Academic Intelligence · Curated Daily

探索全球前沿学术脉络

AcademicHub 汇聚顶级期刊与预印本平台的实时文献。定制您的专属科研雷达,利用大语言模型自动生成交叉领域文献分析简报。

01.
arXiv (CS.AI) 2026-06-15

Think Fast: Estimating No-CoT Task-Completion Time Horizons of Frontier AI Models

arXiv:2606.07157v2 Announce Type: replace Abstract: Many efforts to ensure frontier AI models are safe rely on monitoring their chain-of-thought (CoT) reasoning. If models become able to perform sufficiently complex reasoning internally, without explicit thinking tokens, this would undermine such oversight. We measure how well frontier models reason without CoT across a suite of over 30,000 questions spanning 43 benchmarks in domains including math, coding, puzzles, causality, theory-of-mind, and strategic reasoning. To compare models against humans, we estimate the $50\%$-task-completion time horizon (TH): the human time required for tasks a model completes with $50\%$ success rate. We complement this with a $50\%$ reasoning token horizon: the minimum number of o3-mini reasoning tokens needed for tasks a model solves with $50\%$ success rate. We find that the no-CoT $50\%$ TH of frontier models has been doubling roughly every year over the past six years, with GPT-5.5's TH reaching over 3 minutes and reasoning token horizon exceeding 1,500 tokens. Our median estimates predict that frontier no-CoT THs could exceed 7 minutes by 2028, and 25 minutes by 2030, though these projections carry substantial uncertainty. We recommend frontier developers track this explicitly.

03.
arXiv (CS.LG) 2026-06-19

CAGE: Curvature-Aware Gradient Estimation For Accurate Quantization-Aware Training

arXiv:2510.18784v3 Announce Type: replace Abstract: Despite significant work on low-bit quantization-aware training (QAT), there is still an accuracy gap between such techniques and native training. To address this, we introduce CAGE (Curvature-Aware Gradient Estimation), a new QAT method that augments the straight-through estimator (STE) gradient with a curvature-aware correction designed to counteract the loss increase induced by quantization. CAGE is derived from a multi-objective view of QAT that balances loss minimization with the quantization constraints, yielding a principled correction term that depends on local curvature information. On the theoretical side, we introduce the notion of Pareto-optimal solutions for quantized optimization, and establish that CAGE yields strong convergence guarantees in the smooth non-convex setting. In terms of implementation, our approach is optimizer-agnostic, but we provide a highly-efficient implementation that leverages Adam statistics. CAGE significantly improves upon the prior state-of-the-art methods in terms of accuracy, for similar computational cost: for QAT fine-tuning, it halves the compression accuracy loss relative to the prior best method, while for QAT pre-training of Llama models, its accuracy for 3-bit weights-and-activations (W3A3) matches the accuracy achieved at 4-bits (W4A4) with the prior best method. The official implementation can be found over https://github.com/IST-DASLab/CAGE .

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

Question-Aware Evidence Ledgers for Video Relational Reasoning

The VRR-QA challenge evaluates visual relational reasoning in videos, where answers often depend on implicit spatial relations, event boundaries, target identity, and dialogue context rather than a single salient frame. We present a test-time reasoning pipeline built around a strong GPT-5.5 video QA solver and a set of question-aware evidence ledgers. The initial solver answers each question from a uniform video representation, while routed ledgers are prompted to make the required targets, count units, reference frames, and temporal or spatial scope explicit for counting, spatial, endpoint, viewpoint, and dialogue reasoning. External tools such as open-vocabulary detection, depth cues, pair crops, ASR, and scene-graph ledgers are used only as evidence sources. A conservative gate keeps the current answer unless independent evidence uniquely supports a different option. The final evidence-gated pipeline achieves 92.95% overall accuracy and 93.79% macro accuracy on the challenge test split.

