Search: “dna”

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 · 8d agoAI research 2 sources

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 · 7d agoAI research

ICE Collecting DNA Samples

ICE's DNA collection program projects detainee samples to reach 33% of CODIS offender index by 2030, raising privacy concerns.

A Schneier on Security blog post discusses ICE collecting DNA samples from detainees, citing Georgetown Law research. DHS detainee samples are projected to constitute 33% of the FBI's CODIS offender index in 2030, up from 0.2% in 2019. The post raises concerns that samples collected under civil authority are being searched against crime scenes indefinitely, potentially without legal cause under Fourth Amendment standards.

Schneier on Security·Aug 19, 10:46 UTC · 28d agoPolicy & legal

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 · 7d agoAI research2

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 · 7d agoAI research

Google DeepMind Releases AlphaGenome Atlas

Google DeepMind released AlphaGenome Atlas, a 1-petabyte database pre-computing effects of all 9 billion single-nucleotide variants in the human genome, with a unified AVI score.

Google DeepMind launched AlphaGenome Atlas, a database that predicts the regulatory impact of every possible single nucleotide variant across the roughly 3 billion base pairs of the human genome, yielding a 1-petabyte dataset. It introduces the AlphaGenome Variant Impact (AVI) score, combining coding and non-coding predictions for rapid variant prioritization. Broad Institute researchers used it to support solving an unsolved rare disease case via a predicted DNM1 splice variant, and analysis of 54,000+ UK Biobank participants uncovered 22% more non-coding genetic associations, including 19 regions linked to BMI. The Atlas is available through a no-code web portal.

Hacker News · AI·Sep 8, 14:55 UTC · 8d agoAI researchHN 44↑ · 4 comments

AI Is Learning to Write Genetic Code

AI models generated viable bacteriophage genomes, with 16 designs successfully replicating and some outperforming the original virus at attacking E. coli.

Two AI models generated complete genome designs for bacteriophages modeled on ΦX174, a virus known to infect E. coli. Researchers produced about 700,000 candidate designs, selected 285 promising ones, and synthesized DNA inserted into E. coli, yielding 16 viable viruses. Some of the newly generated viruses proved more effective at attacking E. coli than the original bacteriophage.

Schneier on Security·Aug 21, 16:52 UTC · 26d agoAI research

Reduced-Space Multi-Fidelity Bayesian Optimization of Process Simulation Models

RS-MFBO couples global sensitivity analysis with fidelity-augmented Gaussian processes to slash costly high-fidelity simulation runs in industrial flowsheet optimization.

The paper presents RS-MFBO, a reduced-space multi-fidelity Bayesian optimization framework for high-dimensional, expensive black-box functions. It integrates Global Sensitivity Analysis for dimensionality reduction with a fidelity-augmented Gaussian process and a cost-aware acquisition strategy featuring cooldown and promotion mechanisms. Validation on a plasmid DNA bioprocess (SuperPro Designer) and a green fuel synthesis plant (Aspen HYSYS) shows substantial reductions in high-fidelity evaluations while remaining competitive with single-fidelity baselines.

arXiv cs.AI / cs.LG / cs.CL·Sep 15, 16:46 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 · 12d agoAI research1

Thermo Fisher Patches Flaw That Could Make DNA File Tampering Nearly Undetectable

The Hacker News·Aug 3, 08:05 UTC · Aug 3, 2026Vulnerability in the wildCVE-2026-17583

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 · 2d agoAI research1

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·Sep 10, 16:00 UTC · 6d agoAI industry1

Top 10 Best Enterprise Browsers in 2026

2026 enterprise browser guide ranks Island first and notes Mammoth Cyber's wind-down plus corrections to standard vendor shortlists.

An editorial guide assesses ten enterprise browser options, ranking category creator Island first for last-mile DLP and BYOD controls, followed by Palo Alto's Talon browser as a Prisma Access/SASE surface and Google Chrome Enterprise Premium for DLP on already-deployed browsers. It corrects common lists, noting SlashNext is browser-adjacent phishing and BEC defense rather than a managed browser, and that Mammoth Cyber has wound down independent operations. Microsoft Edge for Business is positioned as effectively free policy depth for Microsoft 365 estates, with Menlo Security offering an isolation-plus-browser blend.

