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NVIDIA Details BioNeMo Inference Runtime (BioIR): 2.90x Higher Boltz-2 Folding Throughput and 58.5K Residues per GPU-Hour on 8xH100

NVIDIA released BioNeMo Inference Runtime (BioIR), an open-source PyTorch-compatible library delivering 2.90x higher Boltz-2 protein-folding throughput on 8xH100 GPUs.

NVIDIA detailed BioIR, a Python library that accelerates Boltz-2, OpenFold2, and OpenFold3 structure-prediction inference on NVIDIA GPUs while preserving standard PyTorch workflows. On a matched benchmark of 1,000 human dimers on 8xH100 80GB GPUs, BioIR delivered 58.5K folded residues per GPU-hour versus 20.2K for a torch.compile baseline, a 2.90x throughput gain. BioIR already powered the AlphaFold Database expansion, generating about 31 million candidate complexes across 4,777 proteomes, with 1.81 million released as high-confidence predictions. Extrapolated to 1 million targets, estimated folding energy drops from 35 MWh to 11 MWh at 8-GPU TDP equivalents.

MarkTechPost · 6d agoAI tools & infra1

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

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

Biology-in-the-loop: Amortized Adaptive Hit Discovery in CRISPR Screens

Researchers release AssayBench-Loop, a 1,389-screen CRISPR benchmark, and AssayLoop, a framework that learns adaptive hit discovery policies.

The paper introduces AssayBench-Loop, a large-scale benchmark of 1,389 CRISPR screens across five phenotype categories for adaptive hit discovery under budget constraints. It also introduces AssayLoop, which combines AssayFormer, a transformer-based amortized acquisition policy trained across historical screens, with LLM-derived biological priors via an adaptive handoff. On temporally held-out screens, AssayLoop achieves 5.67-fold enrichment over random selection and recovers 27.7% of hits after assaying roughly 5% of the candidate library, outperforming existing adaptive-design methods and standalone LLMs.

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

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

A Princeton Researcher Proposes Recurrent Looped Transformer (RLT) that Carries Decoder State across Every Token, Fixing 96 Blocks per Token with Unbounded Temporal Depth

Princeton researcher Yifan Zhang proposes Recurrent Looped Transformer, carrying full decoder state across every token for unbounded temporal depth.

Yifan Zhang's technical report defines the Recurrent Looped Transformer (RLT), pairing a causal encoder with a recurrent decoder whose final output and layerwise sliding-window attention cache carry into every subsequent token with no prompt-response boundary reset. The reference configuration ties 48 encoder and 48 decoder layers, executing 96 logical blocks per token while the state path grows to 48t blocks after t tokens at fixed per-token compute. The report details RL replay contracts that rebuild all states under current parameters and exact prefix snapshots for multi-turn serving, but explicitly reports no measured efficiency, reasoning quality, or scaling results.

MarkTechPost · 3d 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 · 26d agoAI research

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 · 14d 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 · 11d agoAI research

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

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

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 · 6d agoAI industry1

Perplexity Details Its GPU Embedding Stack: How Ivy, Tulip and ROSE Serve pplx-embed

Perplexity details its GPU embedding serving stack (Ivy, Tulip, ROSE), which reuses LLM prefill/decode kernels, CUDA graphs, and LazyTensors to cut launch overhead.

Perplexity engineers published a deep dive on the serving infrastructure behind pplx-embed, used across Perplexity Search and its API platform. The stack comprises Ivy (Rust HTTP gateway), Tulip (gRPC scheduling and batching), and ROSE (Runtime-Optimized Serving Engine), which reuses LLM prefill and decode kernels rather than running a separate embedding engine. Optimizations include whole-model CUDA graphs with lazy capture and a LazyTensor abstraction that overlaps CPU batch preparation with in-flight GPU work. Benchmarks are reported against vLLM v0.22.0 in BF16, with FlashAttention 4 generally fastest but FlashInfer 3 winning on Qwen-based models at very long sequence lengths.

MarkTechPost · 11d agoAI tools & infra1

How Does mHC Use Its Residual Streams? Selective Routing and Near-Identity Mixing

Analysis of DeepSeek-V4-Flash shows four-stream mHC residual blocks use only about two streams effectively, with late-layer mixing providing little benefit.

