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01.
arXiv (CS.LG) 2026-06-17

Conditional Attribution for Root Cause Analysis in Time-Series Anomaly Detection

arXiv:2604.17616v3 Announce Type: replace Abstract: Root cause analysis (RCA) for time-series anomaly detection is critical for the reliable operation of complex real-world systems. Existing explanation methods often rely on unrealistic feature perturbations and ignore temporal and cross-feature dependencies, leading to unreliable attributions. We propose a conditional attribution framework that explains anomalies relative to contextually similar normal system states. Instead of using marginal or randomly sampled baselines, our method retrieves representative normal instances conditioned on the anomalous observation, enabling dependency-preserving and operationally meaningful explanations. To support high-dimensional time-series data, contextual retrieval is performed in learned low-dimensional representations using both variational autoencoder latent spaces and UMAP manifold embeddings. By grounding the retrieval process in the system's learned manifold, this strategy avoids out-of-distribution artifacts and ensures attribution fidelity while maintaining computational efficiency. We further introduce confidence-aware and temporal evaluation metrics for assessing explanation reliability and responsiveness. Experiments on the SWaT and MSDS benchmarks demonstrate that the proposed approach consistently improves root-cause identification accuracy, temporal localization, and robustness across multiple anomaly detection models. These results highlight the practical utility of conditional attribution for explainable anomaly diagnosis in complex time-series systems. Code and models are available at: https://github.com/dfki-av/Conditional-Attribution-for-Root-Cause-Analysis-in-Time-Series-Anomaly-Detection.

02.
arXiv (CS.AI) 2026-06-17

ARVO: Atlas of Reproducible Vulnerabilities for Open-Source Software

arXiv:2606.17283v1 Announce Type: cross Abstract: Achieving reproducibility, quantity, and diversity in vulnerability datasets has long been viewed as an inherent three-way trade-off, where improving one dimension often comes at the cost of the others. In practice, reproducibility has been the dimension most often neglected. This has limited what can be automatically extracted from historical bug datasets, and has reduced their utility for downstream security research. In this work, we propose a method to produce a new security dataset which ensures reproducibility for diverse vulnerabilities at scale by identifying the key obstacles to large-scale bug reproduction and addressing them with general solutions. Using this method, we introduce full reproducibility to the largest open source software vulnerability dataset (OSS-Fuzz) and construct the ARVO dataset (an Atlas of Reproducible Vulnerabilities in Open-source software). ARVO is a large-scale dataset consisting of over 6,100 real-world vulnerabilities across 311 projects. Focusing on reproducibility, ARVO differs from existing datasets by providing each vulnerability in a form that can be consistently rebuilt, triggered, and analyzed across versions. Reproducibility also enables automatic identification of the corresponding patch for each vulnerability and supports direct interaction with vulnerabilities after code changes, capabilities that existing large-scale datasets do not provide. In our evaluation, ARVO successfully reproduces 81% of vulnerabilities and achieves 89.4% accuracy on the located patches. We also discuss ARVO's influence on both upstream practices and downstream security research.

03.
arXiv (quant-ph) 2026-06-15

Certifying Macroscopic Quantum Mechanics via Hypothesis Testing with Finite Data

arXiv:2506.22092v2 Announce Type: replace Abstract: We address the challenge of certifying quantum behavior with single macroscopic massive particles, subject to decoherence and finite data. We propose a hypothesis testing framework that distinguishes between classical and quantum mechanics based on position measurements. While interference pattern visibility in single-particle quantum superposition experiments has been commonly used as a sufficient criterion to falsify classical mechanics, we show that, from a hypothesis testing perspective, it is neither necessary nor efficient. Focusing on recent proposals to prepare macroscopic superposition states of levitated nanoparticles, we show that the likelihood ratio test – which leverages differences across the entire probability distribution – provides an exponential reduction in measurements needed to reach a given confidence level. These results generalize to a broad class of quantum states, and offer a principled, efficient method to falsify classical mechanics in interference experiments, relaxing the experimental constraints faced by current efforts to test quantum mechanics at the macroscopic scale.

