Search: “AlphaFold Database”

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

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 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 · 8d agoAI research2

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 · 5d agoAI tools & infra1

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·Sep 15, 16:00 UTC · 1d agoAI industry

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

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·Sep 15, 16:59 UTC · 1d agoAI research

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

Toolkit Hidden Inside Oracle Database Evades Endpoint Tools

Infosecurity Magazine·Aug 6, 15:30 UTC · Aug 6, 2026Vulnerability

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

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·Sep 14, 13:59 UTC · 2d agoAI industryHN 41↑ · 13 comments1

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·Aug 26, 00:00 UTC · 21d agoAI tools & infra1

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·Sep 8, 20:00 UTC · 8d agoAI research1

Update modules/auxiliary/scanner/http/elasticsearch_tika_xfa_xxe.rb

Rapid7 updated a Metasploit auxiliary scanner module that detects XML external entity injection in Elasticsearch via Apache Tika.

A commit in the Metasploit Framework updated modules/auxiliary/scanner/http/elasticsearch_tika_xfa_xxe.rb, an auxiliary scanner module. The module targets XML external entity (XXE) injection in Elasticsearch through Apache Tika, and was co-authored by jheysel-r7. The terse commit message contains no additional details, CVE references, or exploitation notes.

Metasploit Framework commits·Sep 8, 19:22 UTC · 8d agoTools

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·Sep 10, 17:43 UTC · 6d agoAI research

Towards Scalable and Cost-Efficient Vulnerability Detection: A Study on Automatic Query Generation

A study finds LLM-synthesized CodeQL queries improve average F1-score by 82% over baseline queries, offering scalable vulnerability detection versus direct LLM scanning.

Researchers conducted an empirical study evaluating whether LLMs can synthesize executable CodeQL queries from National Vulnerability Database vulnerability data. LLM-generated queries significantly enhanced baseline CodeQL suites, yielding an 82% improvement in average F1-score across a diverse set of real-world vulnerabilities. A cost-benefit analysis shows direct LLM-based scanning of entire repositories is often computationally and financially prohibitive, while LLM query synthesis offers a scalable and cost-effective alternative for large-scale vulnerability detection.

arXiv cs.CR·Sep 9, 16:31 UTC · 7d agoResearch1

Akamai Valkey Managed Database: Real-Time Memory for Enterprise AI

Akamai launched Valkey Managed Database, a low-latency in-memory data layer aimed at cutting AI inference costs and accelerating RAG.

Akamai introduced Valkey Managed Database, a managed in-memory data service based on the open-source Valkey project. The company positions it as real-time memory for enterprise AI, optimizing inference costs, accelerating retrieval-augmented generation, and powering real-time AI agents.

Akamai Blog·Aug 18, 13:00 UTC · 29d agoAI tools & infra

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·Aug 18, 00:00 UTC · 29d agoAI tools & infra1

Everything in Moderation: Per-Domain Coverage Optima and Alignment-Resistant Domain Gaps in Multi-Domain Mid-Training

Controlled mid-training experiments on Qwen3-8B-Base find each domain has a 10-40% coverage optimum and domain gaps survive alignment SFT.

Using Qwen3-8B-Base (with a 4B replication) across five semantically rule-disjoint KOR-Bench domains, the authors train 30 data allocations spanning the five-domain simplex at five seeds each. All five domains show interior optima in the moderate 10-40% coverage band, and domain gaps persist after a fixed-budget compensatory SFT pass, which raises 116/120 cells yet bridges 0/240 pairs at a 5% threshold. Zero coverage collapses mid-training-only accuracy, though a FineWeb-Edu-only control shows the collapse is partly generic drift. The results argue mid-training data composition requires principled design rather than reliance on later alignment.

arXiv cs.AI / cs.LG / cs.CL·Sep 8, 17:31 UTC · 8d agoAI research1

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·Sep 15, 17:42 UTC · 1d agoAI research

Anchoring Clinical Events in Time: UID-Preserving Multimodal Reconstruction and Source-Grounded Adjudication

UID-preserving multimodal framework plus GAVEL LLM judge improves clinical timeline reconstruction, boosting event recovery 43% over prior matching.

The paper introduces a UID-preserving framework linking each narrative clinical event to its source span through text-only estimation, structured-evidence retrieval, timestamped source-row grounding, and joint revision. GAVEL, an LLM judge, compares UID-aligned timelines against narrative and structured records. Across six open-weight models and 40 mixed-critical-care summaries, GLM 5.2 multimodal revision improved temporal agreement without reducing event recovery and performed competitively with clinician annotations, while DeepSeek V3.2 did not benefit from multimodality. The pipeline achieves 43% increased event recovery with occurrence-level provenance.

arXiv cs.AI / cs.LG / cs.CL·Sep 11, 17:01 UTC · 5d agoAI research1

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·Sep 10, 17:29 UTC · 6d agoAI research1

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 · 11d agoAI research

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, 16:14 UTC · Aug 12, 2026AI tools & infra

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 · 14d agoAI research

Reference-Based Bias Detection in LLMs via Relative Representations of Hidden States

Researchers propose auditing LLM bias via relative hidden-state representations, detecting bias increases with 3-50x less compute than output-level benchmarks.

The paper introduces a reference-based bias auditing method that compares hidden-state representations across model variants, such as before and after fine-tuning, by encoding sentences relative to a fixed anchor set. The resulting Representational Bias Shift (Delta-B) correlates with output-level bias change in 15 of 18 tested settings, reaching |r| = 0.84 under full fine-tuning across WildGuardMix, DecodingTrust, and ToxiGen benchmarks. Thresholding Delta-B detects checkpoints whose bias increased with ROC AUC between 0.65 and 0.99 and beats a SEAT-based baseline, while auditing a model in about three minutes with 3-50x less compute.

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

Think Before You Link: Rarity, Reasoning, and Retrieval in Multilingual Entity Linking

Training-free reasoning-plus-retrieval framework lifts multilingual multimodal entity linking accuracy by 6.9% overall and up to 23.3% on rare entities.

The paper broadens rarity measurement in multimodal entity linking using knowledge-graph structural metrics beyond popularity-based pageview metrics, identifying many rare entities that popularity metrics miss. Across these rare-entity slices, state-of-the-art accuracy drops by 15.4-39.9%, exposing distinct failure modes under different rarity definitions. The proposed training-free framework iteratively searches and reasons over Wikipedia with a reasoning-capable vision-language model; experiments show reasoning and retrieval are complementary. On the MERLIN benchmark covering Hindi, Indonesian, Japanese, Tamil, and Vietnamese, the system improves overall accuracy by 6.9% and up to 23.3% on rare entities, with MERLIN-Rare test slices released.

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

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 · 9d 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·Sep 8, 11:15 UTC · 8d agoMalware in the wild