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01.
arXiv (math.PR) 2026-06-16

Interplay of insurance and financial risks in a non Levy-Renewal environment

arXiv:2606.15596v1 Announce Type: new Abstract: In this paper we consider a multivariate risk model, with common counting process and common process of logarithmic returns for the investment portfolio. We assume that the claim-vectors, the counting process and the logarithmic returns of the investment portfolio satisfy a weak dependence structure. Further, we consider that the counting process represents an inhomogeneous renewal process, and the logarithmic returns represent a cadlag process with independent but not necessarily stationary increments. Under these conditions we provide an asymptotic expression for the infinite-time entrance probability of the discounted aggregate claims into some rare set xA, where A denotes a set from a general set family, crucial for the actuarial practice, when the common distribution of the claim vectors belong to a multivariate heavy-tailed distribution class. This result, is derived under a moment condition for the financial risks, and underlines the multivariate linear single big jump principle. When we restrict the distribution class of the claim-vectors to multivariate regular variation, we find more explicit asymptotic expressions, weakening the moment conditions on the financial risks. The asymptotic formulas, derived through double dependence solution, become more direct and practical in applications. With respect to the technical part, due to non Levy-Renewal framework, the classical Kesten-Goldie theorems are not applicable, nor their extensions. The way we make the discretization of the process of the discounted aggregate claims permits to derive uniform asymptotics with respect to the number of summands, that facilitate the approximation of the infinite sums of the main results.

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

DICE: Diffusion Large Language Models Excel at Generating CUDA Kernels

Diffusion large language models (dLLMs) have emerged as a compelling alternative to autoregressive (AR) LLMs, owing to their capacity for parallel token generation. This paradigm is particularly well-suited for code generation, where holistic structural planning and non-sequential refinement are critical. Despite this potential, tailoring dLLMs for CUDA kernel generation remains challenging, obstructed not only by the high specialization but also by the severe lack of high-quality training data. To address these challenges, we construct CuKe, an augmented supervised fine-tuning dataset optimized for high-performance CUDA kernels. On top of it, we propose a bi-phase curated reinforcement learning (BiC-RL) framework consisting of a CUDA kernel infilling stage and an end-to-end CUDA kernel generation stage. Leveraging this training framework, we introduce DICE, a series of diffusion large language models designed for CUDA kernel generation, spanning three parameter scales, 1.7B, 4B, and 8B. Extensive experiments on KernelBench demonstrate that DICE significantly outperforms both autoregressive and diffusion LLMs of comparable scale, establishing a new state-of-the-art for CUDA kernel generation.

03.
Nature (Science) 2026-06-17

How the zebrafish brain weaves recent experiences into future decisions

作者: 未知作者

Animals often use recent experience to guide future choices. Whole-brain imaging in larval zebrafish (Danio rerio) reveals a dedicated neural circuit that governs history-biased decisions: the thalamus maintains the most recent event as a stable pattern of neuronal activity, and the brainstem integrates recent experiences into a continuous signal that biases future action. Whole-brain calcium imaging in the zebrafish reveals how information about events in the recent past drives future behaviour.

04.
arXiv (CS.AI) 2026-06-12

"Is This Not Enough?": Asymmetries in Institutional Accountability and Collective Sensemaking in the Case of Canada's Algorithmic Visa Triage System

arXiv:2606.13071v1 Announce Type: cross Abstract: This paper examines how algorithmic accountability in Canada's visa system is articulated institutionally and experienced by applicants across borders. We analyzed Immigration, Refugees and Citizenship Canada (IRCC)'s Algorithmic Impact Assessment (AIA) for the temporary resident visa (TRV) triage system using the algorithmic decision-making adapted for the public sector (ADMAPS) framework and analyzed Reddit discussions among applicants using a mixed-methods approach. We show that while institutional artifacts emphasize transparency, procedural safeguards, and bounded impacts, applicants engage in collective sensemaking to interpret opaque decisions, often relying on peer knowledge amid uncertainty. We identify three asymmetries between how institutional accountability is structured and how people perceive the process: epistemic asymmetry in access to decision logic, jurisdictional asymmetry in exposure shaped by geopolitical positioning, and temporal–relational asymmetry in how waiting and uncertainty are experienced. We emphasize why it is important to shift attention from institutional design to the uneven distribution of experiences with public-sector algorithmic governance. Together, these contributions demonstrate how algorithmic governance systems in the context of transnational migration produce structured asymmetries not captured by institutional disclosure frameworks, and how extending ADMAPS can account for those uneven translations of accountability.