04.
arXiv (CS.CL) 2026-06-19

Clusters are All You Need: Pre-Training the Tsetlin Machine with Semantic Clusters from Language Models for Interpretability

Pre-trained language models such as BERT achieve strong text classification performance but lack transparency, limiting their use in high-stakes settings. The Tsetlin Machine (TM) offers fully interpretable, clause-based reasoning but captures little semantic information, and prior attempts to bridge the two rely on static word embeddings that miss contextual meaning. We propose a semantic pre-training framework that transfers knowledge from a pre-trained language model into a TM without using embeddings. Text samples are grouped into semantically coherent clusters with K-means or Top2Vec, and the resulting cluster-sample pairs pre-train a non-negated TM with enhanced Type I feedback. The TM thereby learns interpretable semantic keywords that are fine-tuned on downstream tasks. Across five datasets, our method substantially outperforms vanilla and embedding-based TMs and reaches performance competitive with BERT while remaining interpretable.

05.
arXiv (math.PR) 2026-06-11

Hierarchical Random Measures without Tables

arXiv:2505.02653v2 Announce Type: replace-cross Abstract: The hierarchical Dirichlet process is the cornerstone of Bayesian nonparametric multilevel models. Its generative model can be described through a set of latent variables, commonly referred to as tables within the popular restaurant franchise metaphor. The latent tables simplify the expression of the posterior and allow for the implementation of Gibbs sampling algorithms to approximately draw posterior samples. However, managing their assignments can become computationally expensive, especially as the size of the dataset and the number of levels increase. In this work, we identify a prior for the concentration parameter of the hierarchical Dirichlet process that (i) induces a quasi-conjugate posterior distribution, and (ii) removes the need for tables, leading to more interpretable expressions for the posterior, with both a scalable and an exact algorithm to sample from it. Remarkably, this construction extends beyond the Dirichlet process, leading to a new framework for defining normalized hierarchical random measures and a new class of algorithms to sample from their posteriors. The key analytical tool is the independence of multivariate increments, that is, their representation as completely random vectors.

06.
arXiv (quant-ph) 2026-06-11

Dynamically Optimal Unraveling Schemes for Simulating Lindblad Equations

arXiv:2509.19887v2 Announce Type: replace Abstract: Stochastic unraveling schemes are powerful computational tools for simulating Lindblad equations, offering significant reductions in memory requirements. However, this advantage is accompanied by increased stochastic uncertainty, and the question of optimal unraveling remains open. In this work, we investigate unraveling schemes driven by Brownian motion or Poisson processes and present a comprehensive parametric characterization of these approaches. For the case of a single Lindblad operator and one noise term, this parametric family provides a complete description for unraveling scheme with pathwise norm-preservation. We further analytically derive dynamically optimal quantum state diffusion (DO-QSD) and dynamically optimal quantum jump process (DO-QJP) that minimize the growth rate of the variance of an observable locally in time. Compared to jump process ansatz, DO-QSD offers two notable advantages: firstly, the variance for DO-QSD can be rigorously shown not to exceed that of any jump-process ansatz locally in time; secondly, it has very simple expressions. Numerical results demonstrate that the proposed DO-QSD scheme may achieve substantial reductions in the variance of observables and the resulting simulation error.

