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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.

Hacker News · AI · 8d agoAI researchHN 44↑ · 4 comments

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

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

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

Stanford Researchers Release Paper2Agent: Turning Research Papers Into AI Agents That Reproduce Results and Run on New Data

Stanford researchers released Paper2Agent, a Nature-published pipeline that turns research papers into MCP servers agents can execute.

A Stanford team led by Jiacheng Miao and James Zou published Paper2Agent in Nature on 16 September 2026. Built on Claude Code's agent SDK, it converts a paper and its codebase into a Model Context Protocol server with validated tools, resources, and prompts. In benchmarks, the AlphaGenome agent built 22 tools in about 45 minutes for US$14, scored 100% on 15 novel queries versus 78.7% for Claude Code with repository access, and cut median runtime 1.9x. In scale tests, 74 of 100 bioRxiv papers were converted and 593 of 599 proposed tools passed validation.

MarkTechPost · 9h agoAI research1

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 research 2 sources1

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

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

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

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

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

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

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 · 6d agoAI research1

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 · 9d agoAI research1

harshatheg/Qwen-2.5-1B-RLCD — new model trending #30 on Hugging Face

A community MLX inference engine evaluates constrained JSON schema fields in parallel on Apple Silicon, reporting 5.6-7.0x latency speedups with guaranteed schema validity.

The repository harshatheg/Qwen-2.5-1B-RLCD appeared at #30 on Hugging Face trending, but its content describes Parallel Constrained Decoding, an MLX-based inference engine for structured extraction and classification on Apple Silicon Macs. Benchmarked with mlx-community/Qwen2.5-1.5B-Instruct-4bit on an M4 Max, it reports 5.6x-7.0x latency reductions (e.g., 1,900 ms to 270 ms for a 28-field support triage task) with 100% syntactic validity and calibrated field-level probabilities. The engine prefills a single KV-cache, broadcasts it across all schema fields, and slices logits to valid candidate tokens for enum fields with up to 255 choices.

Hugging Face trending models · 1d agoAI tools & infra

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

Locus: A Framework for Exploring and Optimizing Point Addition Hardware for Zero-Knowledge Proofs

Locus framework automates ASIC and FPGA point-addition designs for elliptic curves, achieving 2.71x speedups and 3.11x area reductions for ZKPs.

Locus is a framework that automatically generates ASIC and FPGA implementations of elliptic curve point addition (PADD) for supported equation forms, enabling exploration of over 1,000 design points. On a 12nm technology node, its designs achieve a 2.71x geomean speedup and 3.11x geomean area reduction versus prior ASICs, plus 34.67x geomean speedup over CPU. Integrated into a prior ZKP accelerator at iso-area, it yields a 3.15x geomean speedup on end-to-end proof generation. The framework is open source on GitHub.

arXiv cs.CR · 15h agoResearch

AIJon: Automated Generation of Annotations for Fuzzing

AIJON uses LLMs to auto-generate IJON-style fuzzing annotations, matching human-expert quality on the Magma benchmark.

Researchers replicate IJON experiments and propose AIJON, a system that uses LLMs to automatically generate expert-style annotations for coverage-guided fuzzing at scale. On the Magma benchmark, LLM-generated annotations performed comparably to human-generated ones, though annotation-based fuzzing was not strictly better than AFL++. The paper analyzes how annotations affect fuzzer energy distribution across campaigns.

arXiv cs.CR · 20h agoResearch

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 · 8d agoAI research2

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 · 26d 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 · 12d agoAI research1

Knowledgator Releases GLiFormer: A 575M-Parameter Encoder That Hits 91.10 F1 on Nested JSON Extraction Without Generating Tokens

Knowledgator released GLiFormer, an Apache-2.0 encoder (264M/575M) handling NER, classification, relations, and nested JSON extraction, scoring 91.10 F1.

Knowledgator Engineering released GLiFormer, a schema-conditioned encoder that performs NER, classification, relation extraction, nested JSON structuring, and embeddings without generating output tokens. GLiFormer Large v1 has 575.6M parameters and scores 91.10 F1 on nested JSON extraction, close to GPT-5.6-luna's 91.96; both checkpoints are Apache 2.0 on Hugging Face. Reported median latency is 69 ms on GPU for the base model, though relation extraction (21.33 micro-F1) still trails GLiNER-Relex and larger LLMs.

MarkTechPost · 9h agoModel release

InceptionRAG: Stealthy Poisoning Attack Against Retrieval-Augmented Generation

InceptionRAG fragments malicious payloads into dormant passages that trigger LLMs to self-deduce misinformation via multi-hop reasoning, bypassing existing RAG poisoning defenses.

Researchers introduce InceptionRAG, a stealthy corpus poisoning attack against retrieval-augmented generation that splits a malicious payload into a chain of individually harmless dormant passages. When retrieved together, the passages induce LLMs to self-deduce target misinformation through multi-hop reasoning, achieving over 80% attack success rate across three datasets and three LLMs under rigorous adversarial constraints. A zeroth-order suffix optimization (ZOSO) method automates authoritative suffix generation in black-box settings. The authors also propose HODOR, a document isolation defense that decouples adversarial logical dependencies.

arXiv cs.CR · 1d agoResearch

AuK Technical Report: An Open-Source Foundational Model for Speech Generation and Editing

Open-source speech foundation model AuK unifies generation and editing, trained on 1.95 million hours, with distilled AuK-Flash achieving 4.5x speedup.

AuK is an open-source foundational model that unifies speech generation and editing through natural-language instructions and audio context, trained on approximately 3.03 billion instruction-audio instances and 1.95 million hours of supervision across five task families including generation, content editing, and acoustic editing. It combines a multimodal LLM for semantic conditioning, a VAE jointly trained on speech, general audio, and music, and a hybrid rectified-flow Transformer using dual-stream MMDiT blocks followed by unified single-stream DiT blocks. Post-training applies human-feedback preference optimization for editing and reward-based reinforcement learning for generation, and the distilled AuK-Flash performs 4-step inference without classifier-free guidance at a 4.5x wall-clock speedup. Source code and model weights are released.

Hugging Face daily papers · 9d agoModel release2

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 · 7d agoAI research1

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 · 6d agoAI research