Search: “molecular-properties”

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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·Sep 8, 14:00 UTC · 8d agoAI research 2 sources

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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

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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 · 11d agoAI research

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Canonical Color as a Lens into Concept Decodability in Vision Encoders and VLMs

Probing study shows vision encoders make canonical color linearly decodable from grayscale images and tie it to object identity.

Researchers use canonical color as a controlled testbed for measuring conceptual (not just visible) information in vision encoder representations. A dataset of objects with canonical colors was built, and probes on both color and grayscale images show canonical color remains decodable even when color is removed from the input, linked to predicted object identity. Extending to full VLMs, they find post-training has a surprisingly large effect on color decodability in the vision encoder.

arXiv cs.AI / cs.LG / cs.CL·Sep 8, 17:50 UTC · 8d agoAI research1

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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

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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 · 6d agoAI research1

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Bridging Control, Inference, Transport, and Thermodynamics: From Theory to Applications in Learning

Review connects control theory, optimal transport, probabilistic inference, thermodynamics, and machine learning via free-energy optimization under constraints.

The review unifies five fields: control theory, optimal transport, probabilistic inference, non-equilibrium thermodynamics, and machine learning. The common conceptual thread is optimization of free-energy-like functionals under dynamical or statistical constraints. Selected applications are presented in reinforcement learning, variational inference, and generative modeling. The tutorial-style text assumes no prior familiarity and begins from physics principles.

arXiv cs.AI / cs.LG / cs.CL·Sep 14, 17:16 UTC · 2d agoAI research

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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·Sep 14, 17:16 UTC · 2d agoAI research1

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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

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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·Sep 15, 13:16 UTC · 1d agoResearch

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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·Sep 10, 21:57 UTC · 6d agoAI tools & infra1

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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 · 14d agoAI research

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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

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Reduced-Space Multi-Fidelity Bayesian Optimization of Process Simulation Models

RS-MFBO couples global sensitivity analysis with fidelity-augmented Gaussian processes to slash costly high-fidelity simulation runs in industrial flowsheet optimization.

The paper presents RS-MFBO, a reduced-space multi-fidelity Bayesian optimization framework for high-dimensional, expensive black-box functions. It integrates Global Sensitivity Analysis for dimensionality reduction with a fidelity-augmented Gaussian process and a cost-aware acquisition strategy featuring cooldown and promotion mechanisms. Validation on a plasmid DNA bioprocess (SuperPro Designer) and a green fuel synthesis plant (Aspen HYSYS) shows substantial reductions in high-fidelity evaluations while remaining competitive with single-fidelity baselines.

arXiv cs.AI / cs.LG / cs.CL·Sep 15, 16:46 UTC · 1d agoAI research

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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

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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

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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·Sep 10, 17:43 UTC · 6d agoAI research

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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 · 8d agoAI research2

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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·Sep 12, 18:51 UTC · 4d agoAI research1

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CUA-Universe: A Scalable and Dynamic Environment for Hybrid GUI+CLI Agents

Researchers introduce CUA-Universe, a pipeline turning real desktop software into hybrid GUI+CLI agent environments, lifting a 9B model's OSWorld success rate.

CUA-Universe is an environment-to-data pipeline that converts real desktop applications into hybrid GUI+CLI environments, scaling to 16 applications via App-Forge, Task-Weave, and Path-Steer. Training on its harvested trajectories shifted a 9B model toward effective GUI+CLI orchestration, yielding +39.3 points on CUA-Verse, +16.8 points success rate on OSWorld, and +7.84 points on OSWorld-MCP while cutting steps and tokens by up to 57% and 60%. The work addresses the scarcity of scalable hybrid environments for computer-use agents.

arXiv cs.AI / cs.LG / cs.CL·Sep 4, 17:26 UTC · 12d agoAI research1

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Does Your Agent's Memory Survive a Model Upgrade? A Controlled Study of Memory Portability

A controlled study finds agent memory portability varies sharply: fixed-schema knowledge graphs survive model swaps while compressed notes degrade.

