Search: “bioinformatics”

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

Thermo Fisher Patches Flaw That Could Make DNA File Tampering Nearly Undetectable

The Hacker News·Aug 3, 08:05 UTC · Aug 3, 2026Vulnerability in the wildCVE-2026-17583

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

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

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 · 7d 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·Sep 9, 13:40 UTC · 7d agoAI research

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 · 10d agoAI research

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

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·Sep 14, 17:44 UTC · 2d agoAI research1

Can Edge-Deployable Vision-Language Models Identify Species?

Evaluation of 2-8B VLMs (Qwen3-VL, Gemma3) against BioCLIP on camera-trap species ID shows all models degrade sharply on field imagery.

The study tests whether edge-deployable 2-8B vision-language models carry genuine taxonomic knowledge, comparing Qwen3-VL 2B/4B/8B and Gemma3 4B against the 300M specialist BioCLIP on a 96-species task across clean iNaturalist photos and six LILA.science camera-trap collections. All models degrade 9.6-26.6 percentage points on field imagery, and BioCLIP outperforms every VLM by 33.2-59.2 points on an expanded 200-image sample, suggesting specialized data rather than scale drives the gap. Under open-set prompting, 5.9-9.6% of responses are syntactically valid but taxonomically nonexistent species names, with fabrication rankings replicating across evaluation sets.

arXiv cs.AI / cs.LG / cs.CL·Sep 10, 17:57 UTC · 5d agoAI research1

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

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

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 · 7d 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·Sep 7, 20:00 UTC · 8d agoAI research1

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·Aug 21, 16:52 UTC · 26d agoAI research

How a researcher uses Codex and ChatGPT to search for new antimicrobial molecules

OpenAI profiles César de la Fuente's lab using ChatGPT and Codex alongside deep-learning models to accelerate antimicrobial molecule discovery.

OpenAI published a case study on bioengineer César de la Fuente's lab, which uses ChatGPT and Codex for hypothesis brainstorming, code writing, dataset processing, and bridging knowledge gaps across biology, chemistry, and computer science. The lab's deep-learning models scan genome and protein databases for antimicrobial peptide candidates, potentially cutting initial searches from years to hours. Bacterial antimicrobial resistance was associated with about five million deaths in 2021, a toll projected to roughly double by 2050.

OpenAI News·Sep 10, 16:00 UTC · 6d agoAI industry1

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·Sep 8, 17:56 UTC · 7d agoAI research2

LongAgent: History-Guided Agentic Search for Longitudinal Outcome Prediction

LongAgent autonomously searches variable sets and temporal windows to predict longitudinal medical outcomes, beating the strongest non-agent baseline on synthetic data.

The paper proposes LongAgent, an agent-based method that searches over combinations of variable sets, temporal windows and aggregation functions for outcome prediction on heterogeneous medical longitudinal data. It uses a history memory of previous searches and numerical evidence to guide exploration. On synthetic data it achieves mean RMSE 1.7376, improving over the best non-agent baseline by 0.0151 (95% CI [0.0045, 0.0260]; p=0.0273), and performs comparably to the best baseline on a real clinical dataset.

arXiv cs.AI / cs.LG / cs.CL·Sep 14, 16:51 UTC · 2d agoAI research

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·Sep 10, 17:53 UTC · 5d agoAI research

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·Sep 15, 17:30 UTC · 1d agoAI research1

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 · 13d agoAI research

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

VidaForge: Open Research Infrastructure for Video Pretraining Data Recipes

VidaForge releases open infrastructure and VIDAFORGE-3M (3.14M clips, 6,475 hours) linking video pretraining data recipes to downstream model performance.

VidaForge is an open research infrastructure that represents a video pretraining data recipe as an executable five-stage workflow from raw videos to training datasets. The team compares data recipes with different coverage and quality during early from-scratch pretraining of Wan 2.1 and V-JEPA 2.1, finding that broader-coverage recipes achieve the highest downstream benchmark scores while loss-based evaluation favors different recipes. They also release VIDAFORGE-3M, containing 3.14 million scene-level clips totaling 6,475 hours with fine-grained annotations and curation signals for video data-recipe research.

Hugging Face daily papers·Sep 5, 20:00 UTC · 10d agoAI research

Type Diversity Enables Transformers to Generalise Compositionally

Researchers show lexical-versus-structural compositional generalization gaps in Transformers stem from type diversity imbalance in datasets, not architectural limits.

The paper argues that Transformers' difficulty with structural compositional generalization is an artifact of low structural type diversity in prior benchmark datasets rather than an architectural limitation. Using Grammatical Framework, the authors create linguistically diverse variants of COGS and SLOG. They find type diversity correlates with compositional generalization equally in lexical and structural test cases, contradicting previous claims that compound divergence explains task difficulty.

arXiv cs.AI / cs.LG / cs.CL·Sep 11, 17:59 UTC · 4d agoAI research

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·Sep 9, 17:32 UTC · 7d 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·Sep 4, 16:26 UTC · 12d agoAI research1

Procedural Graphs: Self-Evolving Execution Structures for LLM Agents

Procedural Graph framework stores procedural knowledge as triplets and self-evolves via LLM refinement, beating memory-based baselines across datasets, tasks, and LLMs.

The Procedural Graph organizes procedural knowledge into (procedure, relation, procedure) triplets; at each decision step the framework localizes the agent's active node and a guidance model translates the surrounding subgraph into step-level guidance that biases the solver's next action. An LLM refiner contrasts failed with successful trajectories and edits the graph's topology and attributes, retaining rejected edits to discourage repetition. Starting from a minimal skeleton, the loop builds graphs that match or surpass hand-designed ones and can repair flawed expert priors, delivering consistent gains over memory-based baselines across multiple datasets, task types, and LLMs.

Hugging Face daily papers·Sep 7, 20:00 UTC · 8d 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

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·Aug 28, 11:26 UTC · 19d agoModel release

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 papers·updated Sep 14, 17:56 UTC · 1d ago·first Sep 13, 20:00 UTC · 2d agoAI research 2 sources