Search: “Cytosol”

HypoEvolve: Genetic Algorithms Enable Multi-Agent LLMs to Discover Scientific Hypotheses

HypoEvolve couples a generational genetic algorithm with specialized LLM agents to generate drug-repurposing hypotheses, beating six baselines on DepMap selectivity (0.171 vs 0.115).

HypoEvolve coordinates specialized LLM agents through a generational genetic algorithm in which scientific judgments and new proposals reshape a hypothesis population. Evaluation centers on drug repurposing, linking mechanistic explanations to target-level biological claims assessed via external measures adapted from DepMap and Open Targets. Across 34 cancer types, HypoEvolve scores highest against six baselines on both measures, with DepMap selectivity of 0.171 versus 0.115 for the strongest baseline, and gains generalize to held-out cancer types.

arXiv cs.AI / cs.LG / cs.CL·Sep 14, 17:44 UTC · 3d agoAI research 2 sources1

AlphaGenome Atlas: A predictive map of every possible DNA letter change in the human genome

Google DeepMind released AlphaGenome Atlas, a free 1-petabyte platform predicting the molecular effects of all ~9 billion possible single-letter DNA variants.

Google DeepMind introduced AlphaGenome Atlas, containing precomputed predictions for the effects of roughly 9 billion single-nucleotide variants across the human genome, spanning hundreds of human and mouse cell types. The 1-petabyte dataset is more than 30 times larger than the AlphaFold Database and includes an AlphaGenome Variant Impact (AVI) score combining AlphaGenome and AlphaMissense predictions for both coding and non-coding regions. External collaborators have already used it to identify and experimentally verify variants in unsolved rare disease research. It is available via a free web portal, the AlphaGenome API, and as a skill in Google Antigravity.

Google DeepMind·Sep 8, 14:00 UTC · 10d agoAI research 2 sources

JEPA-Anything: Learning Predictive Models across Different Worlds

Researchers present JEPA-Anything, a domain-agnostic world-modeling framework improving prediction across vision, biology, control, molecular dynamics, and weather.

JEPA-Anything extends joint-embedding predictive architectures with orthogonal predictive factorization, decomposing latent targets into complementary factors learned through dedicated pathways. It was evaluated across seven domains, including 10 matched dynamics tasks, forecasting of over 1,000 clinical events, and 100-step molecular rollouts across four systems. Against matched JEPA baselines it improves metrics on all 10 dynamics tasks and cuts single-intervention prediction error on Interventional Pong by 34.8%. A factor-nominated biological intervention received experimental support in cell co-cultures, patient-derived organoids, tumor fragments, and mice.

Hugging Face daily papers·updated Sep 17, 17:55 UTC · 20h ago·first Sep 16, 20:00 UTC · 1d agoAI research 2 sources

LimiX-2: A Contextual Mechanism Network Towards General Structured-Data Intelligence

LimiX-2, a tabular foundation model built on Contextual Mechanism Networks, outperforms existing tabular models on TabArena, TALENT, and BCCO.

Researchers introduced LimiX-2, a new model in the LimiX family that adopts the Contextual Mechanism Networks (CMNs) paradigm and is pretrained with Context-Conditional Masked Modeling (CCMM) on synthetic datasets generated by structural causal models. Unlike tabular PFNs centered on p(y | x, D_context), CMNs learn mechanism-oriented joint modeling of p(x, y | D_context). Evaluations on TabArena, TALENT, and BCCO show LimiX-2 outperforms current dataset-specific models and tabular foundation models. Its feature attention also encodes direct causal relationships, enabling accurate causal skeleton recovery.

Hugging Face daily papers·updated Sep 15, 17:30 UTC · 2d ago·first Sep 14, 20:00 UTC · 3d agoAI research 2 sources

Evidence-Grounded Agentic Formulation Development in an Autonomous Laboratory

Andromeda 2, an agentic laboratory system, reaches a 50% high-performance hit rate for paclitaxel SEDDS formulations versus 17% for its predecessor and 2% for DoE.

Andromeda 2 is an agentic system that reasons over structured in-house experimental evidence and invokes computational and experimental tools to design and execute successive formulation batches for self-emulsifying drug delivery systems (SEDDS). For paclitaxel it achieved a 50% high-performance hit rate versus 17% for Andromeda 1 and 2% for a wet-lab DoE campaign, identifying 12 formulations meeting all four target product profile objectives versus 6 and 0. A selected full-TPP formulation reached approximately 19% w/w apparent paclitaxel loading, about 3.3-fold higher than a published paclitaxel S-SEDDS, and an ablation showed structured evidence access increased mean AUC by 34%.

arXiv cs.AI / cs.LG / cs.CL·Sep 16, 17:31 UTC · 1d agoAI research

Molecular Déjà Vu: Digit-Level Retrieval of Published Values in Frontier Language Models

Audit of 22 frontier models finds widespread verbatim retrieval of published molecular property values, with higher reasoning increasing recall of memorized numbers.

