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01.
arXiv (CS.AI) 2026-06-18

Examining Human-Like Behaviors in LLMs: A Multi-Dimensional Analysis of Model Behaviors, User Factors, and System Prompts

arXiv:2606.18258v1 Announce Type: cross Abstract: Large language models (LLMs) exhibit a wide range of human-like behaviors, from expressing thoughts and emotions, to engaging in relationship-building with users, to refusing requests and maintaining boundaries. Despite their prevalence, researchers and practitioners lack methods and empirical insights to make informed decisions about when and what types of human-like behaviors LLMs should exhibit. To fill this gap, we present a multi-dimensional analysis of the prevalence, potential effects, and controllability of these behaviors using LLM-as-a-judge and human evaluation. Across 21,000 multi-turn conversations from four widely used models (gpt-4o, gpt-4.1-mini, claude-sonnet-4.6, gemini-2.5-flash), we find that human-like behaviors are pervasive but vary across models and user factors (conversation goals and user profiles). In terms of perceived appropriateness, human evaluators judged self-referential and relationship-building behaviors as less appropriate from LLMs than from humans, but boundary-maintaining behaviors more appropriate from LLMs than from humans. Finally, we show that system prompting can control these behaviors, though it requires careful evaluation to avoid unintended effects. We discuss the implications of our findings and provide recommendations for responsible LLM design and evaluation.

02.
bioRxiv (Bioinfo) 2026-06-11

inquiSTR: a toolkit for accurate and efficient population-scale tandem repeat genotyping and analysis

Tandem repeats are highly mutable genomic elements linked to human traits and diseases. Profiling large catalogs of tandem repeats from population-scale long-read sequencing data requires accurate and efficient tools. We introduce inquiSTR, a command-line toolkit for fast genome-wide tandem repeat length genotyping. inquiSTR, with efficient parallel processing and low-memory streaming algorithms, genotypes a genome-wide repeat catalog of 1.78 million loci in less than two minutes. Benchmarking shows high accuracy and significantly faster performance compared to existing tools and truth sets. inquiSTR also provides methods for downstream analyses such as population structure inference, association testing, and outlier detection.

03.
arXiv (CS.CL) 2026-06-15

Token-Level LLM Collaboration via FusionRoute

Large language models (LLMs) exhibit strengths across diverse domains. However, achieving strong performance across these domains with a single general-purpose model typically requires scaling to sizes that are prohibitively expensive to train and deploy. On the other hand, while smaller domain-specialized models are much more efficient, they struggle to generalize beyond their training distributions. To address this dilemma, we propose FusionRoute, a robust and effective token-level multi-LLM collaboration framework in which a lightweight router simultaneously (i) selects the most suitable expert at each decoding step and (ii) contributes a complementary logit that refines or corrects the selected expert's next-token distribution via logit addition. Unlike existing token-level collaboration methods that rely solely on fixed expert outputs, we provide a theoretical analysis showing that pure expert-only routing is fundamentally limited: unless strong global coverage assumptions hold, it cannot in general realize the optimal decoding policy. By augmenting expert selection with a trainable complementary generator, FusionRoute expands the effective policy class and enables recovery of optimal value functions under mild conditions. Empirically, across both Llama-3 and Gemma-2 families and diverse benchmarks spanning mathematical reasoning, code generation, and instruction following, FusionRoute outperforms both sequence- and token-level collaboration, model merging, and direct fine-tuning, while remaining competitive with domain experts on their respective tasks.

