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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

Researchers Use Claude to Port Pre-Auth RCE Exploit From One PLC Model to Another

Forescout used Anthropic's Claude to port a working pre-auth RCE exploit for CVE-2021-31886 between WAGO PLCs, executing ARM shellcode on live hardware.

Forescout Vedere Labs used Claude interactively to port an RCE exploit for CVE-2021-31886, a CVSS 9.8 stack buffer overflow in the Nucleus FTP server's USER command, from a WAGO 750-852 to a WAGO 750-831 PLC, running attacker-supplied ARM shellcode. The final RCE stage cost $535.74 in API usage over 8 hours 32 minutes, and a follow-up attempt to build a C2 implant permanently bricked the device. CERT@VDE lists many Nucleus V1-based WAGO models as vulnerable with no updates available; Siemens plans no Nucleus NET remediation. The work follows a joint NSA/CISA/FBI/DOE/EPA advisory warning of AI-generated exploitation scripts targeting internet-exposed Siemens S7 PLCs.

The Hacker News · 14d agoResearchCVE-2021-318862

$536 and 8 Hours: AI Learns to Attack a Different PLC

Forescout used Claude to port a WAGO PLC exploit for $536 in 8 hours, and an AI-generated payload later permanently bricked the test device.

Forescout researchers used Claude Code with Ghidra, terminal access, and physical hardware to port CVE-2021-31886, a pre-authentication buffer overflow in the Nucleus FTP server, from a WAGO 750-852 PLC to the WAGO 750-831 without source code or debugger access. The final RCE development stage cost $535.74 in API fees over an 8-hour, 32-minute session (2.6k input and 1.3M output tokens) and required heavy researcher guidance. Claude produced working ICMP and UDP beacon exploits in 12 minutes after identifying that normal FTP command completion was overwriting its shellcode, fixed by omitting the CRLF terminator. A follow-up session extending the payloads toward a C2 implant wrote to flash-mapped memory and permanently bricked the PLC, underscoring the risks of autonomous agents operating against physical infrastructure.

Security Affairs · 14d agoResearchCVE-2021-318861

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

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

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

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.

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 · 8d agoAI research2

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 · 10d agoAI research

Show HN: LLM Attention Visualization

A developer released a browser-based tool that visualizes which past tokens influence each LLM output token using aggregated, value-weighted attention scores.

A Show HN project presents a React application built on Transformers.js that renders per-token attention influence by aggregating attention weights scaled by value-vector magnitudes across all attention heads and layers. To expose internal tensors, the author instrumented the ONNX computation graph, hosted a modified model on Hugging Face, and pre-generated prompts to avoid long model downloads in the browser. Demos with a 600-million-parameter model show how verbatim copying draws heavily on source tokens and how single outputs blend information from multiple phrases.

Show HN: MultiMatte, a Promptable Image Background Removal Model

Feyn releases MultiMatte, a promptable background-removal model fine-tuned from Meta's SAM 3 via LoRA, outputting alpha mattes that beat SAM 3 on segmentation benchmarks.

Feyn introduced MultiMatte, a promptable image background-removal model built on Meta's SAM 3 (860M parameters). It modifies only 19.49M parameters (2.27%) using a rank-16 LoRA adapter and replaces binary masks with alpha mattes to handle fuzzy boundaries like hair. On the DIS-VD benchmark it scores 0.901 S-measure versus SAM 3's 0.667, and it improves on SAM 3 across all twelve evaluated splits. Training used 19,953 images for 14,000 steps with focal and Dice loss, and the merged weights are available via the nobg library and a web demo.

RelateAnything: Real-Time Open-Vocabulary Relation Prediction From Any Inputs

RelateAnything is a 53M-parameter open-vocabulary relation prediction model running at 20 ms/frame, with 2.3-3.5x higher mean recall than comparable open-vocabulary methods.

RelateAnything predicts scored relations between image regions using any predicate vocabulary supplied at inference as text embeddings, with object labels never required as input, so region sources can change without retraining. Training covers 19,103 predicates using positive-unlabeled supervision; the authors release RA-4M (474k images, 4.3M geometrically verified relations over 10,102 free-text predicates) and the OV-SGG-Bench evaluation suite. The 53M-parameter model runs at 20 ms/frame and achieves 2.3-3.5x the mean recall of the strongest comparable open-vocabulary method across cross-dataset and zero-shot benchmarks. Model, corpus, and benchmark are public.

Hugging Face daily papers · 5d agoAI research

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

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

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

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 · 8d 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 · 8d 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 research1

Show HN: Panel – A research workspace where the agent can build its own panes

Panel is an open-source research workspace where AI agents dynamically build their own panes, posted on Hacker News.

