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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 · 7d agoAI research 2 sources

Building AI to accelerate science and improve lives

Google highlights AI-for-science advances: AlphaGenome Atlas mapping 9 billion genetic variants, WeatherNext 3 weather model, and global health AI tools.

Google detailed AI advances across science and health, including AlphaGenome Atlas, which mapped all 9 billion possible single-letter genetic changes in the human genome and was made openly available. WeatherNext 3 delivers 50% more accurate precipitation forecasts a day or more ahead and is already in products. AlphaFold is used by 4 million researchers in 190 countries, TB chest X-ray screening has processed 25,000+ scans across six nations, and the diabetic retinopathy model has supported 1.15 million screenings. Google also released its AI & Economy ATLAS global usage insights.

Google · AI · 21h agoAI industry

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 · 5d agoAI tools & infra1

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 · 7d agoAI research

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 · 7d agoAI research2

Augustinian BabyLM: What Ostensive Definition Can and Cannot Teach a Small Language Model

Study shows visually grounded token embeddings in a small masked LM persist through training and improve object-property knowledge, but escape standard BabyLM benchmarks.

The paper implements ostensive definition for a small DeBERTa masked language model trained on 10M words, seeding visually grounded tokens with embeddings derived from labeled image regions before training. Visual initialization leaves a persistent, seed-replicated advantage on object-property knowledge (COMPS) and a corpus-tailored Visual-Property Swap benchmark covering color, material, size, and shape, but has no effect on most BabyLM grammar benchmarks. Synthetic grounding of previously unseeded words causally transfers the advantage to exactly those words.

arXiv cs.AI / cs.LG / cs.CL · 5d agoAI research

Tables Decoded: DELTA for Structure, TARQA for Understanding

DELTA extracts tables into compact OTSL text and TARQA fine-tunes LLMs on it, beating VLM baselines on table QA.

DELTA separates physical structure recognition, logical structure recognition, and OCR to output tables in Optimised Table Structure Language (OTSL), a compact unified format encoding cell arrangements and content. It achieves TEDS-Structure scores comparable to state-of-the-art methods across FinTabNet, PubTabNet, and PubTables-1M, with robustness tested on a curated Hindi benchmark, TORQUE. TARQA, an LLM fine-tuned on OTSL sequences, gains 9.3 percentage points on WTQ TabQA and 9.2 points on FinTabNetQA TabVQA; code, models, and the benchmark are released on GitHub.

arXiv cs.AI / cs.LG / cs.CL · 20h agoAI research

Technical Manual for a Toolkit for Measuring Contextual Individuation in Transformer Language Models

An open methodology toolkit measures whether transformer language models contextualize fixed word forms across domains using bridge forms and layer-wise silhouette analysis.

The manual documents an open toolkit built around 'bridge forms' - identical written words recurring across two or more subject domains with a different sense in each - to test whether transformer language models individuate word occurrences by context beyond the embedding layer. It covers declarative specification of bridge forms, Wikipedia corpus acquisition, occurrence localization, layer-wise representation extraction, domain-pairwise silhouette measurement, and visualization, justifying each choice against failure modes such as sense contamination and subword-tokenization misalignment. It is a methodological and implementation reference and reports no empirical results.

arXiv cs.AI / cs.LG / cs.CL · 11d agoAI research

ENCP: Episode-Normalized Conformal Prediction for Vision-and-Language Navigation

ENCP calibrates conformal prediction per navigation episode, giving step-level coverage guarantees for vision-language navigation agents despite within-episode dependence.

Episode-Normalized Conformal Prediction (ENCP) rescales a nonconformity score by a VLN policy's residual confidence and calibrates one maximum score per episode, preserving step-level coverage of at least 1−α despite dependence among steps within an episode. Across four VLN policies and three nonconformity scores on R2R and REVERIE, ENCP meets all reported empirical step-coverage targets in seen-to-unseen evaluation. The model-agnostic uncertainty estimates can signal when an agent should defer to a stronger predictor or human assistance.

arXiv cs.AI / cs.LG / cs.CL · 20h agoAI research

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 · 5d agoResearch

UniH^3: Unifying Hierarchical Homogeneity and Heterogeneity for All-in-One Medical Image Restoration

UniH3 unifies hierarchical homogeneity and heterogeneity modeling for all-in-one medical image restoration across modalities and degradation types.

UniH3 introduces a Hierarchical Homogeneity Memory module that distills shared anatomical priors from high-quality images, injected via a Homogeneity-Guided Attention mechanism. A Hierarchical Heterogeneity Balancer mitigates inter- and intra-task conflicts during multi-task optimization. It achieves state-of-the-art on MedIR-2D-500K and MedIR-3D-3D benchmarks for both all-in-one and single-task restoration, with code released on GitHub.