07.
arXiv (CS.LG) 2026-06-16

Learning Hybrid Biophysical Neuron Models with Neural ODEs

arXiv:2606.16693v1 Announce Type: cross Abstract: Biophysical neuron models link measurements of neural activity to underlying cellular mechanisms. Yet, a central challenge is that the kinetics of many ion channels are poorly characterized, and practical simplifications – omitting channels or reducing morphological detail – introduce systematic gaps between model and biology. Bridging these gaps requires approaches that can flexibly discover unmodeled dynamics while preserving mechanistic interpretability. Here, we introduce a hybrid modeling framework that embeds neural ordinary differential equations into conductance-based biophysical models to capture unknown currents or mis-specified channel kinetics. By parameterizing the neural ODE in terms of voltage-dependent steady-state and time-constant functions, we recover interpretable gating dynamics directly from voltage recordings without assuming a functional form. We show that the hybrid model fits the gating kinetics of 2400 ion channel models and recovers unknown gating dynamics from single current-clamp recordings, generalizing to out-of-distribution stimulus regimes under realistic inputs and parameter misspecification. We also use our method to reduce a multicompartment model of a cortical neuron into a single-compartment hybrid model with a learned axial current, yielding up to an order of magnitude lower computational cost. Together, our results establish a plug-and-play framework for selectively replacing unknown components of conductance-based models with neural ODEs while preserving their mechanistic structure.

08.
bioRxiv (Bioinfo) 2026-06-12

Evaluating cell type annotations in single-cell omics in the absence of ground truth

Accurate cell type annotation is essential for single-cell transcriptomics, directly shaping downstream analyses and biological interpretations. Yet, objective evaluation of annotation quality remains a major challenge. Here, we argue that a cell type or cell state label has practical utility only if it captures a molecular pattern that is reproducible across biological replicates. Based on this principle, we introduce inter-sample consistency (ISC), a quantitative framework to assess annotation quality in single-cell RNA-seq datasets. Unlike existing cluster validation approaches, ISC distinguishes annotations that generalize across samples and individuals from those driven by technical or unwanted variation, thereby providing principled criteria for annotation quality and transferability. When applied to published single-cell atlases, ISC reveals widespread reproducibility gaps and provides actionable guidance for repairing inconsistent annotations. Notably, ISC enables benchmarking of automated cell type annotation tools even when ground-truth labels are unavailable, providing interpretable metrics to guide their development and evaluation. Implemented as the scTypeEval Bioconductor package, this framework offers a broadly applicable resource for evaluating and improving cell type annotations in single-cell RNA-seq experiments.

09.
medRxiv (Medicine) 2026-06-17

Waning protection of long-acting RSV monoclonal antibodies in infants: a Bayesian analysis of clesrovimab and nirsevimab trial data

Clesrovimab and nirsevimab are long-acting monoclonal antibodies used to prevent respiratory syncytial virus (RSV) disease in infants, but waning protection in the first year of life is incompletely characterised. We applied a published Bayesian inference framework to clesrovimab and pooled nirsevimab trial data to estimate time-varying efficacy against medically attended RSV lower respiratory tract infection (LRTI) and RSV-associated hospitalisation, accounting for differences in placebo-arm event timing between trials. Estimated clesrovimab efficacy declined from 60.7% (95% CrI: 46.3-72.6) shortly after dosing to 38.3% (8.6-52.9) at six months against medically attended RSV LRTI, and from 87.1% (71.2-96.2) to 49.6% (10.4-70.7) against RSV-associated hospitalisation. For nirsevimab, corresponding estimates declined from 86.9% (75.4-95.0) to 53.8% (27.4-69.7) against LRTI, and from 77.5% (52.6-91.8) to 49.7% (15.7-68.3) against hospitalisation. After accounting for differences in RSV exposure timing and LRTI endpoint definitions between trials, we found no evidence of a difference in efficacy or waning between clesrovimab and nirsevimab.

10.
arXiv (CS.CL) 2026-06-17

ZeroSyl: Simple Zero-Resource Syllable Tokenization for Spoken Language Modeling

Pure speech language models aim to learn language directly from raw audio without textual resources. A key challenge is that discrete tokens from self-supervised speech encoders result in excessively long sequences, motivating recent work on syllable-like units. However, methods like Sylber and SyllableLM rely on intricate multi-stage training pipelines. We propose ZeroSyl, a simple training-free method to extract syllable boundaries and embeddings directly from a frozen WavLM model. Using L2 norms of features in WavLM's intermediate layers, ZeroSyl achieves competitive syllable segmentation performance. The resulting segments are mean-pooled, discretized using K-means, and used to train a language model. ZeroSyl outperforms prior syllabic tokenizers across lexical, syntactic, and narrative benchmarks. Scaling experiments show that while finer-grained units are beneficial for lexical tasks, our discovered syllabic units exhibit better scaling behavior for syntactic modeling.