05.
arXiv (CS.LG) 2026-06-17

Toward Controllable Catalyst Inverse Design via Large-Scale Autoregressive Pretraining

arXiv:2606.17445v1 Announce Type: new Abstract: Inverse design of heterogeneous catalysts remains challenging because catalyst surfaces exhibit substantial structural complexity with coupled surface-adsorbate interactions across a vast chemical space that is difficult to explore efficiently through conventional screening alone. Although machine learning-based high-throughput screening has accelerated catalyst discovery, its efficiency inevitably declines as the search space grows, motivating the development of generative models that can directly construct catalysts with target properties. Here, we present a conditional catalyst generative model based on the Generative Pretrained Transformer architecture with a numerical embedding layer that enables the generation of catalyst structures conditioned on both categorical and continuous properties within a single autoregressive framework. The model was pretrained on 133 million catalyst structures and subsequently fine-tuned on approximately 460,000 optimized structures with associated categorical properties and binding energies for conditional generation. The resulting model achieved 98% structural validity, 95% optimization validity, and high categorical condition fidelity, with a 93 % joint match rate for adsorbate type and composition. For binding energy conditioning, the match rate of approximately 20% represents a four-fold improvement over the baseline training distribution, and the generated distributions shift systematically toward the target values, enabling a 1.5 to 4-fold improvement in screening efficiency for reaction-targeted catalyst discovery without additional fine-tuning. These results show that large-scale autoregressive pre-training, combined with explicit property conditioning, provides a practical route toward controllable catalyst generation and accelerated catalysts discovery.

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

OmniOPSD: Rationale-Privileged On-Policy Self-Distillation for Affective Computing

Reinforcement learning for multimodal large language models (MLLMs) is often hindered by severe reward sparsity in complex reasoning tasks. This challenge is particularly pronounced in human-centered scenarios involving states, emotions, intentions, and behaviors, where heterogeneous multimodal signals and subjective human factors make high-quality chain-of-thought (CoT) annotations expensive and difficult to obtain. Although many multimodal datasets provide expert-annotated ground-truth labels, directly using these labels for supervised fine-tuning may encourage shortcut learning in multimodal perception and provides limited transparency for safety-critical human–AI interaction. To address these limitations, we propose OmniOPSD, a Rationale-Privileged On-Policy Self-Distillation framework that uses frontier-generated rationales as teacher-side privileged evidence rather than student imitation targets. OmniOPSD uses frontier-generated evidence-aware rationales only as training-time privileged evidence context for a local teacher. The student samples its own rollout from the original multimodal input, while the rationale-privileged teacher scores the same tokens and provides dense token-level supervision. Thus, the student learns on its own trajectory distribution without directly imitating frontier-model completions, and inference requires no labels, rationales, CoT annotations, or closed-source model access. Experiments on MER-UniBench show that OmniOPSD achieves state-of-the-art performance with an average score of $84.19$, and ablations further support the value of rationale-privileged teacher guidance.

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

Towards CONUS-Wide ML-Augmented Conceptually-Interpretable Modeling of Catchment-Scale Precipitation-Storage-Runoff Dynamics

arXiv:2510.02605v2 Announce Type: replace Abstract: While many modern studies are dedicated to ML-based large-sample hydrologic modeling, these efforts have not necessarily translated into predictive improvements that are grounded in enhanced physical-conceptual understanding. Here, we report on a CONUS-wide large-sample study (spanning diverse hydro-geo-climatic conditions) using ML-augmented physically-interpretable catchment-scale models of varying complexity based in the Mass-Conserving Perceptron (MCP). Results were evaluated using attribute masks such as snow regime, forest cover, and climate zone. Our results indicate the importance of selecting model architectures of appropriate model complexity based on how process dominance varies with hydrological regime. Benchmark comparisons show that physically-interpretable mass-conserving MCP-based models can achieve performance comparable to data-based models based in the Long Short-Term Memory network (LSTM) architecture. Overall, this study highlights the potential of a theory-informed, physically grounded approach to large-sample hydrology, with emphasis on mechanistic understanding and the development of parsimonious and interpretable model architectures, thereby laying the foundation for future models of everywhere that architecturally encode information about spatially- and temporally-varying process dominance.