An arXiv audit tests 22 frontier LLMs across 12 molecular regression benchmarks for verbatim retrieval of published values. More than 50% of the LLMs show verbatim retrieval on five datasets, and identical experiments are flagged 89% more often at a high reasoning level than at the lowest one. Suppressing retrieval moves model prediction errors closer together in relative terms, suggesting predictive capability is not determined solely by memorized values.

arXiv cs.AI / cs.LG / cs.CL·Sep 4, 17:32 UTC · 13d agoAI research1

ERCPMP-Gx: Endoscopic Image and Video Dataset for Morphological, Histopathological, and Genomic Characterization of Colorectal Polyposis

Researchers release ERCPMP-Gx, a 160-image endoscopic dataset linking colorectal polyposis imagery with histopathology and germline findings for AI development.

The ERCPMP-GX dataset provides 160 endoscopic images and video clips captured mainly with the Olympus EVIS X1 system in white-light, NBI, and magnifying NBI modes. Roughly 80% of cases are confirmed hereditary polyposis syndromes such as FAP, PJS, JPS, and ganglioneuroma syndrome, with the remainder being non-hereditary mimics for differential classification. Records are linked to standardized endoscopic annotations, histopathology, and germline findings, and the dataset is publicly available on Mendeley.

arXiv cs.AI / cs.LG / cs.CL·Sep 17, 17:59 UTC · 20h agoAI research

Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens

Researchers release AssayBench-Loop, a 1,389-screen CRISPR benchmark, and AssayLoop, a framework that learns adaptive hit discovery policies.

The paper introduces AssayBench-Loop, a large-scale benchmark of 1,389 CRISPR screens across five phenotype categories for adaptive hit discovery under budget constraints. It also introduces AssayLoop, which combines AssayFormer, a transformer-based amortized acquisition policy trained across historical screens, with LLM-derived biological priors via an adaptive handoff. On temporally held-out screens, AssayLoop achieves 5.67-fold enrichment over random selection and recovers 27.7% of hits after assaying roughly 5% of the candidate library, outperforming existing adaptive-design methods and standalone LLMs.

arXiv cs.AI / cs.LG / cs.CL·Sep 10, 17:45 UTC · 7d agoAI research1

Google's AI genome system evaluates every possible one-base change

Google's AlphaGenome AI system predicts functional effects of non-coding DNA variants in humans and mice.

Google's AlphaGenome AI system evaluates genomic sequences to predict gene expression, transcription factor binding, chromatin accessibility, splice site usage, and related genomic features. The system is currently limited to human and mouse sequences and a limited set of well-studied cell types, but its predictions generally match or exceed specialized software tools. Researchers can use it to assess whether non-coding variants are likely significant and generate hypotheses about their function.

Ars Technica · AI·Sep 9, 16:34 UTC · 8d agoAI research

The 2026 PNPL Competition: Word Classification and Efficient Cross-Subject Generalisation in LibriBrain100

The 2026 PNPL competition releases LibriBrain100, a MEG speech dataset with 32 extra subjects, targeting word classification and cross-subject BCI generalization.

The 2025 PNPL competition on non-invasive speech decoding from MEG achieved F1-macro scores of 95.6% for speech detection and 73.6% for phoneme classification, built on LibriBrain's ~50 hours of single-subject data. The 2026 edition extends this with LibriBrain100, adding 32 subjects (~40 minutes each) plus ~80 hours of within-subject data. Two tracks target within-subject word classification at scale and cross-subject generalization with subject-specific fine-tuning shrinking from ~40 to ~20 to ~10 minutes, aiming at clinically feasible non-invasive BCIs for people with profound paralysis.