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

From Correlation to Causation in Lane Change Prediction for Automated Driving: A Causal Explanation Framework

arXiv:2606.15756v1 Announce Type: cross Abstract: Lane-change prediction is a central task in intelligent vehicles, where early maneuver anticipation can support safer decision-making. However, many existing approaches mainly learn statistical associations between observed driving variables and future maneuvers, while overlooking the causal dependencies among the input variables themselves. This limits interpretability, especially when physically related variables such as longitudinal gap, relative longitudinal velocity, and Time-To-Collision (TTC) are treated as independent flat inputs. This article presents a causal-inference-based framework for lane-change prediction and explanation. The proposed approach combines linguistic feature construction, expert-constrained causal discovery, deep structural causal modeling with Deep End-to-end Causal Inference (DECI), intervention-based effect analysis, refutation testing, and recursive causal-chain explanation. The objective is not only to predict the future maneuver, but also to identify candidate variables that directly contribute to the prediction, the upstream factors influencing them, and the causal chains through which these effects propagate. The framework achieves average F1-scores above 95% during the first three seconds before the lane-marking crossing event. Beyond prediction accuracy, the framework uses intervention-based effect analysis to distinguish influential from weakly influential variables under the learned causal structure. It further distinguishes candidate direct contributors from mediated effects and generates contrastive causal-chain explanations that clarify why the predicted maneuver is favored and why the alternative maneuvers are less supported. The main contribution is therefore a mechanism-aware lane-change prediction pipeline that moves beyond correlation-based classification toward more interpretable causal reasoning for maneuver prediction.

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

Atypical Decay Rates for Atypical Heights in Random Recursive Trees

arXiv:2604.20139v2 Announce Type: replace Abstract: We establish the large deviation probabilities for the height of random recursive trees, revealing polynomial upper-tail decay and stretched-exponential lower-tail decay. Remarkably, the lower tail features an atypical prefactor that grows to infinity more slowly than any $n$-fold iterated logarithm.

07.
arXiv (quant-ph) 2026-06-24

Suppressing Self-Discharging of Quantum Batteries by Cavity Interactions

arXiv:2606.23999v1 Announce Type: new Abstract: We analyse a two-cavity architecture, in which a lossy cavity hosting $N$ qubits is coherently coupled to an auxiliary cavity, as a resource for the storage phase of an open quantum battery at non-zero temperature. Within a local Lindblad treatment in the resonant configuration, we find that the inter-cavity coupling enhances the suppression of self-discharging across every initial preparation, battery size, and temperature we examine, with the protection degrading smoothly as the mean thermal occupation increases. For a single qubit, the energy-basis coherence of a pure superposition leads to better long-time retention than fully excited state, highlighting the beneficial role of quantum coherence in protecting stored energy against thermal degradation. For two-qubit batteries, Bell-state preparations exhibit enhanced long-time ergotropy retention compared with the fully excited state, while the inclusion of qubit-qubit interactions produces only a weak dependence on the interaction type and strength within the parameter regime considered. Extending the analysis to multi-qubit GHZ-charged batteries with all-to-all Heisenberg interactions, we find that the normalized retained ergotropy increases monotonically with the number of qubits. This behavior is consistent with the collective enhancement of the qubit-cavity coupling in the symmetric Dicke manifold, indicating that larger quantum batteries can benefit from improved protection against self-discharge. These findings establish cavity-assisted protection as a promising strategy for mitigating self-discharging and realizing of long-lived quantum batteries in experimentally accessible platforms.

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

MDForge: Agentic Molecular Dynamics Pipeline Design under Sparse Simulator Feedback

Molecular dynamics (MD) is the canonical in-silico method for atomistic molecular science, simulating molecular behavior from first-principle physics. Designing an MD pipeline for a new system requires substantial expert knowledge: running it on even one molecule is expensive, ruling out trial-and-error. We automate this expert pipeline-design process with an LLM agent. Unlike existing MD agents that orchestrate a predefined tool set, we treat pipeline design as open-ended code generation in which the agent's behavior is reshaped online by verbal reward. Specifically, we build MDForge, an LLM agent whose in-context update rule densifies the sparse reward via a multi-agent debate among physics experts. On three SAMPL host-guest binding free-energy benchmarks, MDForge automatically designs MD pipelines competitive with human experts. Deployed on a library of unseen candidate guests, its CB[7] pipeline discovers a novel binder that wet-lab competition NMR confirms is a high-affinity, picomolar CB[7] binder. Our data and code are available at https://github.com/Zehong-Wang/MDForge.