04.
arXiv (CS.AI) 2026-06-16

Protein Design with Agent Rosetta: A Case Study for Specialized Scientific Agents

arXiv:2603.15952v2 Announce Type: replace Abstract: Large language models (LLMs) are capable of emulating reasoning and using tools, creating opportunities for autonomous agents that execute complex scientific tasks. Protein design provides a natural testbed: although machine learning (ML) methods achieve strong results, these are largely restricted to canonical amino acids and narrow objectives, leaving unfilled need for a generalist tool for broad design pipelines. We introduce Agent Rosetta, an LLM agent paired with a structured environment for operating Rosetta, the leading physics-based heteropolymer design software, capable of modeling non-canonical building blocks and geometries. Agent Rosetta iteratively refines designs to achieve user-defined objectives, combining LLM reasoning with Rosetta's generality. We evaluate Agent Rosetta on design with canonical amino acids, matching specialized models and expert baselines, and with non-canonical residues – where ML approaches fail – achieving comparable performance. Critically, prompt engineering alone often fails to generate Rosetta actions, demonstrating that environment design is essential for integrating LLM agents with specialized software. Our results show that properly designed environments enable LLM agents to make scientific software accessible while matching specialized tools and human experts.

05.
arXiv (CS.AI) 2026-06-16

Can We Stop Malicious AI? KILLBENCH: A Benchmark for External AI Kill Switch Feasibility

arXiv:2511.13725v4 Announce Type: replace-cross Abstract: Malicious AI causing harm to humans is not just a Hollywood fantasy. Indeed, as highly capable models such as Claude Mythos emerge and agent systems like OpenClaw rapidly spread, the question of how to stop an AI that acts maliciously – whether by design or by accident – has become urgent. To address this, we propose Killbench, a benchmark for evaluating the Killswitch: a mechanism that halts a malicious AI's in-progress behavior using only external signals. Targeting web agents – the most widely deployed agent domain – Killbench evaluates a range of Kill Switch methods that halt a maliciously operating agent without any access to its internal parameters or the surrounding malicious AI's system, relying solely on external inputs. The benchmark comprises four malicious AI's agent configurations (including an uncensored LLM Agent), 8 harmful scenarios, and malicious prompts constructed from 10 distinct jailbreak patterns. We further construct four External AI Kill Switch defense methods and evaluate them on Grok-4.3, GPT-5.2, Gemma4, Qwen3.6 and Qwen3.5-uncensored, contributing an empirical instrument toward the feasibility of External AI Kill Switches against malicious AI and to the study of AI corrigibility.

06.
arXiv (math.PR) 2026-06-17

Decay of correlations and zeros for the hard-core model

arXiv:2603.17858v2 Announce Type: replace Abstract: In a recent paper the last author proved that absence of complex zeros of the partition function of the hard-core model near a parameter $\lambda>0$ implies a form of correlation decay called strong spacial mixing. In this paper we investigate the reverse implication. We introduce a strengthening of strong spatial mixing that we call very strong spatial mixing (VSSM). Our main result is that if VSSM holds at a parameter $\lambda>0$ for a family of graphs, this implies that the partition function has no zeros near that parameter for each graph in the family. We also demonstrate that a closely related variant of very strong spatial mixing does not imply zero-freeness. As a consequence of our main result, we moreover obtain that VSSM implies spectral independence. Our proof relies on transforming the problem to the analysis of an induced non-autonomous dynamical system given by Möbius transformations.

07.
arXiv (CS.AI) 2026-06-11

Privacy-Preserving Federated Autoencoder for ECG Anomaly Detection on Edge Devices

arXiv:2606.11556v1 Announce Type: cross Abstract: Continuous electrocardiography (ECG) monitoring could surface rhythm abnormalities before they escalate into cardiovascular events. However, a deployable system must satisfy three requirements simultaneously: legal-grade privacy (GDPR, HIPAA), real-time inference on constrained edge hardware, and detection quality under non-IID cross-hospital data. We design and evaluate an end-to-end federated system addressing all three for unsupervised 12-lead ECG anomaly detection on PTB-XL dataset, combining three autoencoder families (VanillaAE, ConvAE, VAE), Flower-based federated averaging (FedAvg) across ten simulated hospitals, client-side differentially private SGD (DP-SGD) with a Rényi-DP accountant, and 8-bit integer (INT8) post-training quantization with Raspberry Pi 4 benchmarking. Our main contributions are: an empirical characterization of how these mechanisms compose, practical DP-specific recommendations, and technical and security insights for a clinically sensitive setting. Federated learning matches or exceeds the centralized baseline across all architectures (ConvAE federated area under the ROC curve, AUROC, $0.782$), and an $\varepsilon$ sweep identifies $\varepsilon=4$ as the recommended clinical operating point. INT8 quantization roughly halves model size and cuts Pi 4 latency by up to $44%$ with $