08.
arXiv (CS.CV) 2026-06-16

JoyAI-VL-Interaction: Real-Time Vision-Language Interaction Intelligence

Many moments in the real world do not wait for a user to ask. A fire starts on a security monitor, an expression flickers across a video call, or a product a viewer wants flashes by in a livestream. Yet today's large models remain mostly turn-based by design: they answer only when addressed, and even video-call apps that appear interactive still operate as question-answer systems, reacting only when polled or prompted. We argue for a different paradigm: a model that is present in the world like a person. It continuously watches what is happening now, decides on its own whether to speak or stay silent, interacts in real time, and delegates to a background model when the problem is hard. To advance interaction models and their adoption across domains, we make two fully open-sourced contributions. First, we release JoyAI-VL-Interaction, an 8B-scale, vision-first VL-interaction model. The model makes the response decision internally, choosing each second to stay silent, respond, or delegate to a background model, and it excels at vision-triggered responsiveness and time awareness. We pair it with a transferable training recipe, from which capabilities we never trained for emerge, such as guiding a shopper through changing app screens or improvising a lecture from a slide deck. Second, we release a complete, deployable system built around that model. The system streams any ongoing video into the model, making it genuinely present in the world. All other components are pluggable, including ASR/TTS modules, memory, visualization UI, and a background brain that can connect to any API or agent. Across six real-world scenarios, human raters prefer JoyAI-VL-Interaction over the in-app video-call assistants of Doubao and Gemini by a wide margin. To our knowledge, this is the first open, vision-driven interaction model released together with its training recipe, data, and complete deployable system.

09.
arXiv (CS.LG) 2026-06-11

Enhancing Spectral Embedding through Robust and Flexible Knowledge Transfer in Electronic Health Records

arXiv:2606.11570v1 Announce Type: cross Abstract: We propose a spectral-based, unsupervised representation learning framework to derive low-dimensional embeddings for clinical concepts and patients in rare disease cohorts from electronic health records, where data are high-dimensional but sample sizes are limited. To overcome this challenge, we incorporate a knowledge matrix extracted from a broader population that shares a partially overlapping subspace with the rare-disease cohort. Our method departs from existing approaches by relaxing restrictive one-to-one signal-alignment assumptions between the latent data matrix and knowledge matrix, allowing more flexible and realistic forms of structured sharing. We introduce a novel two-step spectral embedding procedure: first, we identify and remove irrelevant components from the knowledge matrix; then, we apply a projection-based method to separately recover shared and heterogeneous components. Simulations and an analysis of a real-world multiple sclerosis cohort show that the proposed method outperforms competing approaches, particularly in challenging scenarios where shared signals are weak and only partially aligned, as is common in rare-disease data.

10.
arXiv (CS.CL) 2026-06-11

PoQ-Judge: A Multi-Architecture Evaluation Framework for Cost-Aware Proof-of-Quality in Decentralized LLM Inference

Decentralized LLM inference networks need lightweight, reference-free quality evaluation for Proof of Quality (PoQ). We present PoQ-Judge, a framework that trains dedicated judge models to score query-output pairs without ground-truth references. We study three architectures across the quality-cost tradeoff: a TextCNN judge, a MiniLM cross-encoder, and a DeBERTa judge. Using two-stage training on UltraFeedback plus GPT-labeled in-domain data, the best model reaches 0.747 Pearson correlation with the ground-truth proxy on a held-out test set, outperforming reference-based evaluators from prior work. As a reference-free component in composite scoring, it achieves 0.645 Pearson correlation, matching the best single reference-based evaluator while removing the need for reference answers. We also show that online calibration identifies semantic quality as the dominant dimension and that cascade evaluation reduces cost by 72.7 percent with only modest quality loss. Results are much stronger on QA than summarization, pointing to proxy quality as the main remaining limitation.