10.
arXiv (CS.LG) 2026-06-24

Decentralized SGD with Controlled Disagreement Finds Flatter Minima

arXiv:2602.02899v2 Announce Type: replace Abstract: Decentralized training is often regarded as inferior to centralized training because the consensus errors between workers are thought to undermine convergence and generalization. This work challenges this view by introducing decentralized SGD with Adaptive Consensus (DSGD-AC), which uses a time-dependent scaling mechanism to maintain consensus errors throughout the training. We show that adaptive consensus changes the stationary variance of disagreement modes by balancing two effects: it preserves consensus-error magnitude through weaker graph damping while still allowing curvature-dependent damping to shape the disagreement directions. This balance can produce a stronger Hessian-weighted loss-envelope penalty around the deployed model, even when normalized Hessian alignment is weaker than in standard DSGD. Empirical results on image classification show that DSGD-AC reaches flatter solutions and higher test accuracy than standard DSGD and even centralized SGD. Together, these results support consensus errors as a useful implicit regularizer and open a new perspective on the design of decentralized learning algorithms.

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

Temporal Straightening for Latent Planning

arXiv:2603.12231v2 Announce Type: replace Abstract: Learning good representations is essential for latent planning with world models. While pretrained visual encoders produce strong semantic visual features, they are not tailored to planning and contain information irrelevant – or even detrimental – to planning. Inspired by the perceptual straightening hypothesis in human visual processing, we introduce temporal straightening to improve representation learning for latent planning. Using a curvature regularizer that encourages locally straightened latent trajectories, we jointly learn an encoder and a predictor of a Joint-Embedding Predictive Architecture (JEPA) world model. We show that reducing curvature this way makes the Euclidean distance in latent space a better proxy for the geodesic distance and improves the conditioning of the planning objective. We demonstrate empirically that temporal straightening makes gradient-based planning more stable and yields significantly higher success rates across a suite of goal-reaching tasks. Our code is available at https://agenticlearning.ai/temporal-straightening.

12.
medRxiv (Medicine) 2026-06-18

Personalizing Suicide Risk Assessment: Machine Learning Extraction of Cross-Modal Interactions Between Psychosocial and Demographic Factors in Veterans

Background: Veterans face an elevated risk of suicide compared to the general population, motivating national efforts to develop predictive models that can guide proactive care. Current models used by the U.S. Department of Veterans Affairs (VA) rely primarily on structured electronic health record (EHR) data, though clinical notes contain rich contextual information that can be quantified using natural language processing (NLP) to derive psychosocial variables that may improve risk detection. Machine learning methods, particularly classification and regression trees (CART), can also uncover interactions between clinical and psychosocial variables, enabling identification of patient characteristics that modify suicide risk factors. However, integrating structured and unstructured data presents challenges because NLP features often greatly outnumber traditional clinical variables, potentially biasing interaction discovery. In prior work, we addressed this imbalance by introducing a weighted CART framework that balances structured variables with NLP-derived psychosocial features from semantic lexicons (SEANCE). While effective, semantic approaches summarize language into predefined constructs and may overlook important lexical variation present in clinical narratives. Methods: In this study, we extend that framework by replacing semantic features with a high-dimensional bag-of-words (BoW) representation of clinical notes and by evaluating models across cohorts defined by structured suicide risk stratification (low, medium, high) and varying temporal lookback windows. Using a cohort of 27,241 veterans, we analyzed clinical documentation collected up to 30, 90, or 270 days prior to death (or a matched index date for controls), enabling temporally flexible risk modeling. XGBoost models were trained to balance structured and unstructured features and identify cross-modal interactions between textual and clinical variables. Results: When incorporated into generalized linear models, these interactions improved predictive performance, particularly among low- and medium-risk patients, and substantially reduced the performance gap between interpretable and more complex models. Notably, the BoW representation outperformed our prior semantic index-based approach. Discussion and Conclusions: Together, these findings demonstrate the utility of interpretable NLP methods for uncovering clinically meaningful interactions between psychosocial and demographic factors in suicide risk and establish a strong benchmark for future deep learning approaches aimed at capturing richer contextual and temporal information from clinical narratives.