The study examines the four-stream residual pathway of DeepSeek-V4-Flash, finding typical attention or FFN sites effectively use about two streams and that residual mixing is modest, occurring primarily in early layers. Replacing late mixers with identity increases C4 perplexity by only 1.9% while replacing early mixers raises it by 41%. Retaining the three largest routing weights per token increases perplexity by at most 2.7%, showing the model uses only part of the flexibility afforded by the four-stream design.

arXiv cs.AI / cs.LG / cs.CL · 12d agoAI research

Grouped Value Attention: Efficient KV Caching via On-Demand Key Reconstruction

Grouped Value Attention stores grouped values and reconstructs content keys via a learned linear map, cutting KV-cache size about 45-47% versus GQA.

GVA stores only grouped values and reconstructs content keys with a learned linear map absorbed into the query at decode time, while a small shared decoupled RoPE channel preserves positional information via a separately cached positional key. At 350M parameters trained on 30B FineWeb-Edu tokens, the 16-dimensional positional variant scores 44.18 average accuracy across five tasks versus 44.36 for GQA and 43.88 for MLA. Custom decoding kernels are in development with an open-source release planned.

Hugging Face daily papers · 9d agoAI research

Model-Aware Schedules Improve Generation via Fiberwise Optimal Transport

Researchers introduce model-aware diffusion schedules via fiberwise optimal transport, cutting flow-matching FID on CIFAR-10 by 38.6% at 16 function evaluations.

The paper proposes constructing diffusion and flow-matching sampling schedules from a fiberwise prediction risk defined via optimal transport, combined with coefficient-path kinetic action, yielding a closed-form time allocation. Across DDPM and flow-matching experiments spanning targets, datasets, and architectures, the schedules beat model-agnostic baselines, including a 38.6% relative FID reduction for flow matching on CIFAR-10 at 16 function evaluations. Normalized fiberwise-risk profiles from independently trained models align closely, suggesting empirical universality, and a frozen analytic allocation template retains most of the gains.

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

Objective vs. Search: Decomposing What Makes a Good Tokeniser

New tokeniser study shows search procedure, not optimisation objective, drives bits-per-byte performance across model sizes, vocabulary sizes, and multilingual settings.

The paper disentangles BPE and UnigramLM along two axes: optimisation objective (compression vs log-likelihood) and search procedure (bottom-up merging vs top-down pruning). Two new algorithms, BottomUpLL and TopDownComp, complete the 2x2 design space, and trained language models are evaluated on bits-per-byte and BLiMP across model sizes, vocabulary sizes, and English-only vs multilingual domains. Bottom-up tokenisers consistently achieve lower bits-per-byte in most settings, while BLiMP shows no consistent relationship with design choice.

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

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

Quenched Ensemble Sampling

Quenched Ensemble Sampling generalizes nested sampling's hard energy constraint to repulsive potentials, traversing first-order phase transitions where tempering fails.

Quenched Ensemble Sampling generalizes nested sampling's hard energy constraint into a family of repulsive potentials at the energy boundary, preserving monotone energy descent while making the constrained target amenable to scalable gradient-based kernels. On synthetic phase-transition models it estimates marginal likelihood and draws posterior samples across first-order transitions where popular alternatives such as tempering fail. Applications include marginal likelihood estimation for Bayesian neural network architecture comparison and partition function estimation in a high-dimensional continuous lattice field theory.

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

Understanding the Impact of Model Pruning on Long-Tail Forgetting and Explanation Reliability in Medical Imaging

Systematic study finds model pruning causes frequency-dependent long-tail forgetting in medical imaging and that gradient-informed methods best preserve explanations.

Across two long-tailed medical imaging datasets, two CNN architectures, four pruning methods, and sparsity up to 95%, the study measures predictive performance, explanation stability, and faithfulness. Rare classes degrade earlier and more severely than frequent ones, while explanation reliability depends mainly on the pruning strategy, with gradient-informed methods degrading least. Mechanistic analysis ties explanation collapse to loss of class-discriminative gradients rather than vanishing feature activations, recommending class- and explanation-aware evaluation of compression.

arXiv cs.AI / cs.LG / cs.CL · 9d agoAI research

Observational Indistinguishability and Integrity Blind Regions in Hybrid Quantum-Classical Workflows

Framework formalizes integrity blind regions in hybrid quantum-classical workflows, validated across 3,600 label interventions with conformal detection rules.