Cyber Security News·Sep 11, 07:07 UTC · 5d agoIndustry1

Why the current tech backlash feels different

The Verge's Decoder mailbag discusses the current tech backlash, arguing AI hype overstates verifiability outside software engineering.

Nilay Patel's Decoder mailbag episode addresses listener feedback on the widely discussed 'software brain' essay. He argues AI hype is concentrated on software because code is verifiable through compilation, while domains like drug discovery, math and science lack equivalent verifiability. The episode also touches on AI backlash, surveillance, data centers and upcoming midterm coverage.

The Verge · AI·Sep 10, 14:00 UTC · 6d agoAI industry1

Can Edge-Deployable Vision-Language Models Identify Species?

Evaluation of 2-8B VLMs (Qwen3-VL, Gemma3) against BioCLIP on camera-trap species ID shows all models degrade sharply on field imagery.

The study tests whether edge-deployable 2-8B vision-language models carry genuine taxonomic knowledge, comparing Qwen3-VL 2B/4B/8B and Gemma3 4B against the 300M specialist BioCLIP on a 96-species task across clean iNaturalist photos and six LILA.science camera-trap collections. All models degrade 9.6-26.6 percentage points on field imagery, and BioCLIP outperforms every VLM by 33.2-59.2 points on an expanded 200-image sample, suggesting specialized data rather than scale drives the gap. Under open-set prompting, 5.9-9.6% of responses are syntactically valid but taxonomically nonexistent species names, with fabrication rankings replicating across evaluation sets.

arXiv cs.AI / cs.LG / cs.CL·Sep 10, 17:57 UTC · 5d agoAI research1

11 Best CSPM Tools Compared (2026): Features & Pricing

CSPM comparison ranks Wiz first for agentless attack-path analysis; notes Ermetic absorbed into Tenable and Lacework into Fortinet FortiCNAPP.

An editorial comparison of eleven CSPM tools ranks Wiz as the agentless attack-path momentum leader, Prisma Cloud as the breadth benchmark, and Orca as the agentless SideScanning pioneer. It highlights consolidation: Ermetic now powers Tenable Cloud Security and Lacework became Fortinet's FortiCNAPP. The guide recommends starting with free tiers from Defender for Cloud, Prowler, and native cloud tools before buying.

GBHackers·Sep 15, 06:37 UTC · 1d agoIndustry1

Characterizing Language Generation in the Limit: Finite Witnesses and a Separation-Width Hierarch

New work characterizes language generation in the limit via finite witnesses, proves a full separation-width hierarchy, and formalizes all results in Lean.

The paper fully characterizes when language generation in the limit is possible for arbitrary families over a countable universe: each target must admit a finite positive witness such that targets activated by any finite sample share an infinite common intersection. It defines positive separation width and proves every level of the resulting hierarchy occurs, with countable families admitting singleton witnesses and unions of families with infinite common cores requiring unbounded finite witnesses. The characterization, a universal normalization, and a diagonal capture lemma are machine-checked in the Lean proof assistant, with the development maintained on GitHub.

arXiv cs.AI / cs.LG / cs.CL·Sep 9, 17:54 UTC · 7d agoAI research1

Top 10 Best AWS Security Tools in 2026

Editorial roundup ranking the ten best AWS security tools of 2026, from native GuardDuty and Security Hub to CNAPPs like Wiz and Prisma Cloud.

The article recommends enabling AWS-native services first: GuardDuty for threat detection, Security Hub for posture aggregation, the free IAM Access Analyzer, plus CloudTrail logging and Config rules. It then reviews third-party platforms including Wiz, Palo Alto Prisma Cloud, CrowdStrike Falcon Cloud Security, Trend Micro Cloud One, and Orca Security. It is an editorial vendor assessment with pricing described by model only, highlighting cross-account correlation and attack-path prioritization as third-party differentiators.

Cyber Security News·09:57 UTC · 7h agoTools

Fly Language Model (FLM) Wires the Full Fruit Fly Connectome Into a Frozen 1.2B LLM, and Its Own Controls Show the Wiring Does Not Help

Researchers wire the full fruit fly connectome (166,700 nodes) into a frozen LiquidAI LFM2.5-1.2B LLM, but controls show no fly-specific benefit.

