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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 · 8d agoAI research 2 sources

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.

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 · 8d 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 · 7d agoAI research

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 · 1d agoAI industry

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 · 7d agoAI research

ISTA-DASLab/Qwen3.8-27B-GSQ-RCO-GGUF — new model trending #3 on Hugging Face

ISTA-DASLab releases GSQ-RCO non-uniform GGUF quantizations of Qwen3.8-27B down to 2.5 bpw, with task-lossless IQ3_S matching BF16 benchmark scores.

ISTA-DASLab released GGUF quantizations of Qwen3.8-27B produced with GSQ (Gumbel-Softmax Quantization) and RCO (Riemannian Constrained Optimization), non-uniform methods that allocate per-tensor precision via gradient-based search under a total size budget. Four checkpoints range from 2.50 bpw (8.4 GB) to 3.50 bpw (11.8 GB), plus a BF16 vision projector (mmproj) enabling multimodal use. The recommended IQ3_S build is task-lossless, matching the BF16 base exactly on AIME25 (100.00) and LiveCodeBench v6 (85.71) at roughly one fifth of the BF16 size. Optional -mtp variants add a Multi-Token Prediction head for speculative decoding in llama.cpp.

Hugging Face trending models · 19d agoModel release1

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

XHToken/Spark-X2.5-4B-GGUF — new model trending #30 on Hugging Face

XHToken released GGUF weights of Spark-X2.5-4B, a compact model with 1M-token context and 200+ language support, under Apache 2.0.

The Hugging Face repository provides BF16 GGUF conversions of Spark-X2.5-4B, a compact general-purpose language model for conversation, writing, translation, reasoning, coding, tool use, and agentic workflows. The model uses a hybrid attention architecture, supports a native context length up to 1M tokens, and covers more than 200 languages. Local inference is supported through Ollama and LM Studio via an XHToken llama.cpp fork, with a --think=false flag to disable thinking mode for faster responses. Released under Apache License 2.0; it was trending #30 on Hugging Face at publication.

Hugging Face trending models · 19d agoModel release

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 · 6d agoAI tools & infra1

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 · 2d agoAI research1

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 · 12d agoAI research1

Atlas: Efficient Verifiable Semantic Search

Atlas delivers zero-knowledge proofs for HNSW semantic search, verifying RAG retrieval in under a second on SIFT1M and 2.0 seconds at 100M vectors.

Atlas lets a search provider prove that a query was answered correctly against a committed HNSW index without revealing the index, addressing provider deviations like truncation or bias. It combines offline preprocessing, a fixed-size-state restructuring of HNSW with a correctness proof, and timestep-tagged batching of per-step arguments. The system proves queries in under a second on SIFT1M and 2.0 seconds at 100 million vectors while preserving plaintext HNSW recall, and proven retrieval maintains end-to-end RAG answer quality at lower cost than prior verifiable retrieval systems.

arXiv cs.CR · 6d agoResearch3

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 · 4d agoAI research1

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 · 5d 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 · 6d agoAI research1

Implementation of Machine Learning Workflows with NVIDIA cuML, RAPIDS, GPU Benchmarking, Explainability, Clustering, and Model Inference

Hands-on tutorial implements NVIDIA cuML and RAPIDS to GPU-accelerate scikit-learn-style ML workflows with benchmarking, clustering, and inference.

The tutorial demonstrates NVIDIA cuML as a GPU-accelerated machine learning framework, using cuml.accel to speed up unmodified scikit-learn scripts with zero code changes and the native cuML API for CuPy/cuDF interoperability. It benchmarks CPU versus GPU implementations of PCA, K-Means, nearest-neighbor search, logistic regression, random forests, and DBSCAN on datasets up to 200,000 samples with 64 features. It also builds GPU pipelines with UMAP, t-SNE, and HDBSCAN, validates GPU-generated SHAP explanations, uses the FIL library for forest inference, and covers model serialization and GPU/CPU portability.

MarkTechPost · 4d agoAI tools & infra

Cross-Model Agreement as a Deployment-Time Reliability Signal for Automatic Polyp Segmentation

Referee-Based Quality Estimation flags unreliable polyp segmentations at inference without ground truth, reaching ROC-AUC 0.960 with SegFormer-B0 referees.

