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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 · 7d agoAI research 2 sources

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 · 6d agoAI research 2 sources

4.1 Million Impacted by AdaptHealth Data Breach

AdaptHealth disclosed a breach affecting 4,115,802 people after a socially engineered attacker stole health and insurance data from cloud-based patient systems.

A threat actor used social engineering to hijack a user session at a third-party contractor and gained access to AdaptHealth cloud applications, including patient management and document storage systems, in early June. Names, contact and demographic information, and health and health insurance data were exfiltrated; Social Security numbers and financial information were not affected. AdaptHealth reported 4,115,802 affected individuals to HHS, whose breach portal listed the incident this week; Baylor Genetics separately reported 2,810,878 individuals affected in a related June healthcare breach.

SecurityWeek · 6d agoData breach 2 sources

7th September – Threat Intelligence Report

Check Point weekly bulletin: exploited SonicWall SMA 1000 zero-days (CVE-2026-83548/49), JFrog Artifactory auth bypass, and a 2.8M-patient Baylor Genetics breach.

Check Point's weekly bulletin covers breaches including Thomson Reuters' C-Track platform (court records across 11 US states and Canada), Baylor Genetics (2.8M patients and employees, SSNs included), Hit casinos in Slovenia, and Dropbox (~5,000 accounts via abused Lenovo email verification). SonicWall patched two exploited SMA 1000 zero-days, including CVE-2026-83548, a CVSS 10.0 pre-authentication SSRF, while JFrog fixed exploited authentication bypass CVE-2026-82329 (CVSS 9.8). Malware and actor coverage includes Gambling Goblin, JSCeal, Mirage Kitten's NodeRabbit/PollCat campaign, and DPRK Contagious Interview macOS activity, plus a FalconFlank privilege-escalation PoC against CrowdStrike Falcon.

Check Point Research · 8d agoAdvisory in the wildCVE-2026-83548CVE-2026-83549CVE-2026-823291

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 · 7d agoAI researchHN 44↑ · 4 comments

Risky Bulletin: Slovakia finds Russian backdoor in traffic speed cameras

Slovakia's NBU found an SMS-triggered backdoor in Russian-made NERO R-ONE traffic cameras, pausing a 279-unit deployment.

Slovakia's national security service NBU issued an alert against NERO R-ONE high-speed traffic cameras after finding a backdoor that grants shell and network access via SMS from hardcoded Russian phone numbers. The cameras are a rebranded version of the Russian CORDON PRO.M model by St. Petersburg firm Semicon, purchased via a Cyprus shell company under a €30 million EU-funded project. The report also found SecureBoot disabled, vulnerable web management, and unauthenticated live streams; the Interior Ministry paused deployment of 279 cameras pending independent assessment.

Risky Business News · 28d agoThreat actor in the wild1

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 · 7d agoAI research2

Canada’s Hospital for Sick Children attacked by cybercriminals again as employee data stolen

Canada's Hospital for Sick Children reported a data theft incident exposing current and former employee data via a third-party application.

The Hospital for Sick Children (SickKids), Canada's largest pediatric health center, disclosed that hackers stole personal information of current and former employees, job applicants, and SickKids Foundation staff, likely through a third-party software application. The attack briefly took down the hospital's careers website but did not involve clinical systems or patient information. Affected individuals were notified and offered two years of credit monitoring. The hospital was previously hit by ransomware in 2022.

The Record · 25d agoData breach in the wild

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 · 13d agoAI research

Electronic health record company says customer data stolen in breach

Veradigm disclosed that attackers used stolen vendor credentials via an API to steal patient data including Social Security numbers, as the Gentlemen ransomware gang claims 3.5 million patients' records.