Hugging Face daily papers·Sep 2, 20:00 UTC · 15d agoAI research

Deepmind's AlphaGenome Atlas maps every possible DNA change in the human genome

DeepMind's AlphaGenome Atlas precomputes impact predictions for ~9 billion human DNA variants in a 1-petabyte dataset; its AVI score beats CADD in benchmarks

Google DeepMind released the AlphaGenome Atlas, precomputing functional-effect predictions for roughly 9 billion human genome variants (about 27,000 prediction values per variant) in a one-petabyte dataset more than 30 times the size of the AlphaFold database. The accompanying AlphaGenome Variant Impact Score (AVI), a small neural network combining AlphaGenome, AlphaMissense and evolutionary conservation features (18 inputs versus CADD's 150+), outperformed existing tools on clinically classified variants, ranking causal variants in the top 50 candidates for 29.5% of solved GREGoR cases versus 12.5% for CADD. A GREGoR epilepsy case illustrates the impact: AVI elevated a previously unclear DNM1 splice variant that lab experiments confirmed as likely disease-causing. The atlas is available for noncommercial use via web portal, API and a Google Antigravity skill, with a commercial version planned through Google Cloud.

The Decoder·Sep 9, 13:40 UTC · 9d agoAI research1

Google DeepMind Releases AlphaGenome Atlas With Precomputed Molecular Effect Predictions and AVI Scores for 9 Billion Human DNA Variants

Google DeepMind launched AlphaGenome Atlas, precomputing molecular effect predictions and AVI impact scores for ~9 billion human single-nucleotide variants in a 1-petabyte catalogue.

Google DeepMind released AlphaGenome Atlas, a 1-petabyte catalogue of precomputed molecular effect predictions for roughly 9 billion possible single-nucleotide variants in the human genome. It introduces the AlphaGenome Variant Impact (AVI) score, combining AlphaGenome regulatory predictions with AlphaMissense, plus per-variant feature attributions and over 2,500 recurrent DNA sequence motifs. DeepMind reports best-in-class AVI performance on variant pathogenicity and rare disease benchmarks. Early users at the Broad Institute, University of Exeter, and Stowers Institute demonstrated rare-disease variant reprioritization and 22% more non-coding associations across 54,000+ UK Biobank genomes.

MarkTechPost·Sep 8, 19:00 UTC · 9d agoAI research2

'TerminalFix' Campaign Weaponizes PowerShell for Enterprise Attacks

A ClickFix-style campaign called TerminalFix weaponizes PowerShell and reverse tunnels to infiltrate enterprise networks in a multistage attack chain.

Dark Reading reports on the TerminalFix campaign, a sophisticated multistage attack targeting enterprises. It uses a ClickFix-style social engineering lure and heavily weaponizes PowerShell. The chain establishes reverse tunnels into victim organizations' networks, giving operators interactive access for follow-on activity.

Dark Reading·Aug 31, 20:25 UTC · 17d agoThreat actor in the wild

DianShi-RxnDB: A Large-Scale, Fine-Grained Organic Reaction Data Platform Built via a Fully Automated Pipeline for Researchers and AI Agents

Researchers release DianShi-RxnDB, a database of roughly 24 million organic reaction instances extracted automatically from USPTO and EPO patents since 1976.

DianShi-RxnDB is built by a fully automated pipeline integrating patent text, images, and reaction schemes, yielding about 24 million reaction instances, of which 14.8 million (61.7%) pass automated qualification checks. Manual evaluation of 1,300 sampled instances showed 92.95% field-level accuracy, and comparisons with Pistachio found advantages in deduplicated record counts and granularity. The platform offers a web research workbench and a Model Context Protocol (MCP) service enabling AI agents to perform composable structured retrieval.

Hugging Face daily papers·Sep 5, 20:00 UTC · 12d agoAI research1

iceener/files-stdio-mcp-server: sandbox escape in fs_search via a symlinked directory (recursive walker validates only the top level)

iceener/files-stdio-mcp-server allows a read-side sandbox escape: fs_search follows symlinked directories while the recursive walker validates confinement only at the top level.

A vulnerability report describes a read-side sandbox escape in iceener/files-stdio-mcp-server, an MCP server for text-based file access that explicitly promises 'Sandboxed filesystem access. Only these paths are available'. The fs_search tool can follow symlinked directories outside the allowed paths, and the recursive directory-listing walker used by fs_search (and by fs_read) validates confinement only at the top level. The same flaw affects fs_read's directory-listing walker. No CVE identifier was assigned in the provided report text.

oss-security·Sep 10, 01:17 UTC · 8d agoVulnerability

Chainloop: Open-source evidence store and policy engine for the software supply chain

Help Net Security·Aug 10, 00:00 UTC · Aug 10, 2026Policy & legal1

Assessing nnU-Net Generalization across Brain Tumor Populations in BraTS-GoAT 2026

A 3D nnU-Net trained on 1,351 BraTS-GoAT 2026 cases shows mean Dice dropping 0.0747 from out-of-fold to pooled validation, exposing generalization gaps.