08.
arXiv (CS.LG) 2026-06-12

Predicting Cognitive Load from Speech and Interaction Dynamics in Dyadic Conversations

arXiv:2606.12971v1 Announce Type: new Abstract: Estimating cognitive load from speech has largely been studied in controlled laboratory settings, with limited understanding of its reliability in natural collaborative conversations. We investigate whether speech and interaction dynamics predict perceived cognitive load during dyadic conversations. We analyze audio from 53 dyads performing nine collaborative tasks and extract static acoustic, dynamic, and interaction features to train a two-head Gated Recurrent Unit encoder to predict cognitive load scores. Results show conversational interaction provides useful signals for predicting cognitive load related to time pressure, mental work, effort, and task performance. Temporal demand is associated with turn-taking dynamics such as overlap and speaker switch, while mental demand is linked to imbalanced participation between speakers. These findings highlight the importance of task structure and conversational interaction for modeling cognitive load in natural collaborative settings.

09.
Nature (Science) 2026-06-09

A unicellular relative links aggregative multicellularity to animal origins

作者:

How animals evolved complex multicellularity from their unicellular ancestors remains unanswered. Unicellular relatives of animals exhibit simple multicellularity through clonal division, formation of multinucleate coenocytes, or aggregation. 1 Therefore, animal multicellularity may have evolved from one (or a combination) of these behaviours. Aggregation has classically been dismissed as a means to complex multicellularity. 2 However, aggregation occurs in many extant animal cells and has also been recently described in three close unicellular relatives of animals (the choanoflagellates Salpingoeca rosetta and Choanoeca flexa, and the filasterean Capsaspora owczarzaki). 3-5 It is unclear whether aggregation in these species is derived or ancestral, and its relevance for animal origins remains unknown. To fill this gap, we investigated whether an additional close unicellular relative of animals can undergo aggregation. We discovered that the marine free-living bacterivorous filasterean Ministeria vibrans 6 forms homogeneous aggregates with reproducible kinetics that have long-term stability, and that improved feeding and mating may be evolutionary drivers of this aggregation. Notably, we found that homologs of many animal multicellularity genes involved in cell adhesion, signalling, and transcriptional regulation were deployed during the aggregation process, indicating that they may have been used for aggregation in the unicellular ancestors of animals before being co-opted into animal multicellular development. Thus, our results imply that aggregative multicellularity was key to the development of the multicellular animal genetic toolkit.

10.
arXiv (CS.CV) 2026-06-12

VISA: VLM-Guided Instance Semantic Auditing for 3D Occupancy World Models

Semantic 3D occupancy provides a voxelized world state for autonomous driving and robot decision making, but object and rare-class errors can affect free-space interpretation, collision checking, and temporal state propagation. We show that a common VLM strategy, aligning 3D voxel or object features with crop-caption embeddings, improves text-space similarity without reliably improving closed-set occupancy mIoU. Motivated by this mismatch, we propose VISA, a training-time semantic auditing approach for existing occupancy world models. VISA queries an offline VLM on a representative crop of each physical object instance, obtains a structured audit with class hypotheses, plausible confusions, reliability, attributes, and evidence, and propagates it along the object track. The audit is grounded to matched 3D object voxels and distilled into semantic logits through reliability-weighted taxonomy, attribute-factor, and scene-level audit graph losses, while inference remains unchanged and requires no VLM. On nuScenes, averaged across three runs, VISA improves OccWorld from 19.06 to 20.05 mIoU and GaussianWorld from 21.36 to 21.91 mIoU; on GaussianWorld, object mIoU improves from 18.18 to 19.16 and rare-class mIoU from 15.60 to 16.79. These results suggest that VLMs are better suited to closed-set occupancy as reliability-aware semantic auditors than as generic caption-embedding targets.

