashInfer 3 winning on Qwen-based models at very long sequence lengths.

MarkTechPost · 11d agoAI tools & infra1

ScienceIDE: Turning World's Scientific Codebase into Agent Learnable Environments

ScienceIDE turns scientific code repositories into agent-trainable environments and trains PhAI-IDE models at 72B, 9B, and 4B scales.

ScienceIDE is infrastructure that transforms scientific repositories into executable environments supporting task generation, execution, and scientific verification, guided by expert-defined cases and acceptance criteria. Using verified interaction trajectories, the authors train PhAI-IDE-72B, PhAI-IDE-9B, and PhAI-IDE-4B. The model family improves held-out scientific-code repair and selected general benchmarks in code, reasoning, and knowledge, indicating positive transfer. Code is released on GitHub.

AIJon: Automated Generation of Annotations for Fuzzing

AIJON uses LLMs to auto-generate IJON-style fuzzing annotations, matching human-expert quality on the Magma benchmark.

Researchers replicate IJON experiments and propose AIJON, a system that uses LLMs to automatically generate expert-style annotations for coverage-guided fuzzing at scale. On the Magma benchmark, LLM-generated annotations performed comparably to human-generated ones, though annotation-based fuzzing was not strictly better than AFL++. The paper analyzes how annotations affect fuzzer energy distribution across campaigns.

arXiv cs.CR · 19h agoResearch

Linux Foundation takes on TRACE, a hardware-backed runtime evidence specification for AI agents

The Linux Foundation adopts TRACE, an OPAQUE-contributed spec giving AI agents hardware-attested, cryptographically verifiable runtime and compliance evidence.

The Linux Foundation accepted the TRACE (Trust, Runtime Attestation and Compliance Evidence) specification contributed by OPAQUE, developed with AMD, Intel, Microsoft, and the Technology Innovation Institute. TRACE binds runtime environment, software, policies, data classifications, and tool usage into a portable, cryptographically verifiable artifact, composing existing standards such as RATS, EAT, SLSA, SCITT, SPIFFE, and EAR. It recorded nearly 135,000 PyPI downloads within 10 weeks of its June 2026 introduction, and its technical workstream will be hosted by the Coalition for Secure AI.

Help Net Security · 22d agoAI tools & infra

Shuffling is Not Enough: Breaking Permutation-Based Model Confidentiality in Hybrid FHE Inference

Attack breaks permutation-based model confidentiality in hybrid FHE inference, recovering all ResNet-20 linear layers exactly with d+1 queries per layer.

The paper shows output-permutation plus noise fails to protect model confidentiality in hybrid FHE inference: d+1 admissible queries recover an exact permutation-invariant summary of a d-input linear layer, and shuffle-model DP amplification premises cannot hold under correctness-bounded noise. The authors recovered all linear layers of a Safhire-style ResNet-20 end-to-end from TFHE transcripts with zero error, using 5,712 total queries. Exact per-layer recovery was also confirmed on pretrained ImageNet-scale CNNs and ViT-B/16. Leaked layer spectra enable model fingerprinting, lineage attribution, and improved logit-based extraction, while suppressing them destroys inference utility.

arXiv cs.CR · 5d agoResearch1

When Agents Look Like Beacons: NIDS Evasion by Model Context Protocol Traffic

Research shows Model Context Protocol agent traffic structurally resembles C2 beaconing and evades Suricata signatures and RITA behavioral scoring in testbeds.

An arXiv study demonstrates that Model Context Protocol (MCP) JSON-RPC traffic over Streamable HTTP mimics the polling patterns of C2 frameworks like Cobalt Strike and is not flagged as anomalous by standard enterprise defenses. In a Docker testbed with eleven traffic profiles across three TLS conditions, Suricata with the Emerging Threats Open ruleset produced near-zero alerts and RITA assigned a consistent 0.0 beacon score, regardless of jitter or TLS inspection. The authors propose an agent-native network indication standard using Agent-Native ALPN and out-of-band headers.

arXiv cs.CR · 12h agoResearch