Panel, shared as a Show HN project on GitHub, is a research workspace in which the agent can construct its own panes rather than using a fixed interface. The post received 41 points and 8 comments on Hacker News. It targets agentic research workflows with a dynamically generated UI.

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

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

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

arXiv cs.AI / cs.LG / cs.CL · 1d agoAI research1

DynSHAP: Towards Explainable Dynamic Survival Analysis

DynSHAP extends SHAP explainability to dynamic survival analysis, treating time-feature pairs as Shapley players for longitudinal clinical predictions.

DynSHAP adapts marginal SHAP estimators to dynamic survival analysis by treating time-feature pairs as players in the Shapley game, handling longitudinal irregular inputs and functional survival outputs. Temporal DynSHAP learns linear feature dependencies over time and addresses them with conditional sampling. On synthetic data with ground-truth attributions it recovers temporally dependent features more accurately than marginal estimators, and it produces faithful attributions on two real-world clinical datasets across two DSA architectures.

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

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

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

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

Hugging Face daily papers · 15d 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

You've Got a BUD in Me: Authenticated Reads from Per-Block Write Logs

Researchers propose BUD, per-block write-log digests enabling blockchain validators to serve historical membership and exclusion proofs far cheaper than state-wide tries.

The paper introduces Block Update Digests (BUD), which authenticate each block's write log with predecessor pointers, plus a SuperBUD and exponential hierarchy to turn long unchanged intervals into short proofs. Soundness against adversarial provers and up to f Byzantine validators is proven under archive, attestation, and committee evidence assumptions. Benchmarks show a 50x state-size increase raises the base-BUD path only 1.24x versus 3.1x for in-memory and 69.5x for disk-backed Merkle Patricia tries, with read payloads below 800 bytes and p99 warm verification at 146 microseconds.

arXiv cs.CR · 6d agoResearch

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

Graph Machine: Towards Better Pretraining via Edges

Researchers propose Graph Machine, an O(n)-state sparse architecture that replaces 75% of Qwen3-0.6B dense layers with only slight loss change.

The paper introduces the Graph Machine (GM), an architecture that maintains an O(n)-sized state accessed through sparse, dynamic routing via pointer-like edges updated differentiably by a referral mechanism resembling pointer chasing. The authors replaced 75% of dense Transformer layers in Qwen3-0.6B with GM sparse layers and pretrained from scratch on 15.7B tokens. Retrieving 2 of 4,096 tokens per KV head in each sparse layer degrades loss only slightly, while retrieving 4 marginally improves loss over the dense baseline.

Hugging Face daily papers · 14d agoAI research

Beyond the Turing threshold: Productive grammars generate essentially undecidable languages

A theoretical paper designs formal grammars that emulate Post's productive sets, generating languages that are provably beyond Turing decidability.

The paper elaborates on Emil Post's productive sets, which are not even semi-computable, and builds formal grammars that emulate their construction over natural numbers. The resulting languages are shown to be essentially undecidable, placing them beyond Turing decidability. This is pure computability and formal language theory with limited direct security relevance.

arXiv cs.CR · 6d agoResearch1

Convergent Emergence of In-Context Learning Across Modalities

Controlled experiments show few-shot in-context learning emerges across six modalities including language, genomes, images, and proteins, partially supporting a convergence hypothesis.

The paper tests the Convergent Emergence Hypothesis: that few-shot in-context learning, when it emerges, shares a common cross-modality difficulty profile. A controlled framework instantiated the same task suite across six modalities: language, genome, integer sequences, time series, images, and proteins. Paired-mapping ICL emerged in all six modalities, surpassed controlled baselines, and showed correlated per-task effects in five of them, providing partial support for the hypothesis.

Hugging Face daily papers · 4d agoAI research

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

Kaininja: Extending Native 3D Generators to the Part Level

KaiNinja extends TRELLIS.2 native 3D generation to part-level assets via a dual-volume O-Voxel representation, cutting whole-object Chamfer distance by 40%.

KaiNinja extends the TRELLIS.2 native 3D generator to produce part-level assets instead of one fused mesh, enabling downstream editing, rigging, and simulation. A dual-volume form of the O-Voxel representation solves the problem that a single volume cannot represent interfaces where two parts touch. The model needs no segmentation network, is partly trained on LLM-agent-authored part data, lowers whole-object Chamfer distance by 40%, and raises strict part F-score by 16% versus other part-generation pipelines.

Hugging Face daily papers · 2d agoAI research