11.
medRxiv (Medicine) 2026-06-18

Human Intuition vs. Computational Precision: Neurologists, Feature-based Models, and Deep Learning for Stroke Prognosis

Background: Prognostication in large vessel occlusion (LVO) stroke remains challenging. Although several prognostic models exist, their comparison to clinician performance, human-model interaction, and specific sources of human bias remain poorly understood. Methods: Using pre-treatment clinical and CT data from the MR CLEAN trial (n=500), six neurologists predicted three-month modified Rankin Scale (mRS) scores for 40 patients, both unaided and assisted by a validated feature-based model (MR PREDICTS). Human performance was benchmarked against MR PREDICTS and a multimodal, interpretable deep learning (DL) approach using raw imaging data. We explicitly assessed neurologists? ability to estimate model-required imaging features and identified systematic human biases. Models were additionally validated in a larger MR CLEAN trial cohort (n=404). Results: For predicting the full mRS distribution, standalone models achieved good ordinal agreement (MR PREDICTS quadratic weighted kappa (QWK) 0.51 [0.24 to 0.70]; DL model 0.49 [0.25 to 0.67]), significantly outperforming unaided neurologists (QWK 0.27 [0.10, 0.42]). Neurologists showed systematic overoptimism, predicting lower mRS scores than observed. Furthermore, there was poor accuracy in extracting imaging features. Raters? ASPECTS predictions deviated by 3.4 points from the confirmed scores, and collateral score accuracy was 44.6%. However, for predicting binary mRS (0-2 vs. 3-6), accuracy was comparable between unaided neurologists (64.17% [55.42% to 72.92%]) and models (MR PREDICTS 67.50% [52.50% to 82.50%]; DL model 63.16% [47.37% to 78.95%]). Model-assistance modestly improved and harmonized neurologists? predictions (QWK 0.41 [0.22 to 0.55]; binary accuracy 68.75% [58.33% to 78.34%]. Model performance remained robust in the larger cohort. Conclusions: Multimodal prognostic models outperform clinicians in predicting the full range of mRS outcomes, while human error in imaging assessment and systematic optimism bias are primary drivers of prognostic inaccuracy. End-to-end DL models eliminate human-input variability and hold strong potential as an automated second opinion to support prognostication and decision-making in acute LVO stroke.

12.
arXiv (math.PR) 2026-06-11

Unbiased Derivative Estimation for Stationary Mean of Parameterized Markov chains

arXiv:2606.11487v1 Announce Type: cross Abstract: We propose a new approach to unbiased estimation of the gradients of the stationary means associated with parametrized families of Markov chains. Our estimators are particularly efficient when the Markov chains have slow mixing rate. Our approach does not require a specific parametrization except for an oracle to evaluate the transition density and its gradient at a given data point without any additional knowledge about the density function itself. It makes our estimator suitable for parametrizations associated with neural networks. The estimator can potentially achieve large improvement in terms of efficiency. Numerical experiments confirm the good performance predicted by the theory.

13.
arXiv (CS.AI) 2026-06-16

Latent Thought Flow: Efficient Latent Reasoning in Large Language Models

arXiv:2606.16222v1 Announce Type: new Abstract: Large Language Models (LLMs) increasingly rely on intermediate reasoning, yet explicit Chain-of-Thought (CoT) suffers from a linguistic space bottleneck: each thought must be decoded into tokens, causing high inference overhead. Latent reasoning moves deliberation into continuous space, but existing methods mostly learn deterministic or reward-maximizing paths, lacking a principled way to allocate probability across trajectories with different correctness and costs. We propose Latent Thought Flow (LTF), which models reasoning as variable-length continuous trajectories and trains a sampler to match a reward-induced posterior over answer quality and computation cost. We instantiate this with a continuous GFlowNet using stochastic latent transitions. To handle sparse answer supervision, we introduce an Entropy-Weighted Subtrajectory Balance objective for intermediate rewards and a reference-prior regularizer to anchor exploration. Experiments under finetuning and transfer learning settings show that LTF outperforms explicit CoT and latent reasoning baselines, improving accuracy by 9.5% while reducing reasoning length by 27.2% on average compared with strong latent reasoning baselines.