Electronic health records company Veradigm filed an 8-K with the SEC stating that an unauthorized party obtained credentials from a vendor's environment and used them to access a Veradigm API, downloading patients' personal data including Social Security numbers; no clinical or medical data was involved. The Gentlemen ransomware gang added Veradigm to its leak site, claiming theft of 3.5 million patients' health records. Access was limited to the specific API interface, with no operational disruption. Veradigm was previously hit by SamSam ransomware in 2019 and disclosed a December 2024 breach affecting 2,672,036 people.

The Recordupdated · 5d agofirst · 6d agoData breach in the wild 5 sources

Health data of more than 9.5 million people leaked from Aesto record system

Health data firm Aesto reported a breach affecting over 9.5 million people after hackers accessed its AWS infrastructure between December 2 and 18.

Alabama-based healthcare data company Aesto notified the Department of Health and Human Services that more than 9.5 million people had sensitive information leaked in a December cyberattack, after previously warning customers in June without disclosing scope. Attackers broke into the company's Amazon Web Services infrastructure between December 2 and December 18, stealing names, Social Security numbers, medical information, driver's license numbers, financial account numbers, and health insurance data. Aesto provides data migration and archiving services for medical facilities, and at least 30 healthcare organizations were affected, with breach notices filed for customers including Together Women's Health. Related healthcare incidents disclosed this year include Baylor Genetics (2.8 million people), CareCloud (3.7 million), and recent attacks at McKesson, Nutex, Paylogix, and Park Dental Partners.

The Record · 13d agoData breach

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 · 5d 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 · 1d agoAI research1

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 · 11d agoAI research1

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

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 · 7d agoAI research

Evaluating Time-Series Foundation Models and Multimodal Dietary Context for CGM Forecasting

Study finds zero-shot time-series foundation models underperform on CGM forecasting; fine-tuned Chronos-Bolt cuts RMSE up to 18.4% and dietary context adds signal.

The paper evaluates time-series foundation models for continuous glucose monitoring forecasting across eight public datasets covering Type 1 diabetes, Type 2 diabetes, and non-diabetes populations. Under a unified protocol, zero-shot foundation models did not consistently outperform baselines like Elastic Net and PatchTST, but lightweight fine-tuning did, with fine-tuned Chronos-Bolt reducing RMSE by 6.5%-18.4% in the T1D cohort and 8.6%-18.2% in the non-diabetes/T2D cohort. A residual-based fusion framework adding dietary context from CGMacros reduced overall RMSE by about 3% and postprandial RMSE by about 15% versus CGM-only baselines.

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

Bag of Tricks or Bag of Myths? Reducing Modeling Complexity with Task Knowledge in Explainable Suicide Risk Assessment

Researchers audit 31 NLP techniques for clinician-annotated suicide risk prediction, finding only 5 of 31 comparisons yield reliable gains.

A study of 1,635 clinician-annotated social media posts ran roughly 300 controlled experiments across 7 methodological families, auditing techniques such as model scaling, synthetic data, ensembling, and threshold tuning under severe class imbalance. The proposed system reformulates risk factor prediction as entailment between posts and codebook definitions, using architecturally diverse ensembles with class-balanced training and deployment-consistent calibration. It scores 0.8203 for risk, 0.7953 for evidence, and 0.7045 macro-F1 for factors, ranking third among 53 teams.

arXiv cs.AI / cs.LG / cs.CL · 8d agoAI research

Emergency Department Revisit Quality Review Screening: Exploring Human Decision-Making and Artificial Intelligence Support

A retrospective study found GPT-4 over-flagged emergency department revisit cases while an LLM knowledge-graph screener achieved 83-100% positive predictive value.