11.
arXiv (CS.CL) 2026-06-17

Regression Language Models for Code

We study code-to-metric regression: predicting numeric outcomes of code executions, a challenging task due to the open-ended nature of programming languages. While prior methods have resorted to heavy and domain-specific feature engineering, we show that a single unified Regression Language Model (RLM) using a frozen LLM encoder can simultaneously predict directly from text, (i) the memory footprint of code across multiple high-level languages such as Python and C++, (ii) the latency of Triton GPU kernels, and (iii) the accuracy and speed of trained neural networks represented in ONNX. In particular, a relatively small 300M parameter RLM based on T5Gemma, obtains >0.9 Spearman-rank on competitive programming submissions from APPS, and a single unified model achieves >0.5 average Spearman-rank across 24 different programming languages from CodeNet. Furthermore, the RLM can obtain the highest average Kendall-Tau of 0.46 on five classic NAS design spaces previously dominated by graph neural networks, and simultaneously predict architecture latencies on numerous hardware platforms.

12.
arXiv (CS.LG) 2026-06-16

Imbalanced Classification under Capacity Constraints

arXiv:2605.03289v2 Announce Type: replace-cross Abstract: Detecting observations from a minority class under severe class imbalance is a central challenge in applications such as fraud detection, medical screening, and industrial quality control. In these settings, each positive prediction triggers a costly follow-up action, an MRI scan, a transaction audit, whose execution is subject to real operational constraints. This paper proposes a formal classification framework under capacity constraints: given a user-defined bound limit $b$ on the proportion of observations that can be labeled as belonging to the minority class, the goal is to find the classifier that maximizes sensitivity on that class. We characterize the optimal classifier under this constraint and establish its equivalence with the classical Bayes classifier under a reweighting of the prior probabilities. We also introduce a capacity-adjusted performance metric $M$ that accounts for the effective detection rate when the capacity constraint is binding. The framework is implemented on top of standard learning methods, k-NN, SVM, random forests, and neural networks, and statistical consistency is established for each. We further show that these methods reduce to post-hoc thresholding when no hyperparameters are oriented toward the capacity-constrained objective, and introduce a capacity-aware support vector machine that exploits the constraint during training and achieves the strongest empirical performance. Experiments on the Taiwanese credit card default dataset confirm that capacity-constrained classifiers substantially outperform both classical approaches and SMOTE under high imbalance regimes. The framework extends naturally to multiclass settings and online environments.

13.
arXiv (CS.CV) 2026-06-17

Reasoning Text-to-Video Retrieval for Operating Room Clips via Action-Driven Digital Twins

Text-to-video retrieval in operating rooms (OR) is an enabling technology for OR safety, as it allows stakeholders to retrieve and inspect recordings of specific events. However, because the most safety-critical events may not follow the common structure, to unlock its full potential text-to-video retrieval must be able to handle implicit queries that require reasoning to identify the right video (e.g., the step right before clipping). However, existing methods rely on global embeddings that cannot reason over such queries. We propose OR3, a text-to-video retrieval method that converts clips into action-driven digital twins (ActDTs), grouping concurrent subject-action-object triplets under non-overlapping temporal intervals. Moreover, rather than cross-modal matching through paired encoders, OR3 performs imagination-based retrieval where an LLM generates hypothetical ActDTs from queries. This enables intra-modal matching via a single encoder trained with ActDT-tailored hard negatives. Finally, evidence-grounded refinement revises imagined ActDTs based on discrepancies with top candidates to capture procedure-specific patterns. We construct a benchmark from MM-OR with 276 implicit queries across four reasoning categories over 386 clips from robotic knee procedures. OR3 achieves 57.6 R@1 and 77.3 R@5, outperforming the strongest baseline. These results demonstrate that OR3 enables fine-grained discrimination between visually similar OR video clips through temporal action reasoning.