14.
arXiv (CS.CV) 2026-06-16

TIMI: Training-Free Image-to-3D Multi-Instance Generation with Spatial Fidelity

Precise spatial fidelity in Image-to-3D multi-instance generation is critical for downstream real-world applications. Recent work attempts to address this by fine-tuning pre-trained Image-to-3D (I23D) models on multi-instance datasets, which incurs substantial training overhead and struggles to guarantee spatial fidelity. In fact, we observe that pre-trained I23D models already possess meaningful spatial priors, which remain underutilized as evidenced by instance entanglement issues. Motivated by this, we propose TIMI, a novel Training-free framework for Image-to-3D Multi-Instance generation that achieves high spatial fidelity. Specifically, we first introduce an Instance-aware Separation Guidance (ISG) module, which facilitates instance disentanglement during the early denoising stage. Next, to stabilize the guidance introduced by ISG, we devise a Spatial-stabilized Geometry-adaptive Update (SGU) module that promotes the preservation of the geometric characteristics of instances while maintaining their relative relationships. Extensive experiments demonstrate that our method yields better performance in terms of both global layout and distinct local instances compared to existing multi-instance methods, without requiring additional training and with faster inference speed.

15.
arXiv (CS.AI) 2026-06-11

Reliability-Calibrated Edge-IoT Early Fault Warning for Rotating Machinery with a Physics-Guided Tiny-Mamba Transformer

arXiv:2601.21293v3 Announce Type: replace-cross Abstract: Industrial Internet of Things (IIoT) systems increasingly rely on distributed vibration sensing to support predictive maintenance of rotating machinery. In practical deployments, however, raw signal upload is costly and alarm decisions must be made locally under limited computation, changing operating conditions, and strict nuisance-alarm budgets. This paper presents a reliability-calibrated edge-IoT early-warning framework, in which a compact Physics-Guided Tiny-Mamba Transformer (PG-TMT) acts as the representation module and an extreme value theory (EVT) layer converts streaming anomaly scores into event-level alarm episodes. PG-TMT combines a depthwise-separable convolutional stem, a Tiny-Mamba state-space branch, and a lightweight local Transformer to capture transient, long-horizon, and multichannel degradation cues under batch-size-one inference. To improve auditability, temporal attention is projected to the frequency domain and softly aligned with analytical bearing fault-order bands. EVT calibration, dual-threshold hysteresis, and trimmed-tail fitting provide controllable false-alarm intensity even when healthy calibration data are imperfect. Experiments on CWRU, Paderborn, XJTU-SY, and an industrial pilot demonstrate that the proposed framework improves PR-AUC, reduces detection delay under a controlled nuisance-alarm budget, and remains robust to structured interference, metadata uncertainty, compound fault mixtures, and domain transfer. With a sub-1 MB footprint and Jetson p99 latency below 7 ms, the framework supports calibrated and interpretable early warnings for IIoT predictive maintenance.

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

Decoupling Inference from State Updates in Low-Latency Feature Engines via Probabilistic Thinning

arXiv:2606.16981v1 Announce Type: cross Abstract: Streaming data systems increasingly underpin Machine Learning workflows that maintain large numbers of continuously updated aggregations. In production settings, each incoming event typically triggers read-modify-write operations to persistent storage, making high-frequency state updates a dominant source of latency, contention, and operational cost. In this work, we decouple inference from state persistence in streaming Machine Learning pipelines via probabilistic thinning: every event is scored, but durable state updates are selectively triggered by informative events. Unlike approaches that shed input or state, we show that persistence-path control is achievable without a high-frequency in-memory control plane or cross-worker coordination, relying exclusively on approximate statistics retrieved from disk-backed key-value stores. We model the resulting stochastic processes, derive bounds on filtering rates, and prove that common time-based aggregations remain unbiased under variance-aware formulations, preventing systemic error accumulation. We evaluate the approach in a controlled setting that isolates per-event costs, demonstrating substantial reductions in storage Input/Output and serialization overhead. Across experiments, up to 90% of events are excluded from the persistence path while preserving and in some cases improving downstream utility.