The paper presents a claim-relative evidence and reference framework for integrity of hybrid quantum-classical workflows, distinguishing structural blind regions caused by observational indistinguishability from finite-batch statistical misses. Experiments over 3,600 label interventions show exact label-path invariance for feature and prediction views. The geometry-aligned construction detects 343 of 2,700 conclusion-changing interventions using the conformal rule and 1,183 of 2,700 with the uncorrected union, with executed conformal clean false-action rates of 0.048-0.059.

arXiv cs.CR · 1d agoResearch

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 · 12d agoAI research

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

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

Register Tokens for Bounded-State Reasoning in Diffusion Language Models

Register tokens let diffusion language models like LLaDA and Dream carry reasoning state across cleared chunks, gaining up to 19.5 points on code.

Researchers propose register tokens: dedicated fixed-position tokens whose continuous hidden states are trained to carry reasoning progress across generation chunks in masked diffusion language models. After decoding and clearing a chunk, the model continues from the prompt and the carried register state instead of retaining earlier text. On LLaDA and Dream, registers outperform discrete-text carry on every benchmark, with gains up to 8.5 points on math and 19.5 points on code. Registers are especially effective for bounded code generation and can be further refined with reinforcement learning on long-horizon reasoning tasks.

Hugging Face daily papers · 3d agoAI research

Echo: Learning-based Matching Decompilation using Trusted Back Translation

Researchers introduce Echo, a matching decompiler using trusted back-translation that roughly doubles exact-match rates and outperforms GPT-5.6 and Codex on Mirai.

Echo performs matching decompilation by using compilation as trusted feedback for iterative search: a domain-specific model generates candidate code and compilation configurations, which are recompiled, compared at assembly level, and repaired via rule-based rewriting, neural refinement, and reasoning-based refinement. On function-level benchmarks, Echo produces 2.43x more exact matches than the strongest baseline and the highest structural similarity to ground truth. On the Mirai malware binary, it matches 2.75x and 7.4x as many functions as GPT-5.6 and Codex, respectively.

arXiv cs.CR · 15h agoResearch

NCP-ArchPreview Technical Report: Moving towards Latent Space Language Models through Next Concept Prediction

An 8.9B-parameter latent-space language model using next-concept prediction matches OLMo-3-7B pretraining loss with only 51.3% of the training tokens.

NCP-ArchPreview augments next-token prediction with Next Concept Prediction over a product-quantized concept vocabulary built from hidden states, trained jointly end-to-end. The 8.9B model was trained on 5.73T tokens from the Dolma-3 dataset, the largest latent-space language model demonstration to date. It consumes 51.3% of the tokens to reach OLMo-3-7B's final pretraining loss and outperforms it by 2.45 points on the downstream macro-average, including a 5.99-point GSM8K gain. The learned latent space also enables lightweight domain adaptation via a 17M-parameter VQ module and improves speculative drafting accepted length by 4.17%.

Hugging Face daily papers · 8d agoAI research1

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

Studying Image Tokenizers as Visual Languages in Unified Multimodal Models

A controlled pure-autoregressive testbed shows task-specific validation losses rank image tokenizers differently, with I2T loss the most consistent signal.

Researchers built a controlled pure-autoregressive testbed and tracked task-specific validation losses during multimodal continual pretraining across text, image, text-to-image (T2I), and image-to-text (I2T) prediction. They find losses should be analyzed per task because they exhibit distinct scaling behavior and rank tokenizers differently, and that the loss-performance relationship depends on the predicted token space. I2T loss, computed over a shared text vocabulary, correlates consistently with both generation and visual understanding performance after supervised finetuning. Case studies revisit the discriminator, semantic supervision, and vocabulary size as tokenizer design axes.

arXiv cs.AI / cs.LG / cs.CL · 8d agoAI research1