The Fly Language Model (FLM) couples the complete MaleCNS v1.0 fruit fly connectome (166,700 nodes, 25,582,938 edges) to a frozen LiquidAI LFM2.5-1.2B-Instruct backbone, training only a 278,528-parameter readout (~0.0238% of backbone parameters). The fly readout improved NLL by 0.0222 nats/token (perplexity 3.98 to 3.90) on 32 SmolTalk dialogues, but a direct-input control without the graph beat it in all three seeds. Relabeling node identities removes the gain and the recurrence contracts state differences by 0.6 per token, so the connectome adds no long-range memory. The MIT-licensed code runs locally on Python 3.12, but study artifacts remain private, limiting independent reproducibility.

MarkTechPost·Sep 12, 18:51 UTC · 3d agoAI research1

12 Best Browser Isolation Solutions Compared (2026): Features & Pricing

2026 comparison ranks Zscaler, Cloudflare, Menlo Security, Garrison (Everfox), Authentic8 and Kasm among twelve remote browser isolation solutions.

Guide compares twelve RBI products across four architectures: pixel streaming, DOM/vector reconstruction, platform-embedded SSE isolation, and self-hosted containers. Zscaler and Cloudflare lead RBI delivered inside SSE platforms, while Menlo Security leads isolate-everything efficacy and Garrison (Everfox) provides hardware-grade isolation for government use. Most offerings price per user per month.

GBHackers·Sep 15, 06:27 UTC · 1d agoTools

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 · 6d agoAI research1

Driver’s License Data for Sale

Schneier on Security highlights that driver's license data is being sold, underscoring concerns over monetization of driver records and surveillance.

A post on Bruce Schneier's blog is titled 'Driver's License Data for Sale.' The available excerpt contains no article body, so the specifics of the reported data sales are not detailed. The topic concerns the commercial availability of driver's license records, a recurring data-privacy and surveillance theme on the blog.

Schneier on Security·Sep 9, 16:05 UTC · 7d agoData breach

NOAH: Learning the Full Patient Journey. A Longitudinal Multimodal Time-Aware Model for Representation and Forecasting

Researchers introduce NOAH, a time-aware generative transformer trained on 559 million MIMIC clinical events to forecast multimodal patient trajectories.

NOAH is a task-agnostic, time-aware generative transformer trained on over 559 million clinical events from 431,000 hospital visits by 299,000 patients across the MIMIC dataset family. It uses bidirectional time integration and a variational latent space to model the stochastic evolution of patient states, natively processing medical images, time-series signals, categorical events, and structured or unstructured clinical records. The model supports autoregressive forecasting with optional time control, zero-shot classification, and counterfactual intervention simulation, with strong probing performance across clinical outcomes, 15 ICD chapters, and 29 comorbidities.

Hugging Face daily papers·Sep 7, 20:00 UTC · 8d agoAI research1

Mistral X Mozilla: Private, Multilingual AI Browsing

Mistral and Mozilla partnered to power Firefox's Smart Window AI browsing assistant in France and North America, with zero data retention.

Mozilla's Firefox Smart Window (beta) AI browsing assistant is now powered by Mistral models for users in France and North America, with the UK and Germany expected later this year. Conversations are not saved on Mozilla's servers by default, and Mistral agreed to zero data retention. Both companies frame the partnership as advancing open-source, privacy-first, and regionally fine-tuned AI, with models trained on regional languages, dialects, and cultural context.

Hacker News · security·updated 15:01 UTC · 2h ago·first 08:08 UTC · 9h agoAI industry 2 sourcesHN 35↑ · 8 comments

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 · 2d agoAI research

DavidAU/Qwen3.8-27B-TURBO-Fable-Cold-Fusion-735-882-Heretic-Uncensored-NEO-CODER-MAX-MTP-GGUF — new model trending #8 on Hugging Face

A new Qwen3.8-27B GGUF fine-tune claims ARC-C 735 at 8-bit with thinking tokens cut 2x-10x versus the base model.

Independent creator DavidAU released a GGUF fine-tune of Qwen3.8-27B built with Unsloth, claiming ARC-C of 735 at 8-bit and 719 at 4-bit, trending #8 on Hugging Face. The 'TURBO' variant cuts thinking tokens by one half to as much as one tenth while retaining output quality and detail. The repo ships both regular and MTP quants and claims gains over the base model across seven benchmarks, using 'Cold Fusion (GAIN + Unsloth)' and 'Fable Fusion 711' training methods.