Hugging Face daily papers · 6d agoAI research

NCP-ArchPreview Technical Report: Moving towards Latent Space Language Models through Next Concept Prediction

An 8.9B-parameter latent-space language model using next-concept prediction matches OLMo-3-7B pretraining loss with only 51.3% of the training tokens.

NCP-ArchPreview augments next-token prediction with Next Concept Prediction over a product-quantized concept vocabulary built from hidden states, trained jointly end-to-end. The 8.9B model was trained on 5.73T tokens from the Dolma-3 dataset, the largest latent-space language model demonstration to date. It consumes 51.3% of the tokens to reach OLMo-3-7B's final pretraining loss and outperforms it by 2.45 points on the downstream macro-average, including a 5.99-point GSM8K gain. The learned latent space also enables lightweight domain adaptation via a 17M-parameter VQ module and improves speculative drafting accepted length by 4.17%.

Hugging Face daily papers · 7d agoAI research1

Introducing OlmoEarth embeddings: Custom embedding exports from OlmoEarth Studio for downstream analysis

AllenAI's OlmoEarth Studio adds custom embedding exports to support downstream geospatial analysis workflows.

A Hugging Face blog post from AllenAI introduces OlmoEarth embeddings, a feature allowing custom embedding exports from OlmoEarth Studio for downstream analysis tasks. Only the title was available, so no benchmark or performance details are provided. OlmoEarth is Ai2's open geospatial AI model family.

Hugging Face Blog · Aug 12, 2026AI tools & infra

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.

Hacker News · AI · 1d agoAI industryHN 41↑ · 13 comments1

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 · 7d agoAI researchHN 44↑ · 4 comments

Target leakage, not model class, explains reported accuracy in survey-based cardiovascular screening: a leakage-tiered audit of glass-box and tabular foundation models

Audits of 10 classifiers on BRFSS show target leakage, not model class, drives the reported 0.89 AUROC in survey-based cardiovascular screening.

The study benchmarks ten model classes, including glass-box and tabular foundation models, for prevalent myocardial infarction on 442,067 respondents of the 2022 BRFSS across five feature tiers of decreasing leakage risk. Removing two post-diagnostic features costs every model 0.049-0.051 AUROC and collapses performance into a 0.0045-wide band, and the explainable boosting machine matches all alternatives within 0.005 while scoring roughly 104x faster than the strongest foundation model. Frozen models transport within 0.002 AUROC to 2023 data; the authors conclude evaluation practice and feature sets, not model capacity, are the binding constraint.

arXiv cs.AI / cs.LG / cs.CL · 5d agoAI research1

THost9 Android RAT Pairs Packed Loader With ADB Worm

Dark Atlas details THost9, a packed Android RAT paired with an ADB worm that installs itself on devices with exposed Android Debug Bridge services.

Dark Atlas researchers described the Hagaseca cluster, whose THost9 packed loader hides executable code in an embedded asset decoded with single-byte XOR and gzip before loading a tc9.dex second stage. The second stage adds shell execution, file transfer, tunneling, reverse shells, downloadable modules and a self-propagating ADB worm that expands single addresses into 65,025-host scan ranges. Newer builds include anti-analysis checks for Frida, and incident reports connect THost9 and THost4 to Android phones and Redroid containers with exposed ADB from October 2024 through 2026.

Infosecurity Magazine · 8d agoMalware in the wild

Multi-Vector (Late Interaction) Embedding Models with Sentence Transformers

Hugging Face details building and using multi-vector late-interaction embedding models with Sentence Transformers for retrieval workloads.

Hugging Face published a guide on multi-vector, late-interaction embedding models (ColBERT-style) supported through Sentence Transformers. The post covers how practitioners can build and use these models for retrieval and RAG pipelines. It is a developer tooling and technique write-up, not a security advisory.

Hugging Face Blog · 29d agoAI tools & infra1

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 · 6d agoAI research

Right Tool, Right Job: Native-Language Evaluation, Tokenizer Sensitivity, and Methodological Findings from a French-Only BabyLM

French BabyLM entry METRON-FR (125M GPT-2, 92.47M words) shows tokenizer artifacts dominate child-scale zero-shot evaluation; proposes standard diagnostics.