RBQE measures agreement between a primary segmentation model and an independently trained referee on a 1,223-image external benchmark drawn from four public datasets. A cross-architecture SegFormer-B0 referee achieves the strongest signal (ROC-AUC 0.960), beating a Test-Time Augmentation baseline by 0.055 ROC-AUC under an identical protocol. Excluding trivially separable empty-mask cases, ROC-AUC falls to 0.876 (SegFormer-B0) and 0.783 (same-architecture control), but RBQE's margin over baselines widens. Progressive rejection of low-agreement predictions increases mean Dice of retained outputs, supporting selective prediction at the cost of one extra forward pass.

arXiv cs.AI / cs.LG / cs.CL · 7d 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 · 8d agoAI research1

OracleZoom: On-Policy Self-Distillation Inspired Reference-Constrained Recursive Image Super Resolution

OracleZoom enables recursive extreme-scale image super-resolution via reference-constrained on-policy distillation, reducing hallucinations at deep zoom scales.

OracleZoom tackles recursive super-resolution, where repeated feeding of predictions back into the same model leaves deeper-scale outputs unsupervised as required source resolution grows geometrically. The framework trains on its own trajectory while carrying the last ground-truth evidence beyond the supervision boundary, combining direct and cross-scale supervision, a no-reference quality objective, a KL-constrained pretrained latent prior, and EMA consistency. Across seven datasets it achieves state-of-the-art SR quality across zoom scales, averaging 0.713 CLIPIQA with larger gains at deeper scales and significantly reduced hallucinations. Code, data, and models are publicly released.

Hugging Face daily papers · 11d agoAI research

Google Research Releases ToolGrad: Answer-First Framework Hits 99.8% Pass Rate for Tool-Use Data Generation

Google Research and partners introduce ToolGrad, a verified tool-chain-first data generation framework reaching 99.8% pass rate and boosting Gemma-3-12B to 83.1 on BFCL.

Researchers from Google, the University of Tokyo, RIKEN AIP, and Tohoku University released ToolGrad, which inverts query-first tool-use data generation by executing and verifying API chains before annotating them with user queries. On the ToolBench database of 16,000+ APIs, ToolGrad raised generation pass rate from 63.8% to 99.8% while increasing tool uses per sample from 2.1 to 3.4 and cutting tool-use steps from 34.3 to 20.0. Fine-tuning Gemma-3 at 1B, 4B, and 12B parameters on the 500-sample ToolGrad-500 dataset lifted ToolGrad-12B to 83.1 on the Berkeley Function Calling Leaderboard, near Gemini 2.5 Pro at 83.2 and ahead of GPT-5 at 74.4. Code is Apache-2.0, with the dataset, PyPI package, and models available on Hugging Face.

MarkTechPost · 5d agoAI research1

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 · 8d agoAI research1

CodeTD: Topology of Attention Detects Hallucinations in Code LLMs

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

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

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

Discovery Foundation Models: Toward Open-Ended Discovery Intelligence

Paper defines Discovery Foundation Models with seven coupled capabilities for open-ended discovery, demonstrated via Zetema and GALILEO systems.

The paper formulates Discovery Foundation Models (DFMs) as general-purpose model systems for open-ended discovery, supporting seven coupled capabilities spanning problem discovery, formulation, representation construction, hypothesis formation, intervention, evidence-grounded revision, and continual improvement. It instantiates the framework with Zetema, which couples explicit research-state dynamics, verification and experimental gating, and cross-task Discovery Skill evolution. The framework is grounded with GALILEO, a real therapeutic-discovery system combining dry-lab reasoning with robotic wet-lab experimentation in a closed physical discovery loop; code is released on GitHub.

Hugging Face daily papersupdated · 2d agofirst · 3d agoAI research 2 sources

The History Is the Detector: Executing CVE Patch History, End-to-End

BUGSTONE-E2E converts CVE patch history into executable LLM-guided detection rules, yielding 1,033 rules and 644 runtime-verified findings across 14 programs.

The BUGSTONE-E2E framework mines reusable detection rules from verified fixing commits, organized by CWE and language, and applies them through a funnel pipeline that escalates from Tree-sitter anchors and lightweight heuristics to LLM-based agent inspection, runtime verification, and scope-checked patch generation. Built from 19,325 high-severity CVEs published 2022-2026, it produced 1,033 detection rules spanning 56 CWE families, packaged into 172 skills. Applied across 14 programs, it generated runtime evidence for 644 findings, demonstrating that vulnerability history can drive reproducible detection and repair.

arXiv cs.CR · 12d agoResearch

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 · 8d agoResearch1

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 · 1d agoAI research

Speculative Decoding in vLLM on AMD GPUs

vLLM benchmarks speculative decoding on AMD Instinct MI300X and MI355X GPUs across five drafting methods including EAGLE-3 and native MTP.

The vLLM project documents draft-and-verify speculative decoding support for AMD GPUs via ROCm, comparing native MTP, Gemma 4 MTP, EAGLE-3, DFlash, and DSpark drafting approaches. Output-token throughput effects varied with drafting method, proposal length, model family, draft checkpoint, workload, and acceptance behavior. The post also covers how to enable each method plus practical tuning and observability considerations.

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