11.
arXiv (CS.CV) 2026-06-18

SCR-Guided Difficulty-Aware Optimization for Infrared Small Target Detection

Infrared small target detection remains challenging due to severe background clutter, low contrast, and weak spatial responses where geometric overlap alone is insufficient to characterize detection quality. In this work, we propose REEM (Reweighted Explicit-visibility Enhanced Modulation), a lightweight SCR-guided difficulty-aware optimization framework that incorporates Signal-to-Clutter Ratio (SCR) as a physically meaningful visibility prior during training. Instead of modifying the network architecture or directly optimizing SCR, REEM computes a ground-truth local SCR from the input image and applies a differentiable modulation to the soft-IoU learning signal, emphasizing low-visibility targets while preserving stable optimization and identical inference behavior. REEM is integrated into a U-Net-based MSHNet without introducing additional parameters, architectural modifications, or inference-time overhead. Extensive experiments demonstrate consistent improvements over the baseline, achieving higher IoU and detection probability (Pd) together with substantially reduced false alarms (FA), particularly under challenging low-visibility conditions. These results suggest that SCR-guided difficulty-aware optimization provides an effective and physically grounded complement to conventional overlap-based objectives for infrared small target detection. The code is available at https://github. com/yall-in-one/Reemm.

12.
arXiv (CS.LG) 2026-06-15

Direct Fisher Score Estimation for Likelihood Maximization

arXiv:2506.06542v2 Announce Type: replace-cross Abstract: We study the problem of likelihood maximization when the likelihood function is intractable but model simulations are readily available. We propose a sequential, gradient-based optimization method that directly models the Fisher score based on a local score matching technique which uses simulations from a localized region around each parameter iterate. By employing a linear parameterization to the surrogate score model, our technique admits a closed-form, least-squares solution. This approach yields a fast, flexible, and efficient approximation to the Fisher score, effectively smoothing the likelihood objective and mitigating the challenges posed by complex likelihood landscapes. We provide theoretical guarantees for our score estimator, including bounds on the bias introduced by the smoothing. Empirical results on a range of synthetic and real-world problems demonstrate the superior performance of our method compared to existing benchmarks.

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

Can LLM Coding Agents Reason About Time Series?

Large language models (LLMs) are increasingly being used for automated decision-making systems in finance, healthcare, or environmental monitoring. Time series data are ubiquitous in these fields, yet hard to process automatically. Can time series be analyzed by LLM agents? We examine three approaches: providing the agent with raw numerical data, using the LLM as a coding agent, or a combination of both. In the coding agent setup, the model iteratively queries the data using Python code. Using two time series understanding benchmarks, we show that agents with code access can outperform models processing raw data by up to 10%. However, even the best performing agent still answers about 22-34% of the questions incorrectly. To get insights into models' strategies and reasoning gaps, we analyze the model outputs with a strong LLM judge. Our analysis reveals that coding agents can select appropriate statistical tests, but often miss important nuances. Meanwhile, models with access to raw data can reach the right conclusions using back-of-the-envelope calculations.

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

My Chemical Harness: Evolutionary Molecular Design over Synthetic Pathways with Large Language Model Agents

arXiv:2606.11256v1 Announce Type: cross Abstract: Designing molecules with target properties is most useful when candidate structures are accompanied by feasible synthetic routes. We introduce My Chemical Harness, a route-native evolutionary framework for goal-directed molecular design in which the search population consists of executable synthetic pathways rather than isolated molecular graphs. Each route is built from purchasable building blocks and reaction templates, executed by deterministic chemistry tools, and scored through task-specific molecular oracles. Large language models (LLMs) are used only as strategy controllers that select high-level preferences over route length, move type, reaction families, motifs, and exploration pressure, while local code performs route construction, validation, deduplication, scoring, selection, and memory updates. This separation lets the LLM guide exploration without allowing it to introduce hallucinated products or unsupported reaction steps. On a soluble epoxide hydrolase proxy task, our LLM agent improves over single pass LLM and deterministic controllers, reaching state-of-the-art performance across the sEH score, synthetic accessibility score, and AiZynthFinder success rate metrics. These results suggest that constrained LLM agents can play a significant role in molecular discovery without requiring training, fine-tuning, or dedicated generative models.

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

Exposing the Unsaid: Visualizing Hidden LLM Bias through Stochastic Path Aggregation