The study compares preserving an agent's history as raw long context, RAG chunks, compressed natural-language notes, or fixed-schema knowledge graphs across model upgrades, using 48 synthetic histories and two open-weight sub-10B-parameter models. Fixed-schema KG accuracy changed by only +0.0004 ± 0.0020 after a writer swap, while compressed NOTES shifted asymmetrically by +9.91 or -13.28 percentage points depending on migration direction. Mixed 50/50 embedding migrations captured only 4.96 of an 11.90-point RAG re-embedding gain; 80% of the NOTES deficit came from information lost at construction, and 81% of the RAG deficit from retrieval failures. Store-only repair of NOTES failed to reach 90% recovery in all 48 cases, while retaining raw histories enabled recovery in 34 of 48 for one direction.

arXiv cs.AI / cs.LG / cs.CL·Sep 4, 16:44 UTC · 12d agoAI research1

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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 · 8d agoAI research1

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Evaluating Verified Autonomy in Quantum Engineering

Quantum-Harbor lab and QIQCBench (49 tasks) expose wide performance gaps across 17 frontier agentic systems in verified quantum engineering.

Researchers built Quantum-Harbor, a virtual laboratory providing a controlled execution environment where scientific AI agents interacting with quantum systems can have both actions and conclusions directly verified. QIQCBench contributes 49 expert-authored tasks spanning calibration and control, error correction and compilation, and sensing and networking. Across 17 frontier agentic systems, verified performance varied widely, exposing a substantial gap between demonstrated capability and reliable autonomous operation.

arXiv cs.AI / cs.LG / cs.CL·Sep 15, 16:46 UTC · 1d agoAI research1

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LexFlip: A Dissociation Diagnostic for Legal Meaning Preservation Metrics

LexFlip releases 373 minimal perturbations of Quebec statutory French that reverse legal force while preserving tokens, exposing weaknesses in embedding-based meaning preservation metrics.

LexFlip provides 373 minimal perturbations of Quebec statutory French that reverse legal force while preserving 0.93 of tokens, creating dissociation items that break monotone token-overlap metric validation. The seven embedding and BERTScore metrics tested register only 0.022-0.039 of their identical-to-unrelated range on these edits, versus 0.670 for bidirectional NLI. Against FrJudge, with a measured human ceiling of r=0.597, a bare length feature outscores every semantic metric tested.

arXiv cs.AI / cs.LG / cs.CL·Sep 4, 15:49 UTC · 12d agoAI research

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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·Aug 31, 20:00 UTC · 16d agoAI research

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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

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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·Sep 8, 17:57 UTC · 8d agoAI research1

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Large Language Models Develop Belief State Geometry In-Context

Probing six open-source LLMs on HMM-generated data shows belief states are linearly decodable (R² 0.83–0.99), suggesting in-context learning approximates Bayesian prediction.

Researchers prompted six open-source LLMs with data from 40 hidden Markov models selected for non-trivial belief structure and probed residual-stream activations for belief states (posteriors over hidden states). Belief states were linearly decodable with peak R² values of 0.83–0.99 across HMM/LLM combinations, spanning early to late layers. Patching and steering the probe-identified subspace preserved downstream prediction quality while control interventions degraded performance substantially, establishing functional relevance. The results provide representation-level evidence that in-context learning approximates optimal Bayesian prediction over a context-inferred generative model.

arXiv cs.AI / cs.LG / cs.CL·Sep 15, 16:17 UTC · 1d agoAI research1

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Studying Image Tokenizers as Visual Languages in Unified Multimodal Models

A controlled autoregressive testbed shows validation losses must be analyzed per task, and image tokenizer choice affects joint multimodal text modeling.

Researchers built a pure-autoregressive testbed to study image tokenizers as the 'visual language' of unified multimodal models, tracking task-specific validation losses during multimodal continual pretraining across text, image, text-to-image (T2I), and image-to-text (I2T) prediction. They found that losses exhibit distinct scaling behavior per task and rank tokenizers differently, and that I2T loss over a shared text vocabulary gives a more consistent loss–performance signal than T2I loss. Better reconstruction does not necessarily yield lower task-specific losses or stronger downstream performance, and tokenizer choice can affect text modeling under joint optimization. Case studies examine the discriminator, semantic supervision, and vocabulary size design axes.

Hugging Face daily papers·Sep 7, 20:00 UTC · 9d agoAI research1

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