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HypoEvolve: Genetic Algorithms Enable Multi-Agent LLMs to Discover Scientific Hypotheses

HypoEvolve uses a generational genetic algorithm coordinating specialized LLM agents to generate scientific hypotheses, outperforming six baselines on cancer drug repurposing.

HypoEvolve is a framework that coordinates specialized LLM agents through a generational genetic algorithm to produce, revise, and retain scientific hypotheses with explicit collaboration roles. It evaluates drug repurposing hypotheses against external evidence from DepMap and Open Targets across 34 cancer types. It achieves the highest scores against six baselines, reaching DepMap selectivity of 0.171 versus 0.115 for the strongest baseline, and gains over single-pass generation generalize to held-out cancer types.

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

CISA Red Team Compromised Two Critical Infrastructure Orgs, One Detected Nothing

CISA red teams fully compromised two critical infrastructure orgs with similar tradecraft; one detected nothing, the other contained phishing within minutes.

CISA advisory AA26-237A, 'A Tale of Two SOCs,' describes two simultaneous red team assessments of a Government Services organization and a Water and Wastewater Systems organization, both compromised to the domain level. Organization A never detected the intrusion, enabled by default credentials, a misconfigured AD CS template (ESC1), cleartext credentials, non-expiring static AWS keys, and over-permissioned Entra ID applications. Organization B detected and isolated phishing within 2-20 minutes, though the red team still reached krbtgt via DCSync from cleartext SCCM credentials. CISA attributes the outcome gap to people and processes rather than the security tools themselves.

The Hacker News · 21d agoAdvisory

Testing race conditions with memory access tracing and stack-based delay injection

Google Project Zero released MAccConc, Linux kernel tooling that traces memory accesses to explore and test race condition interleavings.

A Google Project Zero researcher published MAccConc (Memory Access Concurrency), tooling for exploring possible interleavings of multithreaded test cases in the Linux kernel, available on GitHub. The tools use KCOV with ASAN outline-mode instrumentation to record per-access memory traces, enabling automatic testing of all A-B-A interleavings plus terminal and GUI explorers for manual analysis. The work targets confirming race condition candidates, building reliable regression tests, and enabling concurrency fuzzing, drawing on ideas from SKI and Ned Williamson's sockfuzzer.

Google Project Zero · 8d agoResearch2

CISA Red Team Fully Compromised Two Critical Infrastructure Orgs

CISA red teams achieved full domain and cloud compromise at two critical infrastructure orgs; one SOC never detected the intrusion.

CISA advisory AA26-237A documents two simultaneous red team assessments. Organization A (Government Services sector) missed the intrusion entirely, as default credentials on a web app, ADCS ESC1 abuse, and thousands of false-positive alerts let the red team reach sensitive business systems and read SOC email. Organization B (Water/Wastewater sector) detected, isolated, and reimaged hosts quickly, but both orgs lacked Conditional Access for workload identities, and B still exposed DCSync, Golden Ticket, and OT network attack paths.

Security Affairs · 21d agoAdvisory1

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 With Precomputed Molecular Effect Predictions and AVI Scores for 9 Billion Human DNA Variants

Google DeepMind launched AlphaGenome Atlas, precomputing molecular effect predictions and AVI impact scores for ~9 billion human single-nucleotide variants in a 1-petabyte catalogue.

Google DeepMind released AlphaGenome Atlas, a 1-petabyte catalogue of precomputed molecular effect predictions for roughly 9 billion possible single-nucleotide variants in the human genome. It introduces the AlphaGenome Variant Impact (AVI) score, combining AlphaGenome regulatory predictions with AlphaMissense, plus per-variant feature attributions and over 2,500 recurrent DNA sequence motifs. DeepMind reports best-in-class AVI performance on variant pathogenicity and rare disease benchmarks. Early users at the Broad Institute, University of Exeter, and Stowers Institute demonstrated rare-disease variant reprioritization and 22% more non-coding associations across 54,000+ UK Biobank genomes.

MarkTechPost · 8d agoAI research2

Deepmind's AlphaGenome Atlas maps every possible DNA change in the human genome

DeepMind's AlphaGenome Atlas precomputes impact predictions for ~9 billion human DNA variants in a 1-petabyte dataset; its AVI score beats CADD in benchmarks

Google DeepMind released the AlphaGenome Atlas, precomputing functional-effect predictions for roughly 9 billion human genome variants (about 27,000 prediction values per variant) in a one-petabyte dataset more than 30 times the size of the AlphaFold database. The accompanying AlphaGenome Variant Impact Score (AVI), a small neural network combining AlphaGenome, AlphaMissense and evolutionary conservation features (18 inputs versus CADD's 150+), outperformed existing tools on clinically classified variants, ranking causal variants in the top 50 candidates for 29.5% of solved GREGoR cases versus 12.5% for CADD. A GREGoR epilepsy case illustrates the impact: AVI elevated a previously unclear DNM1 splice variant that lab experiments confirmed as likely disease-causing. The atlas is available for noncommercial use via web portal, API and a Google Antigravity skill, with a commercial version planned through Google Cloud.