14.
arXiv (CS.LG) 2026-06-11

PAWS: Preference Learning with Advantage-Weighted Segments

arXiv:2606.11982v1 Announce Type: new Abstract: Preference-based reinforcement learning (PbRL) learns policies from human trajectory-level comparisons, avoiding explicit reward design and expert demonstrations. Existing methods typically train utility functions on trajectory or segment-level preferences while relying on per-step utility estimates during policy optimization. This training and inference mismatch induces a distribution shift that severely degrades temporal credit assignment and limits policy learning. We analyze this issue and propose PAWS, a segment-based preference learning method that performs policy updates directly using segment-level advantage functions. By aligning utility training with policy optimization, PAWS preserves trajectory-level preference information and avoids unreliable per-step learning signals. Experiments on simulated robotic manipulation and locomotion tasks demonstrate that PAWS consistently outperforms existing PbRL approaches, highlighting the importance of distribution-consistent preference learning.

15.
arXiv (CS.LG) 2026-06-19

Closing the Social-Semantic Gap: SPSD for Edge-Based Prompt Compression in Cloud LLM Inference

arXiv:2606.19364v1 Announce Type: new Abstract: The prefill stage of Large Language Model (LLM) inference is a growing contributor to cloud-scale energy cost. Many consumer-support and conversational prompts contain social scaffolding: politeness markers, apologetic preamble, repetition, and rapport-building language that is important for human communication but carries low marginal information for machine reasoning. We call this discrepancy the Social-Semantic Gap. We present SPSD (Sentiment Preserving Semantic Distillation), an edge-based pipeline that compresses user prompts using a 4-bit quantised Small Language Model before transmission to a cloud-deployed LLM. Evaluation on a 248-prompt corpus using Gemma-2-2B-Instruct (Q4_K_M) as the SLM and Llama-3.1-8B-Instruct as the cloud evaluation model yields a mean input token saving of 99.9 tokens per distilled call, with all 146 distilled calls yielding positive savings. Response quality, assessed by blind LLM-as-judge scoring across 121 pairs, is non-inferior to the raw path within a pre-specified 1-point margin on a 15-point rubric; the judge awarded 43 percent ties, 28 percent distilled wins, and 29 percent raw wins. Cosine similarity is mixed: mean 0.682, median 0.712, with 54.1 percent of pairs above the 0.70 reference threshold. Safety-critical domains are conservatively routed to passthrough via rule-based gates. Per-call net energy saving is estimated at 70-270 uWh under stated assumptions. SPSD shows that on-device prompt distillation can reduce cloud LLM input-token cost while preserving response quality within a practical non-inferiority margin.

16.
arXiv (CS.CL) 2026-06-19

CREDENCE: Claim Reduction for Decomposition & Enhanced Credibility – Semantic Metrics and Convergence Analysis

Decomposing compound sentences into atomic, verifiable claims is a prerequisite for reliable automated fact-checking. Prior work has relied on token-overlap (Jaccard) metrics that systematically underestimate decomposition quality for paraphrastic claims, and has lacked formal termination analysis for the repair loop. We present Credence, a revised claim decomposition and evaluation framework addressing both shortcomings. Our contributions are: (1) Semantic-F1: we use BGE-large cosine similarity fidelity metric that resolves Jaccard's penalisation and improves downstream fact-checking accuracy; (2) Convergence theorems: we formally characterise four properties of the repair pipeline, establishing that rule-based repair is monotone and finitely terminating under an oracle parser assumption; LLM-based self-repair is provably non-monotone and requires an early-exit guard; (3) Three evaluation benchmarks spanning social-media, encyclopaedic, and news domains for cross-domain generalisation measurement; (4) Multi-model benchmarking across four decomposer models (3.8B-12B) and a closed API model. Experiments on SocialClaimSplit, WikiSplitBench, and ClaimDecompBench show that Semantic-F1 outperforms Jaccard-F1 by +15-32pp. EPR ranges from 0.94 to 1.00 on SocialClaimSplit and WikiSplitBench, while ClaimDecompBench includes lower base EPR cases (down to 0.824) due to harder news-domain constructions, and rule-repair reduces the Atomicity Violation Rate (AVR) by 47-100% relative to the base model without degrading fidelity.