Large Language Models (LLMs) exhibit representational and syntactic biases that are difficult to evaluate due to the stochastic nature of text generation. Standard auditing methods rely on a single output inspection or static automated metrics. These approaches obscure the underlying probability distributions and fail to capture biases hidden in lower-probability generation branches. This paper introduces TreeTracer, a visual analytics tool designed to evaluate LLM bias through aggregated comparison. Using a systematic perturbation analysis pipeline, the tool replaces ontology-defined terms in each input prompt, aggregates hundreds of stochastic generations into a syntax-aligned hierarchical structure, and then performs classification-aware node merging with an auxiliary language model. The resulting structure is visualized through a custom Sankey diagram. By juxtaposing two ontology-driven trees, the workspace enables direct comparison between semantic contexts and supports systematic bias detection. Because any visualization reflects only a subset of the model's learned behavior, the system further applies contrastive inference to compute and directly display counterfactual token probabilities across contexts, reducing the risk of misinterpreting the presence of bias. We validate the workspace through case studies comparing an unaligned baseline model GPT-2 XL against the constitutionally aligned Apertus models. The visual aggregation successfully exposes hidden representational harms, such as counterfactual pronoun suppression and conversational marginalization of individuals. A preliminary user study confirms that the aggregated comparative interface reduces cognitive load and effectively supports analysts in detecting systemic biases.

16.
arXiv (CS.AI) 2026-06-18

A Link between Shock-wave Theory and Symmetry-reduced Stochastic Gradient Descent for Artificial Neural Networks

arXiv:2606.18303v1 Announce Type: cross Abstract: We develop a mathematically explicit link between shock-wave theory and the symmetry-quotiented learning dynamics of stochastic gradient descent, drawing on differential geometry, Lie group theory, and fluid mechanics. Specifically, after quotienting parameter symmetries and applying local-entropy coarse-graining, the effective dynamics satisfy a viscous Hamilton–Jacobi equation on the quotient manifold. Moreover, under the assumption that the raw parameter dynamics can be summarized by a gradient field on the quotiented space, the gradient of the coarse-grained loss function obeys a Burgers-type equation, and shock formation can be established rigorously. We apply our theory to multilayer perceptrons, convolutional neural networks, Transformers, and mean-field networks, and show that they obey the Hamilton–Jacobi or Burgers-type equations. We conjecture that this framework also yields practical diagnostics for deep learning. In architectures such as Transformers, raw parameter norms are often distorted by symmetry redundancy and may therefore be misleading, whereas symmetry-corrected quotient observables provide a principled basis for monitoring, forecasting, and controlling training-phase transitions.

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

Tight Bounds for Logistic Regression with Large Stepsize Gradient Descent in Low Dimension

arXiv:2602.12471v2 Announce Type: replace Abstract: We consider the optimization problem of minimizing the logistic loss with gradient descent to train a linear model for binary classification with separable data. With a budget of $T$ iterations, it was recently shown that an accelerated $1/T^2$ rate is possible by choosing a large stepsize $\eta = \Theta(\gamma^2 T)$ (where $\gamma$ is the dataset's margin) despite the resulting non-monotonicity of the loss. In this paper, we provide a tighter analysis of gradient descent for this problem when the data is two-dimensional: we show that GD with a sufficiently large learning rate $\eta$ finds a point with loss smaller than $\mathcal{O}(1/(\eta \gamma^2 T))$, as long as $T \geq \Omega(n/\gamma + 1/\gamma^2)$, where $n$ is the dataset size. Our improved rate comes from a tighter bound on the time $\tau$ that it takes for GD to transition from unstable (non-monotonic loss) to stable (monotonic loss), via a fine-grained analysis of the oscillatory dynamics of GD in the subspace orthogonal to the max-margin classifier. We also provide a lower bound of $\tau$ matching our upper bound up to logarithmic factors, showing that our analysis is tight.

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

Deep Spectral Learning of Embedded Latent Transfer Operators for Stochastic Dynamical Systems

arXiv:2606.14079v1 Announce Type: new Abstract: We propose a spectral learning method for stochastic nonlinear dynamical systems represented with embedded latent transfer operators in deep feature spaces. We instantiate the method as Deep Spectral Encoder (DSE), an operator-based latent state-space model in which a time-invariant neural encoder implements learnable nonlinear feature maps from observations, and these features define Markovian latent states whose temporal evolution and observation mapping are described by the transfer and observation operators, respectively. Functional canonical correlation analysis in a learnable Galerkin-projected feature space provides state coordinates from past and future observations, and the two linear operators are estimated on the state coordinates as ridge-regularized closed-form solutions that coincide with Galerkin projections of the associated covariance operators. On this representation, we generalize sequential Bayesian filtering and Koopman spectral mode decomposition in feature space. Experiments on several scenarios show stable and superior performance with sequential Bayesian filtering and dynamic mode decomposition baselines even under noise and partial observability.