Researchers trained a conventional 3D nnU-Net on 1,351 labeled brain tumor cases with five-fold cross-validation and 1,000 epochs per fold, averaging folds with test-time mirroring for the final predictor. On pooled official validation, global Dice scores were 0.7805 for enhancing tumor, 0.8288 for tumor core, and 0.8854 for whole tumor. Under matched fold-0 inference, mean regional Dice fell from 0.9058 on source out-of-fold cases to 0.8310 on pooled validation, and failures correlated with smaller and more disconnected enhancing tumor components rather than volume alone.

Hugging Face daily papers·Sep 13, 20:00 UTC · 4d agoAI research1

Harm Laundering in GPT Models: Evidence That Gender Discrimination Is Transformed Rather Than Reduced Across Safety-Trained Generations

Study of 450,000 GPT-lineage completions finds safety training transforms gender discrimination into subtle 'harm laundering' that toxicity classifiers miss.

The paper analyzes 450,000 gender-directed completions across 15 OpenAI GPT-lineage models from GPT-2 to GPT-5 under three demographic conditions. Sexual-violence clusters in GPT-2 women-directed output disappear by GPT-4, but men-directed completions gain positive representational territory women-directed output lacks, and a GPT-5 cluster (1,997 documents) frames breast cancer as a men's rights debate while three independent classifiers score it non-toxic. Women-directed topic diversity falls 36% at the GPT-4 alignment boundary (W/M=0.58 from 0.91), and representational harm disparity correlates with release date (rho=+0.55) while Detoxify toxicity does not. The authors formalize a three-criteria harm-laundering test and a three-stage detection protocol, arguing toxicity score reduction is an insufficient proxy for harm reduction.

arXiv cs.AI / cs.LG / cs.CL·Sep 17, 17:49 UTC · 20h agoAI safety & security

LongAgent: History-Guided Agentic Search for Longitudinal Outcome Prediction

LongAgent autonomously searches variable sets and temporal windows to predict longitudinal medical outcomes, beating the strongest non-agent baseline on synthetic data.

The paper proposes LongAgent, an agent-based method that searches over combinations of variable sets, temporal windows and aggregation functions for outcome prediction on heterogeneous medical longitudinal data. It uses a history memory of previous searches and numerical evidence to guide exploration. On synthetic data it achieves mean RMSE 1.7376, improving over the best non-agent baseline by 0.0151 (95% CI [0.0045, 0.0260]; p=0.0273), and performs comparably to the best baseline on a real clinical dataset.

arXiv cs.AI / cs.LG / cs.CL·Sep 14, 16:51 UTC · 3d agoAI research

Testing race conditions with memory access tracing and stack-based delay injection

Google Project Zero released MAccConc, Linux kernel tooling that traces memory accesses to explore and test race condition interleavings.

A Google Project Zero researcher published MAccConc (Memory Access Concurrency), tooling for exploring possible interleavings of multithreaded test cases in the Linux kernel, available on GitHub. The tools use KCOV with ASAN outline-mode instrumentation to record per-access memory traces, enabling automatic testing of all A-B-A interleavings plus terminal and GUI explorers for manual analysis. The work targets confirming race condition candidates, building reliable regression tests, and enabling concurrency fuzzing, drawing on ideas from SKI and Ned Williamson's sockfuzzer.

Google Project Zero·Sep 8, 07:00 UTC · 10d agoResearch2

AI-designed drug appears to turn back the body's biological clock in early trial

Insilico Medicine's AI-designed drug rentosertib showed reduced predicted biological age in IPF trial blood analysis, published in Nature Biotechnology.

Insilico Medicine reported that rentosertib, an AI-designed drug candidate in Phase III trials for idiopathic pulmonary fibrosis, showed reduced predicted biological age in blood protein analysis of 42 trial patients. Six independent aging-clock models built by teams at Harvard, Oxford, Beijing, and Insilico all predicted lower biological age versus placebo, with drops of three to four years by week 4 and up to six years on one clock. The drug targets TNIK and was developed with two generative AI systems in about 18 months; Eli Lilly recently invested in the company. Experts including Eric Topol and Harvard's Vadim Gladyshev called the results encouraging but not definitive, citing small sample size.

The Decoder·Sep 7, 16:34 UTC · 10d agoAI industry

PEEP: A Browser RAT Posing as a Chrome Extension

SOCRadar's STRU analyzed PEEP, an emerging Chromium-based RAT disguised as a Chrome extension enabling post-exploitation control of browsers.

SOCRadar's Threat Research Unit (STRU) identified and analyzed PEEP, a Chromium-based post-exploitation toolkit distributed as a browser extension. PEEP provides RAT-style capabilities while posing as a legitimate Chrome extension. It is assessed as an emerging threat worth monitoring by defenders.