17.
arXiv (CS.LG) 2026-06-16

David vs. Goliath in Next Activity Prediction: Argmax vs. LSTM, Transformer, and LLM

arXiv:2606.15868v1 Announce Type: new Abstract: Next activity prediction (NAP) is a cornerstone of predictive process monitoring (PPM), enabling organizations to move from retrospective analysis to proactive process steering. The PPM field has progressed from classical machine learning through deep learning architectures such as LSTMs and Transformers to large language models (LLMs). Despite growing model complexity, no benchmark jointly compares LLMs, Transformers, LSTMs, and simple baselines in a direct sequence modeling setting for NAP. In this paper, we fill this gap with a systematic benchmark. We compare vocabulary-adapted LLMs, Transformers trained from scratch, LLM-distilled Transformers, and LSTMs against a simple counting-based argmax baseline across seven real-life event logs. Our results tell a David vs. Goliath story: pretraining confers no consistent improvement over training from scratch, model size shows little effect on performance, and on most datasets the argmax baseline matches or approaches the performance of billion-parameter LLMs.

18.
arXiv (CS.LG) 2026-06-15

Cluster LOCO: Feature Importance For Interpreting Clusters

arXiv:2606.14592v1 Announce Type: cross Abstract: Clustering is widely used for exploratory analysis and scientific discovery, driving insights from market segmentation to biological data analysis, but its outputs can be difficult to interpret, audit, and reproduce as modern datasets become increasingly large and complex. Reliable use of clustering requires understanding which features drive the discovered structure, yet feature-level explanations for clustering remain scarce compared with methods in supervised learning. Furthermore, existing clustering feature importance scores are often tied to specific algorithms and data assumptions. To address these challenges, we propose Cluster LOCO (Leave-One-Covariate-Out), a family of model-agnostic feature importance scores for clustering. Cluster LOCO is built on feature occlusion and clustering generalizability, defined as whether cluster labels learned on one subset of the data can be accurately predicted on held-out samples. For any chosen clustering algorithm, Cluster LOCO quantifies a feature's importance by measuring how much its removal degrades generalizability. We first introduce Cluster LOCO-Split, which relies on data splitting, and then extend it to Cluster LOCO-MP, a minipatch ensemble-based version designed for large-scale data. Across synthetic simulations and an application to cell-type discovery in single-cell transcriptomics, we show that Cluster LOCO more reliably recovers informative features than existing clustering feature importance methods.

19.
arXiv (CS.CV) 2026-06-15

Representation Forcing for Bottleneck-Free Unified Multimodal Models

Unified multimodal models (UMMs) aim to handle perception and generation in a single model. Yet existing UMMs still rely on a frozen, separately pretrained VAE for image generation, imposing a structural bottleneck. Naively removing it introduces a quality gap, as the model must learn both high-level structure and low-level details from raw pixels. In this paper, we propose Representation Forcing (RF), a technique that closes this gap by making representation prediction a native capability of the model. Concretely, RF forces the decoder to autoregressively predict visual representations as intermediate tokens before pixels; these tokens then stay in context to guide pixel diffusion within the same backbone. By turning representations from perception outputs into generation targets, RF eliminates the need for any external generative latent space. We find that RF benefits both understanding and generation. On image generation, our pixel-space model with RF matches state-of-the-art VAE-based unified models. On image understanding, pixel-space RF generally outperforms its VAE-based variant. Together, these results offer an effective step toward end-to-end, bottleneck-free UMMs.