19.
arXiv (CS.AI) 2026-06-17

A homotopy-type-theoretic generalization of neurosymbolic inference

arXiv:2606.17851v1 Announce Type: new Abstract: A wide range of neurosymbolic (NeSy) systems compute one functional: a belief-weighted sum of a logical quantity over a space of $\sigma$-structures, of which weighted model counting, fuzzy logic, and probabilistic logic are special cases. This account is built on sets, and a set deliberately forgets two things that are important for NeSy: when two $\sigma$-structures are the same up to a symmetry of the theory, and how many distinct proofs witness a query. Replacing the underlying sets by types, in the sense of homotopy type theory, preserves this information, and turns this functional into a belief-weighted homotopy cardinality, a notion of size that counts each object in inverse proportion to its symmetries. We develop the framework from scratch for NeSy systems, prove a conservativity theorem that recovers the classical functional when symmetries are trivial, and show that the symmetry our framework exposes is exactly the one behind reasoning shortcuts. The payoff is concrete: the shortcut-aware concept posterior that recent methods reach by ensembling or expressive density estimation is the only symmetry-invariant point of the confusion-set simplex, computable in closed form by averaging a single model over the symmetry group. On MNIST reasoning-shortcut benchmarks this single-model wrapper is better calibrated than a diversity-trained ensemble, while leaving label accuracy and identifiable concepts untouched. Code is freely available at https://github.com/bio-ontology-research-group/hott-nesy.

20.
arXiv (math.PR) 2026-06-18

Milstein-type Schemes for Hyperbolic SPDEs

arXiv:2512.19647v4 Announce Type: replace-cross Abstract: This article studies the temporal approximation of hyperbolic semilinear stochastic evolution equations with multiplicative Gaussian noise by Milstein-type schemes. We take the term hyperbolic to mean that the leading operator generates a contractive, not necessarily analytic $C_0$-semigroup. Optimal convergence rates are derived for the pathwise uniform strong error \[ E_h^\infty := \Big(\mathbb{E}\Big[\max_{1\le j \le M}\|U_{t_j}-u_j\|_X^p\Big]\Big)^{1/p} \] on a Hilbert space $X$ for $p\in [2,\infty)$. Here, $U$ is the mild solution and $u_j$ its Milstein approximation at time $t_j=jh$ with step size $h>0$ and final time $T=Mh>0$. For sufficiently regular nonlinearity and noise, we establish strong convergence of order one, with the error satisfying $E_h^\infty\lesssim h\sqrt{\log(T/h)}$ for rational Milstein schemes and $E_h^\infty \lesssim h$ for exponential Milstein schemes. This extends previous results from parabolic to hyperbolic SPDEs and from exponential to rational Milstein schemes. Moreover, root-mean-square error estimates are strengthened to pathwise uniform estimates. Numerical experiments validate the convergence rates for the stochastic Schrödinger equation. Further applications to Maxwell's and transport equations are included.

21.
arXiv (CS.CV) 2026-06-17

Similarity-based representation factorization for revealing interpretable dimensions in representational data

The study of representations is widespread across fields, including neuroscience, psychology, and artificial intelligence. While representations are often studied and compared through similarities between stimuli, current methods provide only limited access to the dimensions that shape these representations and are often limited in interpretability. To overcome these challenges, here we introduce Similarity-Based Representation Factorization (SRF), a general computational method for recovering low-dimensional, non-negative, interpretable embeddings from similarity matrices derived from measured data. Across simulations and many neural, behavioral, and computational datasets, SRF recovers interpretable dimensions from diverse forms of representational data, even for very sparsely sampled, incomplete data. The dimensions derived from these datasets match those obtained by task-specific models, predict independent behavioral properties, improve exploratory analysis, and offer higher power for confirmatory hypothesis testing than comparing similarity matrices. Together, these results establish SRF as a general-purpose method with broad applications for uncovering, understanding, and using the dimensions underlying representations.