Hugging Face trending models·Sep 1, 07:01 UTC · 15d agoModel release

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 · 10d agoAI research

Top 10 Best Endpoint Privilege Management (EPM) Tools in 2026

A 2026 scorecard ranks ten endpoint privilege management tools, led by BeyondTrust, ThreatLocker and Delinea for elevation, coverage and policy depth.

The article ranks ten endpoint privilege management (EPM) tools using weighted criteria covering elevation workflow, platform coverage, policy depth, time-to-value and value. BeyondTrust scored highest overall (8.4) for cross-platform breadth, with ThreatLocker (8.2), Delinea (8.1) and Admin By Request (8.0) highlighted for allowlisting integration, cloud administration and deployment speed respectively. It also notes that Netwrix acquired CoSoSys in 2024, which affects bundling when shortlisting both EPM and device control.

Cyber Security News·Sep 10, 07:58 UTC · 6d agoIndustry

NOAH: Learning the Full Patient Journey. A Longitudinal Multimodal Time-Aware Model for Representation and Forecasting

Researchers introduce NOAH, a generative time-aware transformer trained on 559 million MIMIC clinical events to model and forecast patient trajectories.

NOAH is a task-agnostic, time-aware generative transformer designed to represent and forecast the full multimodal patient journey across medical images, time-series signals, categorical events, and clinical text. It was trained on over 559 million clinical events from 431,000 hospital visits covering 299,000 patients in the MIMIC dataset family. The architecture combines bidirectional time integration with a variational latent space to capture continuous patient state evolution and clinical stochasticity. NOAH supports autoregressive forecasting with time control, zero-shot classification, and counterfactual intervention simulation, with evaluations on 15 ICD chapters, 29 comorbidities, and time-to-event prediction.

arXiv cs.AI / cs.LG / cs.CL·Sep 8, 17:56 UTC · 7d agoAI research2

12 Best CWPP Solutions Compared (2026): Features & Pricing

Editorial comparison ranks twelve CWPP vendors, with Sysdig leading K8s runtime depth, Prisma Cloud workload breadth, and Wiz agentless speed.

A 2026 buyer's guide compares twelve cloud workload protection platforms across features and pricing models. Sysdig is rated deepest for container/Kubernetes runtime via its Falco lineage, Prisma Cloud broadest across hosts, containers, and serverless, Aqua strongest on cloud-native lifecycle, and Wiz/CrowdStrike lead agentless speed and platform correlation. Category notes flag Illumio as microsegmentation and Fidelis as NDR/XDR rather than classic CWPP.

GBHackers·updated 09:52 UTC · 8h ago·first Sep 15, 06:43 UTC · 1d agoIndustry 14 sources

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 · 13d 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 · 8d agoResearch1

Canonical Color as a Lens into Concept Decodability in Vision Encoders and VLMs

Probing study shows vision encoders make canonical color linearly decodable from grayscale images and tie it to object identity.

Researchers use canonical color as a controlled testbed for measuring conceptual (not just visible) information in vision encoder representations. A dataset of objects with canonical colors was built, and probes on both color and grayscale images show canonical color remains decodable even when color is removed from the input, linked to predicted object identity. Extending to full VLMs, they find post-training has a surprisingly large effect on color decodability in the vision encoder.

arXiv cs.AI / cs.LG / cs.CL·Sep 8, 17:50 UTC · 8d agoAI research1

Decomposition Buys Integrity, Not Yield

Study of 600 production deep-research traces finds agent-tree decomposition loses findings at rate N^(1-δ); flat architectures maximize yield.

The paper models multi-agent decomposition as a tree where an agent holding b items retains each with probability r(b); with r(b)=1/b every tree delivers exactly one finding regardless of shape. Analysis of 600 production deep-research traces estimates delta=0.34 retention decay, and 1,012 annotated traces show one brief in sixteen goes off-target per tier, giving an alignment penalty of 0.536. Depth still cuts root context exposure from N to N^(1/k) and is cheaper at scale, with a hazard model over 743,819 production tool calls showing delegation is an opening move rather than a response to filling context.

arXiv cs.AI / cs.LG / cs.CL·Sep 15, 17:04 UTC · 1d agoAI research

StudyBench: Can Self-Evolution Squeeze Textbooks for Olympiad Capability?

Researchers introduce StudyBench, a physics benchmark showing self-evolution gains on textbook problems rarely transfer to olympiad-level questions.