13.
arXiv (CS.AI) 2026-06-12

HybridCodeAuthorship: A Benchmark Dataset for Line-Level Code Authorship Detection

arXiv:2606.12620v1 Announce Type: cross Abstract: Thanks to the rapid adoption of AI code assistants powered by large language models (LLMs), industry codebases are, increasingly, a hybrid of AI- and human-authored code. For risk management and productivity analysis purposes, it is crucial to enable fine-grained location detection of AI-generated code. To develop algorithms for this task, quality benchmarks are needed to assess performance. However, existing benchmarks tend to comprise academic, LeetCode-style problems and presume a code snippet is either completely human-authored or completely AI-authored, which is not reflective of the diverse intents and styles of industry codebases utilizing AI code assistants. To fill these gaps, we introduce HybridCodeAuthorship, a novel benchmark of Python code files with interleaved human- and AI-authored lines of code to simulate authentic utilization of AI code assistants. In this paper, we first present our dataset construction pipeline, which leverages CodeSearchNet, a massive collection of links to open sourced repositories on GitHub. We then benchmark the performance of two state-of-the-art AI-generated code detection algorithms at both the line- and chunk-level. Experimental results demonstrate that HybridCodeAuthorship is a challenging benchmark with a top-scoring algorithm, AIGCode Detector, obtaining a highest F1 score of 0.48 and 0.56 on chunk-level and line-level code detection tasks, respectively.

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

Koshur Diacritizer: A Byte-Level Sequence-to-Sequence Model for Kashmiri Diacritic Restoration

Kashmiri, an Indo-Aryan language written in a modified Perso-Arabic script, frequently omits diacritic marks in digital text, creating ambiguity and challenging downstream NLP applications. We present Koshur Diacritizer, a ByT5-small byte-level sequence-to-sequence model for restoring diacritics in Kashmiri text. To support this task, we release a publicly available dataset of 23.7k aligned undiacritized diacritized Kashmiri sentence pairs. The proposed framework combines script-aware normalization, alignment validation, and skeleton-preserving inference to ensure reliable restoration while maintaining the original base-letter sequence. Experimental results on a held-out test set achieve a DERm of 0.2012 and a WER of 0.2159. Additionally, evaluation by a native Kashmiri linguistic expert yields a mean accuracy of 77.5%. The dataset, model, and source code are publicly released to provide a reproducible baseline for Kashmiri diacritic restoration and future low-resource language research.

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

Evaluating Pluralism in LLMs through Latent Perspectives

The growing need to represent diverse perspectives has increased interest in pluralistic LLM generation. Although difficult to operationalize, identifying perspectives expressed in text would provide clear guidance on pluralistic alignment and more clearly articulate the pluralistic gap in LLM generation. While models have been shown to reduce the diversity of training data and generate homogeneously, this has been demonstrated primarily on multiple-choice questionnaires or using high-level characteristics of free-form text. In this paper, we introduce and implement a domain-agnostic multi-layered framework for unsupervised extraction of perspectives suitable for identifying the pluralistic gap in LLM-generated text. We evaluate our framework on book reviews, a highly opinionated dataset representing diverse perspectives, and compare various prompts and models. Our results show that while some models and prompting techniques come close to covering a broad spectrum of perspectives, rarer perspectives remain disproportionately underrepresented, resulting in distributions that diverge from human text.

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

GOT-JEPA: Generic Object Tracking with Model Adaptation and Occlusion Handling using Joint-Embedding Predictive Architecture

The human visual system tracks objects by integrating current observations with previously observed information, adapting to target and scene changes, and reasoning about occlusion at fine granularity. In contrast, recent generic object trackers are often optimized for training targets, which limits robustness and generalization in unseen scenarios, and their occlusion reasoning remains coarse, lacking detailed modeling of occlusion patterns. To address these limitations in generalization and occlusion perception, we propose GOT-JEPA, a model-predictive pretraining framework that extends JEPA from predicting image features to predicting tracking models. Given identical historical information, a teacher predictor generates pseudo-tracking models from a clean current frame, and a student predictor learns to predict the same pseudo-tracking models from a corrupted version of the current frame. This design provides stable pseudo supervision and explicitly trains the predictor to produce reliable tracking models under occlusions, distractors, and other adverse observations, improving generalization to dynamic environments. Building on GOT-JEPA, we further propose OccuSolver to enhance occlusion perception for object tracking. OccuSolver adapts a point-centric point tracker for object-aware visibility estimation and detailed occlusion-pattern capture. Conditioned on object priors iteratively generated by the tracker, OccuSolver incrementally refines visibility states, strengthens occlusion handling, and produces higher-quality reference labels that progressively improve subsequent model predictions. Extensive evaluations on seven benchmarks show that our method effectively enhances tracker generalization and robustness.