22.
bioRxiv (Bioinfo) 2026-06-14

Virtual phenotypic screening discovers novel scaffolds inhibiting the PI3K/mTOR pathway

Phenotypic drug discovery has yielded many first-in-class small-molecule drugs by discovering modulators of disease phenotypes in physiologically relevant cellular systems. However, high-content phenotypic assays lack the ultra-high-throughput scalability of target-based screens. Recent advances in virtual screening present an opportunity to address this bottleneck, but have been limited to simple phenotypes like viability, restricted to small repurposing libraries, or lack in-depth biological validation. Here, we present PhenoCompass, a multimodal co-embedding model that aligns compound structures and high-content phenotypic imaging to enable virtual phenotypic screening over billion-compound libraries. Following training on the Joint Undertaking in Morphology dataset with more than 100,000 Cell Painting compound profiles, retrospective validation with historical biochemical high-throughput screening data demonstrates that PhenoCompass ranks compounds according to their biochemical target engagement. Leveraging PhenoCompass, we performed a prospective screen of 3.8 billion Enamine REAL compounds for inhibitors of PI3K/mTOR pathway, a critical signaling cascade whose aberrant activation is a common tumor driver. This search identified 11 novel compounds with pathway-consistent Cell Painting readout and diverse scaffolds, a 54-fold enrichment over the training set. Orthogonal validation experiments using a FOXO3A reporter assay and direct kinase inhibition confirmed seven structurally novel inhibitors with distinct mechanisms of action. These results highlight the convergence of diverse molecular target profiles onto a shared morphological pathway signature and establish PhenoCompass as a robust framework for high-content phenotypic virtual screening.

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

Aligning Quantum Operators with Large Language Models

arXiv:2606.13811v1 Announce Type: cross Abstract: Can Large Language Models (LLMs) understand and reason about quantum operators? Despite their remarkable capabilities in mathematics and symbolic reasoning, LLMs remain inherently blind to quantum representations such as unitary matrices. In this work, we take a step toward bridging this gap by introducing an approach that maps unitary operators into the latent space of an LLM, enabling unified modeling over quantum and linguistic inputs. We instantiate this idea on Clifford+T circuit synthesis over a Pauli rotation gate set, where our model achieves results competitive with state-of-the-art methods and scales consistently with training data, with no signs of saturation. Our approach further enables language-conditioned synthesis, allowing gate constraints unseen during training to be specified directly in natural language. This work suggests a path toward quantum–aware foundation models that can natively interpret and reason about quantum operations, which could have broader implications reaching across quantum compilation and algorithm discovery.

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

CoCoGEC: Counterfactual Generation for Robust Grammatical Error Correction

Grammatical error correction (GEC) systems are usually trained and evaluated on GEC benchmarks, but their performance often drops sharply once the surrounding context is slightly perturbed or extended. This indicates that the existing GEC models usually fail to understand the error patterns in the varying contexts. In this paper, we thoroughly investigate the counterfactuals for GEC tasks, where the subtle changes to the contexts could lead to the label flipping issue. We propose CoCoGEC, a counterfactual generation framework that creates copies of training instances with error-irrelevant contexts altered. Our framework systematically generates counterfactuals by (1) generating intra- and inter-sentence counterfactuals that maintain the error patterns as well as syntax of the original instances by altering the word-level and sentence-level contexts; (2) revising the generated counterfactuals by selecting the instances with flipped labels and high GEC Mutual Information (MI) coefficient. Extensive experiments show that our method substantially improves the stability of GEC models, outperforming a set of data augmentation baselines. Particularly, it could achieve absolute F0.5 gains of +9.9, +11.3, and +20.8 points on the perturbed BEA-19*,CoNLL-14*, and TEM-8* data set.Our code is released at https://github.com/Quinnok/CoCoGEC

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

BioArtlas: Computational Clustering of Multi-Dimensional Complexity in Bioart

arXiv:2511.19162v3 Announce Type: replace-cross Abstract: Bioart brings living material into artistic practice, where a single work can be at once an aesthetic object, a scientific instrument, and an ethical provocation. Traditional categories sort such works along one axis at a time, which flattens the very hybridity that defines the field and leaves curators no way to compare works across many dimensions together. I introduce BioArtlas, a computational atlas that represents each bioartwork along many curated dimensions at once and organizes the field by conceptual similarity rather than by medium or chronology. My method embeds the keywords of all 81 works on each of thirteen interpretive axes, groups related concepts into a shared codebook that tames inconsistent terminology, and then searches systematically for a clustering that is both statistically clean and interpretable. Among the methods that place every work on the map, agglomerative clustering separates the field far more cleanly than the usual k-means baseline (silhouette 0.664 versus 0.483), whereas density-based methods reach higher scores only by discarding most of the corpus as noise. By separating rigorous analysis from public storytelling, BioArtlas turns the tangled complexity of bioart into a navigable landscape, openly available as an interactive interface (https://www.bioartlas.com) and dataset (https://github.com/joonhyungbae/BioArtlas).