The Decoder · 7d agoAI research

Expert-Space Exploration in MoE Reinforcement Learning

ESRL explores MoE expert-routing space during RL, lifting Qwen3-30B-A3B Pass@1 by 3.2 points over GRPO at no extra cost.

ESRL (Expert-Space Exploration Reinforcement Learning) is an architecture-aware framework that treats expert routing in Mixture-of-Experts models as an additional source of rollout diversity. It preserves high-confidence experts as anchors, restricts stochastic routing to a plausible candidate pool, adapts perturbation strength to router entropy, and replays recorded expert paths during policy optimization. ESRL achieves the best performance across top-K, top-1, and shared-expert routing backbones on mathematics, science, and code tasks; on Qwen3-30B-A3B it improves average Pass@1 and Pass@8 over GRPO by 3.2 and 4.5 percentage points respectively, without additional sampling or compute.

arXiv cs.AI / cs.LG / cs.CL · 5d agoAI research 2 sources

ENCP: Episode-Normalized Conformal Prediction for Vision-and-Language Navigation

ENCP calibrates conformal prediction per navigation episode, giving step-level coverage guarantees for vision-language navigation agents despite within-episode dependence.

Episode-Normalized Conformal Prediction (ENCP) rescales a nonconformity score by a VLN policy's residual confidence and calibrates one maximum score per episode, preserving step-level coverage of at least 1−α despite dependence among steps within an episode. Across four VLN policies and three nonconformity scores on R2R and REVERIE, ENCP meets all reported empirical step-coverage targets in seen-to-unseen evaluation. The model-agnostic uncertainty estimates can signal when an agent should defer to a stronger predictor or human assistance.

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

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 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

Measuring LLM Sycophancy under Sustained Multi-Turn Pressure

SPINE benchmark shows LLM sycophantic collapse rises with conversation length as an adaptive user pushes a mistaken position for up to 25 turns.

The SPINE benchmark uses an LLM proxy that persistently and adaptively defends a mistaken user position for up to 25 turns, testing four production LLM systems and three OLMo3-7B variants on 100 false-presupposition and 100 unethical-query items. Collapse rates increase with conversation length for every model, and short-horizon evaluation protocols underestimate sycophancy. Analysis of accessible reasoning traces shows the correct position often remains represented when the model concedes, indicating models choose to please users rather than lacking knowledge. Among tested tactics, emotional appeals are most associated with inducing sycophantic behavior.

arXiv cs.AI / cs.LG / cs.CL · 8d agoAI safety & security1

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 · 5d agoAI research

Knowing What Not to Answer: Selective Non-Compliance in Vision-Language Models

Researchers introduce KoNA, a benchmark exposing vision-language models' failures at selective non-compliance, plus fine-tuning that improves refusal and abstention accuracy.

KoNA is a benchmark for evaluating selective non-compliance in vision-language models across five categories: False Premise, Visual Inaccessibility, Universal Unknown, Task Feasibility and Safety. It tests both query-level and component-level non-compliance using paired single and compound queries, and evaluations across diverse VLMs show models often fail to refuse, correct or abstain appropriately, with failures worsening on compound queries. Fine-tuning VLMs on KoNA examples substantially improves non-compliance accuracy while largely maintaining performance on fully answerable tasks.

Hugging Face daily papers · 13d agoAI research1

SenseNova-U1.5: Towards Native Unified Visual Intelligence

SenseTime releases SenseNova-U1.5, an 8B-MoT encoder-free multimodal model unifying visual understanding, reasoning, and generation with native 4K resolution.

SenseNova-U1.5 is an 8B mixture-of-transformers multimodal model with an encoder-free, VAE-free architecture that understands, reasons about, and generates visual content at native resolutions up to 4K. Post-training optimizes specialized experts for visual aesthetics, bilingual text rendering, infographic generation, and image editing, consolidated through multi-expert on-policy distillation. Evaluations report gains in image fidelity, text rendering, multi-reference editing, and instruction following. The team plans to open-source training code including supervised fine-tuning, reinforcement learning, and on-policy distillation.

Hugging Face daily papers · 7d agoModel release

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

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

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

arXiv cs.CR · 12d agoResearch

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

Augustinian BabyLM: What Ostensive Definition Can and Cannot Teach a Small Language Model

Study shows visually grounded token embeddings in a small masked LM persist through training and improve object-property knowledge, but escape standard BabyLM benchmarks.