SOCRadar·Sep 4, 09:50 UTC · 14d agoMalware

[0day-rubbish] core-admin 1.0.164 (build 16468) Systemic shell command injection via ineffective quote escaping (8.8)

0day Rubbish discloses a CVSS 8.8 shell command injection in core-admin 1.0.164 via ineffective quote escaping, enabling authenticated remote code execution.

0day Rubbish Research Team publicly disclosed a systemic shell command injection (CWE-78) in core-admin 1.0.164 (build 16468). The flaw stems from ineffective quote escaping and scores 8.8 (AV:N/AC:L/PR:L/UI:N/S:U/C:H/I:H/A:H). The disclosure does not mention a CVE identifier or observed exploitation in the wild.

Full Disclosure·Sep 8, 17:31 UTC · 9d agoVulnerability1

NVIDIA Details BioNeMo Inference Runtime (BioIR): 2.90x Higher Boltz-2 Folding Throughput and 58.5K Residues per GPU-Hour on 8xH100

NVIDIA released BioNeMo Inference Runtime (BioIR), an open-source PyTorch-compatible library delivering 2.90x higher Boltz-2 protein-folding throughput on 8xH100 GPUs.

NVIDIA detailed BioIR, a Python library that accelerates Boltz-2, OpenFold2, and OpenFold3 structure-prediction inference on NVIDIA GPUs while preserving standard PyTorch workflows. On a matched benchmark of 1,000 human dimers on 8xH100 80GB GPUs, BioIR delivered 58.5K folded residues per GPU-hour versus 20.2K for a torch.compile baseline, a 2.90x throughput gain. BioIR already powered the AlphaFold Database expansion, generating about 31 million candidate complexes across 4,777 proteomes, with 1.81 million released as high-confidence predictions. Extrapolated to 1 million targets, estimated folding energy drops from 35 MWh to 11 MWh at 8-GPU TDP equivalents.

MarkTechPost·Sep 10, 21:57 UTC · 7d agoAI tools & infra1

PEEP Turns Chrome and Edge Into Post-Compromise Backdoors for Host Command Execution

SOCRadar disclosed PEEP, a post-exploitation Chromium extension toolkit that turns Chrome and Edge into host-level backdoors via native messaging and C2 polling.

SOCRadar researchers detailed PEEP, a Chromium-based post-exploitation toolkit masquerading as a 'Smart Bookmarks' extension injected directly into Chrome and Edge profiles by forging Secure Preferences integrity values, bypassing Web Store checks. A native-messaging host binary (nm_host.exe) extends the browser agent to host-level command execution, file management, credential theft, and session hijacking, while the extension polls C2 endpoints at 206.237.30.232 or xfjcc.fun every 30 seconds over plaintext HTTP and exfiltrates browsing history, cookies, and tab metadata. PEEP is derived from the open-source RedExt red teaming framework, adds PowerShell persistence scripts, and includes a Linux-targeting Python script, suggesting cross-platform intent. The activity is unattributed but contains Chinese-language artifacts; a C2 /health endpoint showed 34 agent entries and 10 active sessions.

The Hacker News·Sep 7, 18:12 UTC · 10d agoMalware in the wild1

Sandworm-Linked Cyclops Blink Returns With Network Scanning and Packet-Sniffing Capabilities

Sophos uncovers a 64-bit Cyclops Blink variant on hacked Cisco FMC appliances, adding internal network scanning and selective packet capture; linked to Sandworm.

Sophos CTU analyzed a new 64-bit x86-64 Cyclops Blink implant (timezone_check) deployed on Cisco Secure Firewall Management Center appliances compromised via CVE-2026-20079 authentication bypass and CVE-2026-20316 low-privileged login. The activity is assessed with high confidence as Russian-nexus, with a moderate-confidence link to Sandworm (IRON VIKING, also tracked as Seashell Blizzard). The implant runs a parent controller plus five worker modules, masquerades as [kworker/0:1], persists via SysV init scripts at /lib/tz/timezone_check, and beacons to hard-coded C2 89.34.96.56 over a custom TLS protocol on ports 43856 and 49172. New module 0x11 scans internal IPv4 networks for SSH, SMB, LDAP, VMware, HTTP/HTTPS and VPN services, while module 0x12 performs filtered packet capture that can expose cleartext credentials, cookies and tokens.

GBHackers·Sep 14, 09:27 UTC · 4d agoMalware in the wildCVE-2026-20079CVE-2026-203161