METRON-FR is a 125M-parameter GPT-2 pretrained on 92.47M French words, submitted to the BabyLM 2026 Strict track, scoring 85.97% on the native Quebec-French QFrBLiMP benchmark and 62.80% on the BabyLM-weighted leaderboard. A cross-lingual GLUE protocol combining French task-data translation with rank-16 LoRA shows relational tasks gain while world-knowledge tasks regress. Bilingual Lexicon Induction reaches p@1 of 68.84%, 18x above chance, and ablations show single-token zero-shot scoring is dominated by tokenizer and template artifacts at child scale.

arXiv cs.AI / cs.LG / cs.CL · 21h agoAI research

Building a Production Greek-English Speech Recognizer

Engineering report details Sophea, a production Greek-English ASR reaching 4.26% WER on public English sets via ROVER ensemble and data-pipeline calibration.

Across 23 training iterations, two architectures, and nine production gates, no single data composition passed all gates; a three-model ROVER ensemble reached 9 of 9 gates and cut overlapping-speech WER from 53.35% to 37.87%. Calibrating an audio-quality filter against in-domain anchors reduced discarded scored Greek audio from 98.7% to 10.6%, and a pre-registered ablation traced a hallucination defect to one training-data package. The sophea/asr-k1 preview arbiter lists 4.26% average WER on eight public English test sets and 25.88% WER on live Greek noisy traffic; no weights or training data are released.

Hugging Face daily papers · 5d agoAI research

HoneyRoute: Honeypot-Model Routing for Adversarial LLM Serving

HoneyRoute detects malicious LLM serving requests and diverts them to a honeypot model, reaching F1 0.911 with 38 ms median added latency.

HoneyRoute is an inference-serving layer pairing a streaming router (a frozen 0.8B embedding backbone with per-domain MLP heads) with a dual-implementation honeypot and an analysis loop that converts trapped interactions into attacker fingerprints for router retraining. On a production trace plus a seven-domain attack corpus it matches 96% of a two-tier guard-LLM cascade's F1 at 1/385th of its latency with 0% evasion under 13 adversarial transformations. Diverting malicious traffic cuts production token consumption under GCG-suffix flooding by 97.8%, and loop training raises detection F1 to 0.933.

arXiv cs.CR · 8d agoAI safety & security

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 · 10d agoAI tools & infra1

MAxBench: A Multinomial Concept Recovery Benchmark

MAxBench evaluates multinomial concept recovery methods, finding affine subspaces steer most reliably but none consistently beats prompting.

MAxBench is a geometry-agnostic evaluation framework for multinomial concept representations in language models, based on sampling from recovered concept representations. It compares 10 localization methods covering 5 geometry types across 6 concepts and 4 models. Findings show affine subspaces steer more reliably than rank-one or linear subspaces due to better non-zero offsets, manifold steering is competitive where applicable, and no method consistently outperforms prompting.

arXiv cs.AI / cs.LG / cs.CL · 4d agoAI research

MOONWALK: Mediating Operations with Intent-Evidence-Action Alignment Across Junior-Supervisor Review Workflows in Animation/VFX Pre-Production

MOONWALK introduces an intent-evidence-action alignment workflow for animation/VFX reviews where AI handles administrative coordination while artists keep creative authority.

MOONWALK is a pre-production review system that articulates creative intent into a shared project record, anchors review judgments to grounded evidence, and converts authorized decisions into concrete revision tasks. AI components handle administrative coordination such as flagging missing context and organizing notes, not creative direction. An in-studio study against a chat-only AI interface showed stronger intent alignment, decision traceability, and checklist executability.

arXiv cs.AI / cs.LG / cs.CL · 6d agoAI research

Training and Finetuning Multi-Vector Embedding Models with Sentence Transformers

Hugging Face published a tutorial on training and finetuning multi-vector embedding models using the Sentence Transformers library.

Hugging Face's blog walks through training and finetuning multi-vector embedding models with Sentence Transformers. Multi-vector approaches store multiple vectors per document to support late-interaction retrieval. The post is a practical guide for developers building retrieval pipelines with the library.

Hugging Face Blog · 21d agoAI tools & infra1

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 · 11d agoAI research1

VDiff-Bench: A Challenging Benchmark for Fine-Grained Image Difference Identification

VDiff-Bench, a 1,756-question benchmark, shows multimodal LLMs struggle with fine-grained image-difference identification, scoring as low as 8.7% on low-level changes.

VDiff-Bench is a multiple-choice benchmark of 1,756 four-way questions over image pairs covering 10 change categories including position, motion, color, texture, OCR/text and illumination, with curated hard negatives. Evaluation of 11 state-of-the-art open- and closed-source MLLMs shows fine-grained visual comparison remains brittle: 7-8B-scale open-source models score 52.5-70.6% on semantic changes but only 8.7-33.3% on low-level changes like noise and texture. Notably, Grok 4.3 shows a sharp performance drop on noise and texture differences, falling behind large open-source models like Kimi K2.5 and K3.

Hugging Face daily papers · 11d agoAI research