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

Ricci-Filtration: Boosting Retrieval-Augmented Generation Reranker to Query-Answer Tasks by Discrete Ricci Flow

arXiv:2606.15482v1 Announce Type: cross Abstract: Ricci flow is a curvature-guided diffusion process that deforms space by shrinking regions of high positive curvature and expanding those with negative curvature. Similarly, discrete Ricci flow on weighted graphs modifies edge weights by shrinking edges with positive Ricci curvature and stretching those with negative Ricci curvature, effectively increasing the separation between clusters. Inspired by these two cornerstone works, we propose a geometry-based RAG reranker enhancement procedure called Ricci-Filtration. By modeling the input query and initial retrieved chunks as a network, where the input query and chunks serve as nodes and embedding-based pairwise relations define an initial graph, Ricci-Filtration leverages discrete curvature and Ricci flow to evaluate the structural importance of each chunk with respect to the user query. The system first filters the initial chunks based on their geometric curvature relative to the query; then, a reranker processes the remaining chunks to enhance generative performance. We theoretically prove that normalized discrete Ricci flow can detect community structures by identifying distinct asymptotic behaviors in edge weights. This supports the removal of ``noisy'' document chunks characterized by large weights and negative Ricci curvature relative to the query node. Extensive experiments confirm that Ricci-Filtration outperforms several baseline reranking methods in accuracy, precision, recall, and F1 scores. Furthermore, ablation studies demonstrate that the Ricci-Filtration generally outperforms the baseline under various settings, highlighting the framework's robustness across different architectures.

18.
bioRxiv (Bioinfo) 2026-06-11

Integrating Spatially Adjusted Protein Summaries for Survival Prediction in Spatial Proteomics

Recent advances in spatial proteomics, particularly imaging mass cytometry, enable the measurement of protein expression at the single-cell level while preserving a spatial context. Conventional survival analyses, however, typically rely on patient-level averages of protein intensities and therefore overlook spatial heterogeneity and tissue architecture. To address this limitation, we introduce a framework that incorporates spatial information into survival modeling by generating spatially adjusted protein summaries (SAPS). In this approach, cell-level protein intensities within each patient are modeled using spatial spline regression to capture spatial trends. From these models, we extract two complementary features: a spatially adjusted mean expression and a residual variance that reflects cell-to-cell variability unexplained by spatial effects. These summaries are then incorporated into Cox proportional hazards models in combination with clinical covariates. In simulation studies, our proposed framework achieved improved predictive performance compared to other alternative methods. The application of the method to breast cancer imaging mass cytometry data indicate that spatially adjusted summaries may enhance survival prediction and reveal biologically interpretable spatial protein patterns, suggesting high translational potential. This methodology offers an efficient means of translating complex spatial proteomics data into patient-level features, providing both improved survival prediction and new insights into the role of spatial heterogeneity in cancer outcomes.

19.
medRxiv (Medicine) 2026-06-15

Dysplasia-Stratified Management of Barrett's Esophagus: An Incidence-Based U.S. Cost-Effectiveness Analysis

作者:

Background and Aims Barrett's esophagus (BE) is the principal precursor of esophageal adenocarcinoma (EAC), whose incidence has risen sharply in Western countries since the 1960s. Effective, dysplasia stratified surveillance strategies are needed to prevent progression. This study evaluated the cost effectiveness of dysplasia stratified surveillance intervals and endoscopic eradication therapy (EET) across the BE spectrum. Methods We developed an incidence-based Markov state transition model of BE progression calibrated to U.S. epidemiologic data from a healthcare sector perspective over a lifetime horizon. Four hypothetical cohorts of 50-year-old individuals with short segment BE (SSBE), nondysplastic BE (NDBE), low grade dysplasia (LGD), or high-grade dysplasia (HGD) were evaluated. Strategies included no surveillance; surveillance at 1-, 2-, 3-, 4-, 5-, or 10-year intervals; standard or AI assisted endoscopy; non endoscopic screening (sponge, breath, miRNA tests); and EET for LGD and HGD. Outcomes included costs, quality adjusted life years (QALYs), incremental cost effectiveness ratios (ICERs), net monetary benefits (NMBs), EAC cases, and EAC-related deaths. Sensitivity analyses used a willingness to pay threshold of US$100,000 per QALY. Results No surveillance was the most cost-effective strategy for SSBE and NDBE. For LGD, upfront EET was more cost effective than all surveillance strategies, with results sensitive to EAC incidence and recurrence. For HGD, EET was cost saving and yielded the greatest QALYs, with findings robust in 99.9% of simulations. EET prevented 12,614 and 44,295 EAC related deaths per 100,000 individuals with LGD and HGD, respectively. Conclusion Dysplasia-stratified management is essential for optimizing surveillance and treatment strategies in BE. Any degree of dysplasia should receive EET followed by targeted post-treatment monitoring, establishing EET as the central therapeutic pathway for dysplastic BE.

20.
arXiv (CS.AI) 2026-06-24

JEDEL: Zero-Shot DNA-Encoded Library Design for Early-Stage Drug Discovery

arXiv:2606.23745v1 Announce Type: cross Abstract: We present JEDEL, a framework for generating synthesis-ready DNA-encoded libraries (DELs) directly from three-dimensional pharmacophore representations of active ligands. JEDEL is the first model to map pharmacophore interaction patterns to actionable, scalable synthesis instructions, enabling the design of targeted libraries comprising potentially millions of molecules. Unlike existing generative approaches that produce virtual compounds requiring downstream synthesis planning, JEDEL operates within the space of purchasable building blocks and validated reactions, ensuring that every output is experimentally realizable by construction. JEDEL learns a predictive alignment between pharmacophore geometry and molecular structure and decodes this into combinatorial synthesis routes at scale. Across 18 protein targets, it generates focused libraries that outperform random and diversity-based baselines in predicted binding affinity, pharmacophore recovery, and sample efficiency, without target-specific retraining. JEDEL enables a shift from virtual molecule generation to experimentally deployable library design.

21.
arXiv (quant-ph) 2026-06-12

Coulomb crystallization of xenon highly charged ions in a laser-cooled Ca+ matrix

arXiv:2512.12266v2 Announce Type: replace-cross Abstract: We report on the sympathetic cooling and Coulomb crystallization of xenon highly charged ions (HCIs) with laser-cooled Ca$^+$ ions. The HCIs are produced in a compact electron beam ion trap, then charge selected, decelerated, and finally injected into a cryogenic linear Paul trap. There, they are captured into $^{40}$Ca$^+$ Coulomb crystals, and co-crystallized within them, causing dark voids in their fluorescence images. Fine control over the number of trapped ions and HCIs allows us to realize mixed-species crystals with arbitrary ordering patterns. By investigating Xe$^{q+}$–Ca$^+$ strings, we confirm the HCI charge states, measure their lifetime and characterize the mixed-species motional modes. Our system effectively combines the established quantum control toolbox for Ca$^+$ with the rich set of atomic properties of Xe highly charged ions, providing a resourceful platform for optical frequency metrology, searches for signatures of new physics, and quantum information science.

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

Universal Time Series Generation with Neural Controlled Differential Equations

arXiv:2605.28507v2 Announce Type: replace Abstract: Recent work on the sequence universality of State Space Models (SSMs) has introduced efficient, maximally expressive continuous-time approaches for time-series modelling. While these works focus on discriminative settings, we extend this perspective to generative time-series modelling by proving that maximally expressive Structured Linear Controlled Differential Equations (SLiCEs) are universal time-series generators, in the sense that they can approximate the induced path laws of continuous causal pushforwards on compact latent sets in $W_\infty$. Building on these theoretical results, we propose Generative SLiCEs (G-SLiCEs), a maximally expressive continuous-time model for flow matching on path-space. Empirically, we show that expressivity improves performance in probabilistic forecasting and downstream tasks, while retaining the advantages of continuous-time models such as generalising to arbitrary observation grids. This is particularly beneficial for irregular grids, where fixed-grid models often struggle.