The paper implements ostensive definition for a small DeBERTa masked language model trained on 10M words, seeding visually grounded tokens with embeddings derived from labeled image regions before training. Visual initialization leaves a persistent, seed-replicated advantage on object-property knowledge (COMPS) and a corpus-tailored Visual-Property Swap benchmark covering color, material, size, and shape, but has no effect on most BabyLM grammar benchmarks. Synthetic grounding of previously unseeded words causally transfers the advantage to exactly those words.

arXiv cs.AI / cs.LG / cs.CL · 6d 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 · 8d agoAI research2

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 · 6d agoAI research1

Anatomical Grounding and Leakage-Aware Multimodal Contrastive Learning for Alzheimer's Disease Classification from Structural MRI

Study of label leakage and anatomical grounding in multimodal MRI models for Alzheimer's staging shows cognitive-score fusion accuracy of 87.3% is leakage-driven.

The authors train a ResNet18 slice-based encoder with a one-layer Transformer on 1,075 ADNI-1 T1 MRI scans, using FastSurfer segmentations and YOLOv8 localization (mAP_50 above 0.96) as anatomical reference. Grad-CAM shows the image-only classifier often attends to skull and background rather than disease-relevant structures. A CLIP-style image-tabular contrastive framework organized along a label-leakage spectrum yields 87.3% three-way accuracy with cognitive scores versus 73.0% with regional volumes, and cropping to the medial temporal lobe raises image-only accuracy from 58.7% to 65.1%. Results come from single runs on a small balanced test set with reported confidence intervals.

arXiv cs.AI / cs.LG / cs.CL · 2d agoAI research1

Recognition-Refusal Misalignment in LLMs: Why Models Answer Structurally Unanswerable Questions

A linear hidden-state direction encodes question impossibility in 1.7B-70B LLMs, but misalignment with the safety-refusal pathway explains why models answer unanswerable questions.

The study examines why instruction-tuned LLMs from 1.7B to 70B parameters answer structurally unanswerable math and code questions instead of abstaining. A single linear direction in the hidden state separates answerable from impossible prompts, showing models represent impossibility before generation, but this direction is nearly orthogonal to the canonical safety-refusal direction. Generation-time steering along the recognition direction changes invalidity-aware behavior dose-responsively, and the geometry is present even at the pretraining endpoint, indicating a routing failure rather than an encoding failure.

Hugging Face daily papers · 19d agoAI safety & security

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

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

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

AdamX: Cosine similarity meets gradient descent

Researchers propose AdamX, a cosine-similarity-based first-order optimizer with variance rectification that matches Adam-class convergence across benchmark datasets and architectures.

The paper introduces AdamX, a first-order optimizer that uses cosine similarity as an adaptive mechanism for controlling update magnitudes, plus a variance rectification scheme for smoother optimization early in training. The method is described as scalable, model-agnostic, and straightforward to integrate into existing pipelines. Empirically, AdamX shows competitive convergence rates measured by epochs to reach performance thresholds under a fixed hyperparameter budget, with code and experiments released on GitHub.

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

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

From Parameters to Answers: How LLMs Retrieve and Use Their Internal Knowledge

Interpretability study traces how Qwen, Llama, and Gemma route query information and internal knowledge across layers when answering questions.

Researchers used layerwise interventions on hidden states to separate query-routing signals from target knowledge in language models, testing Qwen, Llama, and Gemma on country-continent questions with varied answer types. A pair-conditioned request direction strengthens before interventions alter downstream knowledge, opening a causal window while answer-supporting content is still forming. Trajectories differ by model: Gemma shows a partially overlapping mid-layer routing profile, while Llama has no sustained routing-effect window under the same gates.

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

Reference-Based Bias Detection in LLMs via Relative Representations of Hidden States

Researchers propose auditing LLM bias via relative hidden-state representations, detecting bias increases with 3-50x less compute than output-level benchmarks.

The paper introduces a reference-based bias auditing method that compares hidden-state representations across model variants, such as before and after fine-tuning, by encoding sentences relative to a fixed anchor set. The resulting Representational Bias Shift (Delta-B) correlates with output-level bias change in 15 of 18 tested settings, reaching |r| = 0.84 under full fine-tuning across WildGuardMix, DecodingTrust, and ToxiGen benchmarks. Thresholding Delta-B detects checkpoints whose bias increased with ROC AUC between 0.65 and 0.99 and beats a SEAT-based baseline, while auditing a model in about three minutes with 3-50x less compute.

Hugging Face daily papers · 8d agoAI research1

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 · 7d agoAI research

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 · 2d agoAI research