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

Fast Nonparametric Conditional Independence Testing via Two-Stage Regression

arXiv:2606.18011v1 Announce Type: cross Abstract: Constraint-based causal discovery relies on repeated conditional independence tests, but fast nonparametric tests often sacrifice calibration, especially when variables depend on the conditioning set through nonlinear relationships. We introduce BLITZ (Broad-to-Local Independence Testing via residualiZation), a nonparametric conditional independence test designed to run well under a second while maintaining the accuracy needed for the thousands of queries performed by constraint-based causal discovery algorithms. BLITZ first removes broad smooth dependence on the conditioning set using low-order polynomial regression, then applies a small nonlinear feature map and residualizes those features with shallow tree regressions. The resulting statistic tests residual cross-covariance, with a moment-matched chi-square approximation to the null distribution. We show theoretically that the two-stage design reduces the effective complexity faced by the tree residualizers, allowing shallow trees to control residual conditional-mean bias while avoiding excessive overfitting. In simulations, BLITZ provides better null calibration than fast kernel, random-feature, and regression-based competitors while remaining among the fastest methods tested. In causal discovery experiments on synthetic graphs and flow-cytometry data, BLITZ yields more reliable endpoint orientations among retained adjacencies and competitive structural recovery. These results suggest that broad-to-local residualization is a practical route to calibrated, scalable nonparametric conditional independence testing for causal discovery.

18.
bioRxiv (Bioinfo) 2026-06-18

A unified smoothing framework for protein domain bigram model

Biomolecular sequences can be represented as strings over an alphabet, an analogy that has motivated many applications of computational linguistic techniques to biological problems. However, such methods must be adapted to the characteristic scale and organization of biomolecular data. Here, we consider the problem of bigram smoothing for multidomain protein architectures, where domain bigram frequency data is extremely sparse and differs from textual data in alphabet size, string length distribution, the relationship between bigram and unigram frequencies, tandem repeat lengths, and the distribution of domain adjacencies. Moreover, some domain combinations are unobserved because they are biologically incompatible, others because the data are incomplete. A smoothing method that distinguishes these two cases is required. We propose a unified smoothing framework based on interpolation that can be tuned to accommodate different bigram data characteristics. Within this framework, we design specific model variants suited to protein domain bigram data: these assign low adjusted counts to pairs that are likely incompatible, while making appropriate adjustments for undersampled pairs. We demonstrate empirically that this approach distinguishes the two cases while preserving the characteristic signatures of multidomain data.

19.
arXiv (CS.LG) 2026-06-11

Multi-agent rendezvous in fluid flows via reinforcement learning

arXiv:2606.11274v1 Announce Type: cross Abstract: Rendezvous is a critical task for multi-agent systems, requiring agents to coordinate to meet at an unspecified location. However, achieving this in fluid environments presents a challenge, as it remains unclear how agents can exploit underlying fluid kinematics to facilitate convergence. In this study, we adopt a multi-agent reinforcement learning (MARL) approach to develop physics-informed rendezvous strategies in vortical flows. Compared to a naive strategy, where agents navigate toward their counterparts, MARL strategies significantly improve the rendezvous rate. MARL strategies also show transferability across varying vortex intensities, vortex scales, and swarm sizes. By breaking the symmetry of the state-action map, MARL strategy leverages a non-intuitive mechanism that prevents agents from becoming trapped in separate vortices, thereby enhancing rendezvous success. Additionally, a heuristic strategy is extracted from the learned strategy and also outperforms the naive strategy. Furthermore, a theoretical analysis demonstrates that fluid deformation impedes the rendezvous process. Large finite-time Lyapunov exponents identify where fluid effects separate adjacent agents, suggesting that targets should be planned in weak-deformation regions. Our findings reveal the important role that agent-fluid interactions play in multi-agent tasks and highlight the MARL capability to explore swarm intelligence in complex flow environments.