StudyBench is a controlled physics benchmark splitting test data into an Application Set of difficult textbook problems and a Transfer Set of olympiad-level problems. Across three base models, representative self-evolution methods improved on the Application Set but rarely transferred to the harder Transfer Set. A guidance ablation reveals a Guidance Gap, and every method hits a Compute Plateau, indicating the remaining limits are method problems rather than data or compute problems.

Hugging Face daily papers·Aug 31, 20:00 UTC · 15d agoAI research

Revoked but Still Authoritative: An Empirical Study of Revocation Enforcement in Agent-Memory Systems

An empirical study finds no major agent-memory system enforces fact revocation at retrieval, causing agents to act on superseded, unsafe information.

Researchers tested five agent-memory systems across nine policy scenarios, nine models, and six defense conditions, tracking whether revoked facts are returned and acted upon. No system enforces revocation by default: revoked records are returned whenever the revocation label is visible to the retrieval layer, outrank their replacements, and lead agents to unsafe actions. The authors propose a backend-agnostic guard that sits between the agent and any memory store and withholds revoked or conflicting records at retrieval time.

arXiv cs.CR·Sep 8, 05:03 UTC · 8d agoAI safety & security

Embedded Graph Flows for Categorical Graph Generation

Researchers propose Embedded Graph Flows, a generative model with learned categorical embeddings that beats DiGress and GruM on molecular graph benchmarks.

Embedded Graph Flows (EGF) learns continuous embeddings for node and unordered-edge categories and transports Gaussian noise toward these endpoints using a permutation-equivariant graph transformer. On QM9 it achieves the best result on all four reported metrics, with a Fréchet ChemNet Distance of 0.150 versus 0.717 for DiGress and 0.812 for GruM. On ZINC250k it retains the lowest NSPDK MMD, indicating close agreement with local substructures of reference molecules. Code is released on GitHub.

arXiv cs.AI / cs.LG / cs.CL·Sep 4, 16:26 UTC · 12d agoAI research1

Large Language Models Develop Belief State Geometry In-Context

Probing six open-source LLMs on HMM-generated data shows belief states are linearly decodable (R² 0.83–0.99), suggesting in-context learning approximates Bayesian prediction.

Researchers prompted six open-source LLMs with data from 40 hidden Markov models selected for non-trivial belief structure and probed residual-stream activations for belief states (posteriors over hidden states). Belief states were linearly decodable with peak R² values of 0.83–0.99 across HMM/LLM combinations, spanning early to late layers. Patching and steering the probe-identified subspace preserved downstream prediction quality while control interventions degraded performance substantially, establishing functional relevance. The results provide representation-level evidence that in-context learning approximates optimal Bayesian prediction over a context-inferred generative model.

arXiv cs.AI / cs.LG / cs.CL·Sep 15, 16:17 UTC · 1d agoAI research

CausalArena: Benchmarking Causal Discovery in the Foundation Model Era

Researchers introduce CausalArena, a unified benchmark revealing that causal discovery rankings shift substantially across structural causal model families and protocols.

The paper presents CausalArena, a unified and evolvable benchmark for causal discovery combining synthetic structural causal models, semantically grounded operational SCMs, formula-grounded scientific SCMs, and public real-world datasets. Experiments across classical, neural, and pretrained causal discovery foundation models show large ranking shifts between benchmark regimes. The authors identify pretraining-evaluation overlap and benchmark diversity as central evaluation challenges.

arXiv cs.AI / cs.LG / cs.CL·Sep 10, 17:53 UTC · 6d agoAI research

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

LimiX-2 scales Contextual Mechanism Networks pretrained via context-conditional masked modeling, beating tabular foundation models on TabArena, TALENT, and BCCO benchmarks.

LimiX-2 is a new tabular model in the LimiX family, developed through model and data scaling guided by previously established scaling laws under the Contextual Mechanism Networks (CMNs) paradigm. It is pretrained with Context-Conditional Masked Modeling (CCMM) on synthetic datasets generated by structural causal models spanning diverse graph structures, functional mechanisms, and observation processes. It outperforms dataset-specific models and tabular foundation models on TabArena, TALENT, and BCCO, and its feature attention encodes direct causal relationships, enabling accurate causal skeleton recovery.

arXiv cs.AI / cs.LG / cs.CL·Sep 15, 17:30 UTC · 1d agoAI research1