20.
arXiv (CS.AI) 2026-06-19

Modeling Day-Long ECG Signals to Predict Heart Failure Risk with Explainable AI

arXiv:2601.00014v2 Announce Type: replace-cross Abstract: Heart failure (HF) affects 11.8% of adults aged 65 and older, reducing quality of life and longevity. Preventing HF can reduce morbidity and mortality. We hypothesized that artificial intelligence (AI) applied to 24-hour single-lead electrocardiogram (ECG) data could predict the risk of HF within five years. To research this, the Technion-Leumit Holter ECG (TLHE) dataset, including 69,663 recordings from 47,729 patients, collected over 20 years was used. Our deep learning model, DeepHHF, trained on 24-hour ECG recordings, achieved an area under the receiver operating characteristic curve of 0.80 that outperformed a model using 30-second segments and a clinical score. High-risk individuals identified by DeepHHF had a two-fold chance of hospitalization or death incidents. Explainability analysis showed DeepHHF focused on arrhythmias and heart abnormalities. This study highlights the feasibility of deep learning to model 24-hour continuous ECG data, capturing paroxysmal events essential for reliable risk prediction. Artificial intelligence applied to single-lead Holter ECG is non-invasive, inexpensive, and widely accessible, making it a promising tool for HF risk prediction.

21.
Nature (Science) 2026-06-10

Gene ancestries reveal diverse microbial associations during eukaryogenesis

The origin of eukaryotes remains a central enigma in biology1. Continuing debates agree on the pivotal role of a symbiosis between an alphaproteobacterium and an Asgard archaeon2,3. However, the nature, timing and contributions of other potential bacterial partners4–6 and the role of interactions with viruses7–9 remain contentious. To address these questions, we used advanced phylogenomic approaches and comprehensive datasets spanning the known diversity of cellular life and viruses. Our analysis provided a revised reconstruction of the last eukaryotic common ancestor (LECA) proteome, in which we traced the phylogenetic origin of each protein family. We found compelling evidence for multiple waves of horizontal gene transfer from diverse bacterial donors, with some likely to have preceded mitochondrial endosymbiosis. We inferred plausible traits of the major donors and their functional contributions to the LECA. Our findings support a contribution of horizontal gene transfers to shaping the proteomes of pre-LECA ancestors and suggest a facilitating role of Nucleocytoviricota viruses. Taken together, our results suggest that ancient eukaryotes may have originated within complex microbial ecosystems through a succession of diverse associations that left a footprint of horizontally transferred genes. Phylogenomic reconstruction of the proteome of the last eukaryotic common ancestor sheds light on the origin of eukaryotes, indicating an important role of horizontal transfer of genes from diverse bacterial and viral donors.

22.
arXiv (CS.CL) 2026-06-12

MARD: Mirror-Augmented Reasoning Distillation for Mechanism-Level Drug-Drug Interaction Prediction

Mechanism-level drug-drug interaction (DDI) prediction requires identifying which enzyme or pharmacodynamic axis is implicated, in which direction, and with which evidence – not merely whether two drugs interact. We introduce a reproducible mechanism-level DDI labelling and evaluation protocol with a structured 7-family/147-subtype taxonomy, leakage-safe cold-split protocols, and auditable reasoning metrics for evaluating pharmacological prediction beyond flat interaction classification. We propose a pipeline that produces a 7B reasoning MARD (Mirror-Augmented Reasoning Distillation), combining three training innovations: a single-token KL divergence on direction tag that ties the model's prediction, per-loss PRM-weighted DPO with programmatic hard negatives, and a leakage-safe mechanism-aware retrieval channel. Process-reward step labels are automatically verifiable against DrugBank-structured fields, requiring no human or LLM judges. On the April-2026 DrugBank release, our MARD-7B is the only system in a 32-system comparison whose accuracy survives drug-pair novelty, beating the best baseline by +13.9 pp and GPT-4o by +6.7 pp at ~1% of frontier API cost. Further analysis reveals an anti-memorisation signature where accuracy improves on rarely seen drugs, suggesting that gain comes from structured pharmacological reasoning rather than drug-frequency memorisation. We release corpus, DDI-PRM, retrieval index, and training code.