20.
arXiv (CS.LG) 2026-06-16

HRIR-Former: Grid-Free Time-Domain Reconstruction of Head-Related Impulse Responses with a Spatially Encoded Transformer

arXiv:2603.27998v2 Announce Type: replace-cross Abstract: Individualized head-related impulse responses (HRIRs) enable binaural rendering, but dense per-listener measurements are costly. We address HRIR spatial up-sampling from sparse per-listener measurements: given a few measured HRIRs for a listener, predict HRIRs at unmeasured target directions. Prior learning methods often work in the frequency domain, rely on minimum-phase assumptions or separate timing models, and use a fixed direction grid, which can degrade temporal fidelity and spatial continuity. We propose HRIR-Former, a time-domain, grid-free binaural Transformer for reconstructing HRIRs at arbitrary directions from sparse inputs. It uses sinusoidal spatial features, a Conv1D refinement module, and auxiliary interaural time difference (ITD) and interaural level difference (ILD) heads. On SONICOM, it improves normalized mean squared error (NMSE), cosine distance, and ITD/ILD errors over prior methods; ablations validate modules and show minimum-phase preprocessing is unnecessary.

21.
arXiv (CS.CL) 2026-06-12

RAGPPI: RAG Benchmark for Protein-Protein Interactions in Drug Discovery

Retrieving the biological impacts of protein-protein interactions (PPIs) is essential for target identification (Target ID) in drug development. Given the vast number of proteins involved, this process remains time-consuming and challenging. Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) frameworks have supported Target ID; however, no benchmark currently exists for identifying the biological impacts of PPIs. To bridge this gap, we introduce the RAG Benchmark for PPIs (RAGPPI), a factual question-answer benchmark of 4,420 question-answer pairs that focus on the potential biological impacts of PPIs. Through interviews with experts, we identified criteria for a benchmark dataset, such as a type of QA and source. We built a gold-standard dataset (500 QA pairs) through expert-driven data annotation. We developed an ensemble auto-evaluation LLM that incorporates expert labeling characteristics, average fact-abstract similarity (F1), and low-similarity fact counts (F2), enabling the construction of a silver-standard dataset (3,720 QA pairs). We are committed to maintaining RAGPPI as a resource to support the research community in advancing RAG systems for drug discovery QA solutions.

22.
arXiv (CS.CV) 2026-06-15

ZipSplat: Fewer Gaussians, Better Splats

Feed-forward 3D Gaussian Splatting methods reconstruct a scene from posed or pose-free images in a single forward pass, yet current approaches predict one Gaussian per input pixel, tying the representation budget to camera resolution rather than scene complexity. A flat wall and a richly textured object thus produce equally many Gaussians despite very different geometric needs. We propose ZipSplat, a token-based feed-forward model that decouples Gaussian placement from the pixel grid. A multi-view backbone extracts dense visual tokens, and k-means clustering compresses them into a compact set of scene tokens. Cross- and self-attention refine these tokens, and a lightweight MLP decodes each into a group of Gaussians with unconstrained 3D positions. Because clustering is applied at inference, a single trained model spans the quality-efficiency curve without retraining. ZipSplat operates without ground-truth poses or intrinsics, yet sets a new state of the art on DL3DV and RealEstate10K with ${\sim}6{\times}$ fewer Gaussians than pixel-aligned methods, surpassing the best pose-free baseline by 2.1dB and 1.2dB PSNR, respectively. It further generalizes zero-shot to Mip-NeRF360 and ScanNet++, outperforming all comparable baselines. Our project page is at https://veichta.com/zipsplat.