23.
arXiv (CS.LG) 2026-06-18

Contextualizing Biological Language Models across Modalities via Logit-Space Contrastive Alignment

arXiv:2606.18703v1 Announce Type: new Abstract: Pretrained biological language models expose per-token probability distributions through masked-token prediction, providing the likelihood interface central to sequence design, variant scoring, and mechanistic interpretation. Yet these distributions are learned from broad unlabeled corpora and are not naturally conditioned on task-specific biological contexts such as interaction partners, cellular environments, or therapeutic interventions. Existing contextual matching methods often distort this interface through pooled embeddings, contrastive latent spaces, or task-specific prediction heads. We introduce LOGICA (Logit-space Contrastive Alignment), a framework for context-conditioned prediction that performs contrastive learning directly in output-logit space. Using gated cross-modal adapters compatible with each model's native token head, LOGICA preserves the pretrained likelihood interface and converts contextualized token log-likelihoods into matching scores. Alignment is defined through context-sensitive token probabilities rather than proximity in a shared embedding space, enabling learning from sparse paired data across models with distinct vocabularies, without a shared tokenizer or decoder. LOGICA is particularly effective for mutation-local variant ranking, where comparisons reduce to context-conditioned likelihoods of mutant tokens at perturbed sites. Across protein–ligand binding, TCR–peptide activity, and drug-conditioned resistance prediction, LOGICA improves over prior state-of-the-art methods, including matched latent-contrastive and conditional MLM baselines, while retaining a token-level interface for interpretation and generation. On held-out-gene single-mutation drug-resistance prediction, LOGICA improves AUC from near-random latent-space baselines of $\sim$0.55 to $\sim$0.65.

24.
arXiv (CS.LG) 2026-06-19

AgentArmor: A Framework, Evaluation, \& Mitigation of Coding Agent Failures

arXiv:2606.19380v1 Announce Type: cross Abstract: Software engineering and deployment are increasingly being delegated to AI coding agents. The scale of their adoption is surfacing rare, but highly destructive, failure modes. In this paper, we study these failure modes as stemming from three distinct mechanisms: underspecification, where default model behavior is unsafe; capability errors, where the safe action is available but the model does not adhere to it due to bias or capability limitations; and agent harness errors, where the model fails to execute the safe action through the harness. We evaluate these across 8 different evaluations, each inspired by real-life deployment failures, totaling 20 coding environments and 59 synthetic transcript templates. Based on this evaluation, we propose AgentArmor, an agent harness modification, to mitigate these errors. By adding an extended system prompt, a separate command classifier, a ``3 strikes'' policy, deterministic guardrails, and tools for the agent to edit its own context, we show that AgentArmor is safer across a statistically significant number of samples. Thus, we suggest concrete mitigations for current coding agents and a design philosophy for future agent harness features.

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

Quantum Batteries as Work Sources for Phase-Locked Parametric Amplification

arXiv:2606.20306v1 Announce Type: new Abstract: Quantum batteries have been proposed as locally precharged work sources for superconducting quantum technologies, suggesting a route to reduce continuously supplied microwave drives. Here we ask whether the pump tone of a quantum-limited parametric amplifier can be replaced, or strongly duty-cycled, by a finite bosonic quantum battery. Quantizing the pump of a nondegenerate parametric amplifier exposes a resource distinction hidden in the classical description: stored pump energy can generate signal-idler photons, but pump phase coherence is required to generate a phase-locked amplifier field. In a closed trilinear model, coherent and phase-randomized coherent pumps with the same photon-number distribution produce comparable pair numbers, yet only the coherent pump produces anomalous two-mode coherence and an EPR-squeezed interference dip. Including leakage, we collect the emitted fields into cascaded temporal modes. At matched collector bandwidth, the coherent pump gives \(I_{\min}^{(f)}=0.553\), whereas the phase-randomized pump gives \(I_{\min}^{(f)}=1.94\) at nearly identical collected energy. Weak amplitude squeezing slightly improves the dip by reducing finite-pump number fluctuations while preserving the coherent displacement. Thus battery-powered parametric amplification requires phase-coherent stored energy, possibly assisted by number-noise reduction, rather than stored energy alone.