In an exploratory retrospective study of 99 emergency department diagnosis pairs from a multihospital health system, clinicians and GPT-4 independently judged whether revisit pairs warranted further assessment. GPT-4 responses correlated poorly with clinicians, flagging 94% of pairs for follow-up, 4.4-13.3 times more than clinicians, though prompt engineering was minimal. An algorithm leveraging an LLM-populated knowledge graph (KGA) achieved 83-100% positive predictive value against at least one clinician rater, suggesting LLM-based screening could broaden revisit quality review without substantially increasing reviewer workload.

arXiv cs.AI / cs.LG / cs.CL · 6d 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 · 5d agoAI research1

Lightweight Vision Transformer Compression for On-Device Plant Disease Detection in Resource-Constrained Agricultural Field Conditions

A unified ViT compression pipeline (H-BAC pruning, quantization, distillation) cuts plant-disease models 54.5x to 6.01 MB while keeping 95.13% accuracy.

Researchers combined Hessian-Balanced Adaptive Block Pruning (H-BAC), guided by second-order sensitivity estimation, with quantization and attention-based knowledge distillation to compress Vision Transformers for on-device chilli plant disease detection in India. On a 3-class cross-village, cross-device out-of-distribution dataset, the integrated pipeline reduced model size from 327.42 MB to 6.01 MB (54.5x) at 95.13 +/- 2.32% accuracy, matching the 95.13% FP32 baseline. Ablations also show a directly trained 6.01 MB INT8 student reaches 94.87% accuracy, indicating where pruning and distillation add limited value.

arXiv cs.AI / cs.LG / cs.CL · 11d agoAI research

K-Bench: a clinically calibrated benchmark for evaluating large language models in high-risk mental health conversations

Clinician-calibrated K-Bench evaluates 125 LLM configurations on 200 high-risk mental health vignettes, exposing wide variation in suicide and violence risk handling.

K-Bench is a clinician-calibrated, protected benchmark evaluating 125 model configurations from 33 base models across 14 providers on 200 multi-turn vignettes covering suicide, self-harm, domestic violence, substance misuse and no-risk presentations. A frozen GPT-4o judge achieved 94.2% exact agreement with clinician consensus across 6,751 eligible comparisons from 151 clinician-rated transcripts. Leading models combined supportive conversation with combined-risk scores above 95, while risk exploration varied substantially among weaker configurations; therapeutic prompting helped weaker models and elevated reasoning produced no average improvement. A continuously updated public leaderboard is hosted at k-bench.ai with protected test materials.

arXiv cs.AI / cs.LG / cs.CL · 1d agoAI safety & security

IdeaAMBIG: Benchmarking Implementation-Critical Gaps in Research-Idea Specifications

IdeaAMBIG benchmark with 660 instances measures whether LLMs can spot and fix underspecified research-method details for faithful implementation.

Researchers introduce IdeaAMBIG, a benchmark of 660 evidence-grounded instances (163 real-world gaps from reproducibility reports and GitHub issues, 497 controlled synthetic gaps) built from papers, codebases, and reproduction artifacts. It evaluates codification-readiness assessment, defect localization, and clarification action generation. Across 13 LLMs, the best model achieved only 9.6% Macro Defect Recovery Rate on real-world instances but 80.6% clarification success when given the annotated defect. An oracle study showed gold resolutions raise the codification-ready rate from 14% to 98%, identifying defect localization as the main bottleneck.

arXiv cs.AI / cs.LG / cs.CL · 6d agoAI research2

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

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 · 7d agoAI research1

ActReview: Rebuttal-Guided Training Data and Rubric Rewards for Actionable Peer Review Generation

ActReview post-trains Qwen3-8B-Base on OpenReview rebuttals to generate actionable peer-review feedback with grounded revision suggestions, benchmarked on 1,000 curated instances.

The paper defines Actionable Peer-review Generation as diagnostic claim generation plus revision suggestion generation and introduces ActReview, a rebuttal-guided post-training framework. From OpenReview review-rebuttal threads the authors build ActReview-40K, aligning reviewer weaknesses with author responses grounded in localized paper evidence, and post-train Qwen3-8B-Base with multi-task SFT followed by GRPO using weakness-specific rubric rewards. They also release ActReview-Bench, a human-curated 1,000-instance benchmark, on which ActReview outperforms prior specialized review-generation models on actionability and grounding while remaining competitive with strong prompt-based LLMs. Human evaluation confirms improved revision usefulness but identifies a remaining gap in technical accuracy.