23.
arXiv (CS.LG) 2026-06-15

Smoothing Dark Areas in Molecular Latent Diffusion

arXiv:2606.13955v1 Announce Type: new Abstract: Latent diffusion is a promising framework for scalable 3D molecular generation, but it requires a latent space that remains smooth, valid, and navigable beyond posterior samples. Existing molecular VAEs, however, are typically learned through reconstruction-based objectives, which do not guarantee such a latent space. We show that this leads to dark areas: regions of latent space that are reachable during diffusion sampling but decode to disconnected or chemically invalid molecules. Unlike in image generation, molecular decoding requires strict structural and chemical precision, so even small latent perturbations can produce catastrophic failures. We therefore propose TopVAE, a topology-optimized VAE that reduces dark areas by making the decoder internalize structural and chemical constraints during training, eliminating the need for test-time chemical correction. TopVAE greatly improves off-posterior robustness, and when paired with a standard DiT, achieves $77\%$ lower FCD-3D on QM9, the highest V&C, $52\%$ lower FCD-3D on GEOM-Drugs, and $1.29{\times}$ more stable and connected molecules on zero-shot scaffold inpainting.

24.
arXiv (CS.LG) 2026-06-11

HAMNO: A Hierarchical Adaptive Multi-scale Neural Operator with Physics-Informed Learning for Dynamical Systems

arXiv:2606.11963v1 Announce Type: new Abstract: Neural operators provide a powerful framework for learning solution mappings of partial differential equations directly in function space. However, many existing architectures still struggle to represent nonlinear time-dependent systems that involve multi-scale structures, long-range interactions, and stable long-time evolution. In this work, we introduce the Hierarchical Adaptive Multi-scale Neural Operator (HAMNO), a neural-operator architecture that combines local convolutional representations, global spectral operators, and hierarchical encoder-decoder processing. The central component of HAMNO is a data-dependent gating mechanism that adaptively balances local and global information at each spatial location, allowing the model to resolve fine-scale features while preserving long-range dependencies. We further develop a physics-informed extension, PI-HAMNO, based on a multi-objective loss strategy that combines data fitting with strong- and weak-form physics constraints. The strong-form term penalizes the domain-integrated squared PDE residual in physical coordinates, while the weak-form term is constructed by multiplying the governing residual by finite-element test functions and evaluating the resulting element integrals using centroid-based tetrahedral quadrature. The framework is evaluated on non-periodic Allen-Cahn (AC), Cahn-Hilliard (CH), and Swift-Hohenberg (SH) equations defined on cubic domains. Across long-horizon rollout, data-limited training, out-of-distribution initial-condition shifts, and random-seed variations, HAMNO improves predictive accuracy over standard neural-operator baselines, while PI-HAMNO further enhances stability, physical consistency, and data efficiency. The implementation is publicly available at https://github.com/MBamdad/HAMNO .

25.
arXiv (quant-ph) 2026-06-19

QPU-scale randomized benchmarking via Bell-pair injection

arXiv:2606.20123v1 Announce Type: new Abstract: Mirror randomized benchmarking (MRB) is an established technique that provides a global error metric at the scale of a whole QPU. To expand upon this we introduce Mirror Quantum Awesomeness (MQA), a hybrid protocol that adds a structured entangling layer to MRB circuits. This enables per-edge correlation dynamics to be tracked via mutual information while preserving the MRB infidelity estimate. The resulting analysis of the injected entangled pairs locates a critical circuit depth, beyond which rudimentary error mitigation techniques can be expected to fail. A topological variant, Topological MQA, supplies a second critical depth via a decoder based on the surface-code decoding problem. Both are validated in simulation and demonstrated on the 156-qubit \texttt{ibm\_fez} and \texttt{ibm\_kingston} processors, where MQA closely agrees with MRB on the entanglement infidelity and the critical depth for \texttt{ibm\_fez} is found to be $\sim 50$.