23.
arXiv (CS.LG) 2026-06-19

UltraEP: Unleash MoE Training and Inference on Rack-Scale Nodes with Near-Optimal Load Balancing

arXiv:2606.04101v3 Announce Type: replace-cross Abstract: Large-scale expert parallelism (EP) is becoming pivotal for training and serving frontier MoE models, but it also amplifies device-level expert load imbalance into compute stragglers, token all-to-all bottlenecks, and activation-memory spikes. Existing balancers redistribute experts periodically based on historical load, which becomes unreliable for production deployments with non-stationary load patterns. We present UltraEP, the first exact-load, real-time balancer for large-EP MoE training and serving prefill on rack-scale nodes (RSNs). Leveraging the extended scale-up connectivity among dozens of GPUs within RSNs, UltraEP rebalances every microbatch and layer on critical paths, which requires nontrivial co-design of plan solving and expert replication communication to minimize exposed overhead. To this end, UltraEP eagerly reacts to post-gating load with an efficient quota-driven planner, and executes the resulting irregular expert-state transfers with RSN-native persistent tile streaming and relay-based fan-out mitigation. We evaluate UltraEP in a multi-RSN deployment of up to 256 GPUs, using cutting-edge MoE models from 106B to 671B parameters. Averaged across training and serving, UltraEP achieves 94.3% of the force-balanced ideal throughput, delivering 1.49$\times$ improvement over no-balancing, while reducing the final inter-rank imbalance from 1.30$-$4.01 to 1.01$-$1.04.

24.
arXiv (CS.CV) 2026-06-16

Geometric Action Model for Robot Policy Learning

Generalist robot policies must follow user instructions while reasoning about how objects, cameras, and robot actions interact in the 3D physical world. Recent vision-language-action models (VLAs) and video world-action models (WAMs) inherit strong semantic or temporal priors from large-scale foundation models, but they still operate primarily on 2D image frames or 2D-derived latent spaces, leaving implicit the 3D geometry required for contact-rich manipulation. We propose the Geometric Action Model (GAM), a language-conditioned manipulation policy that directly repurposes a pretrained geometric foundation model (GFM) as a shared substrate for perception, temporal prediction, and action decoding. GAM splits the GFM at an intermediate layer: the shallow layers serve as an observation encoder, and a causal future predictor inserted at the split layer forecasts future latent tokens conditioned on language, proprioception, and action history. The predicted future tokens are then routed through the remaining GFM blocks for feature propagation and decoding, allowing a single backbone to produce both future geometry and actions. This design equips the GFM with language-conditioned temporal world modeling through minimal architectural modification while preserving its rich geometric priors. Across a broad suite of simulation and real-robot manipulation benchmarks, GAM is more accurate, more robust, faster, and lighter than current foundation-model-scale baselines.

25.
arXiv (CS.CV) 2026-06-17

GASE: Gaussian Splatting-Based Automated System for Reconstructing Embodied-Simulation Environments

Training embodied agents in the real world requires skilled operators and expensive hardware. Simulation environments offer a compelling alternative by enabling large-scale, cost-effective data augmentation. Consequently, rapidly constructing high-fidelity simulation scenes with a minimal sim-to-real gap has become a critical objective in robot learning. While reconstruction-based methods provide superior visual quality, current workflows are hindered by inefficient data acquisition and subpar foreground object extraction. We thus propose GASE, a highly automated system for simulation scene construction. GASE leverages multi-view video streams from panoramic camera arrays to enable rapid environment scanning. To ensure high-quality asset generation, our pipeline introduces a camera-pose-based strategy that robustly extracts objects across frames in the 2D domain, followed by high-fidelity scene inpainting. Foreground objects and the static background are then reconstructed independently and seamlessly imported into physics simulators for policy training. Extensive experiments demonstrate that GASE outperforms existing 3D Gaussian-based methods in segmentation accuracy by over 10\% while achieving state-of-the-art inpainting quality. Furthermore, real-robot deployments across manipulation and navigation tasks maintains a performance gap of less than 10\% compared to policies trained purely on real-world data. These results confirm that GASE provides an efficient and highly effective solution for bridging the sim-to-real gap. Code will be released.