Hugging Face daily papers · 8d agoAI research

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 · 7d agoAI research2

IdeaAMBIG: Benchmarking Implementation-Critical Gaps in Research-Idea Specifications

IdeaAMBIG benchmark of 660 specification-gap instances shows LLMs localize implementation-critical research gaps poorly, with best model at 9.6% defect recovery.

IdeaAMBIG is a benchmark of 660 evidence-grounded instances evaluating whether research-method specifications provide enough information for faithful implementation: 163 real-world gaps from reproducibility reports and GitHub issues plus 497 controlled synthetic gaps. It tests codification-readiness assessment, defect localization, and clarification action generation across 13 LLMs. The best model achieves only a 9.6% Macro Defect Recovery Rate on real-world instances, though 80.6% clarification success when given the annotated defect, and an oracle study shows gold resolutions raise codification-ready rates from 14% to 98%. Defect localization emerges as the main bottleneck across all evaluated models.

Hugging Face daily papers · 7d agoAI research

When Should LLMs Abstain? Chain-of-Self-Questioning for Selective Risk Control

Chain-of-Self-Questioning prompting cuts LLM wrong-answer commitments 32% relative while raising answered accuracy, holding across eleven model families.

The paper introduces Chain-of-Self-Questioning (CoSQ), a prompt-only framework that makes LLM answer commitment conditional on an explicit assessment of the information required to answer. On an 817-item TruthfulQA multiple-choice set, Grounded-CoSQ at τ=0.90 reduced mean unconditional wrong-commitment rate from 13.1% under chain-of-thought to 8.9% (a 32.1% relative reduction), while raising answered accuracy from 86.9% to 89.7% at 87.6% coverage. Improvements held across eleven open-weight and hosted model families and at every evaluated threshold, with convergent evidence from a Natural Questions short-answer evaluation.

arXiv cs.AI / cs.LG / cs.CL · 18h agoAI research

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 · 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 · 25d 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 · 19h agoAI research1

DianShi-RxnDB: A Large-Scale, Fine-Grained Organic Reaction Data Platform Built via a Fully Automated Pipeline for Researchers and AI Agents

Researchers release DianShi-RxnDB, a database of roughly 24 million organic reaction instances extracted automatically from USPTO and EPO patents since 1976.

DianShi-RxnDB is built by a fully automated pipeline integrating patent text, images, and reaction schemes, yielding about 24 million reaction instances, of which 14.8 million (61.7%) pass automated qualification checks. Manual evaluation of 1,300 sampled instances showed 92.95% field-level accuracy, and comparisons with Pistachio found advantages in deduplicated record counts and granularity. The platform offers a web research workbench and a Model Context Protocol (MCP) service enabling AI agents to perform composable structured retrieval.

Hugging Face daily papers · 10d agoAI research

CiteShade: Citation Laundering in Multi-Source Retrieval-Augmented Generation and Its Counterfactual Defense

CiteShade attack makes RAG models cite trusted sources for attacker-chosen wrong answers, raising wrong-answer rate from 0.01 to 0.68.

CiteShade is presented as the first citation laundering attack against multi-source retrieval-augmented generation: an attacker controlling a single source induces a wrong answer falsely attributed to a trusted source, even while correct evidence remains in context. The attack is formalized via three necessary conditions (retrieval, generation, citation) constructible without any instructions, raising wrong-answer rate from 0.01 to 0.68 on multi-hop QA, with source deletion confirming the malicious source as causal driver. Vulnerability tracks a model's citation propensity rather than scale, reaching CLR 0.84 with explicit instruction and 0.64 without on the most citation-prone model. Perplexity filtering and citation-support checking prove insufficient; the authors propose a counterfactual defense verifying which source actually drove the answer.

arXiv cs.CR · 1d agoAI safety & security1