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

Detecting Historical Turning Points in Italian Media: A Complex Systems Approach to a Diachronic News Corpus

Authors:
Dario Zarcone↗Salvatore Miccich\`e↗David Sanchez↗

The increasing availability of large-scale textual corpora has opened new possibilities for data-driven, quantitative approaches to historical analysis using Natural Language Processing (NLP). However, diachronic corpora with historical relevance from the pre-digital era remain scarce and often incomplete. We present a quantitative approach to historical analysis based on the reconstruction and exploration of a diachronic corpus of around 600,000 articles from the Italian newspaper "La Repubblica", covering all the articles published from the 1st of January 1985 to the 31st of December 2000 - a period of major political, social, and geopolitical change in Italy and globally. Using NLP techniques, we analyze the text at both lexical and semantic levels; we then apply tools from complex systems and statistical physics to trace shifts in media discourse over time. This allows us to detect key transition periods, such as the transition from the First Republic to the Second Republic in Italy, or major international conflicts like the Gulf War or the Kosovo War, without relying on prior labeling. The results show how combining computational linguistics with ideas from complex systems can offer new quantitative insight into historical changes, opening up new paths for studying the dynamics of media and society through large-scale textual data.

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02.
arXiv (CS.CV) 2026-06-19

3D Scene Graphs: Open Challenges and Future Directions

Authors:
Dennis Rotondi↗Francesco Argenziano↗Sebastian Koch↗Nathan Hughes↗Martin Buechner↗Johanna Wald↗Lukas Rosenberger Schmid↗Daniele Nardi↗Abhinav Valada↗Liam Paull↗Federico Tombari↗Luca Carlone↗…

3D Scene Graphs (3DSGs) have emerged as a powerful representation for spatial AI by combining geometric grounding with semantic and relational abstractions of the environment. Their expressiveness has made them relevant to a broad range of problems in robotics and computer vision, including manipulation, navigation, task planning, scene understanding, and many others. However, the field remains fragmented: different communities adopt distinct formulations, construction pipelines, and evaluation protocols, making it difficult to compare methods, identify common assumptions, and assess remaining challenges for robust real-world deployment. This survey provides a unified and critical review of 3DSGs, with particular emphasis on open challenges and future directions. We first formalize 3DSGs under a common definition and analyze the principal modeling choices that characterize existing formulations, including node and edge attributes, hierarchical structure, dynamic scene representations, and affordance-aware extensions. We then review how 3DSGs are built from raw sensory observations, discussing the most common terminologies, conventions, and techniques. Finally, we examine downstream applications and evaluation strategies, from intrinsic graph quality to task-level performance. To support the community, we also provide a dedicated website that organizes and extends the surveyed content, accessible at https://3dscenegraphs.com/.

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03.
bioRxiv (Bioinfo) 2026-06-16

RetroMol: Parsing a shared encoding from natural products and their biosynthetic gene clusters

Authors:
Meijer↗Williams↗S. E↗Terlouw↗Charusanti↗Kok↗Skinnider↗M. A↗Weber↗van der Hooft↗J. J. J↗Healy↗…

Natural products such as polyketides and nonribosomal peptides (NRPs) are important sources of bioactive compounds, including many antibiotics. Many of them are assembled by modular enzyme complexes and further modified and diversified by tailoring reactions encoded by biosynthetic gene clusters (BGCs). Although natural products and their coding BGCs describe different data modalities of the same biochemical process, a unified language to jointly describe their biochemistry is lacking. Here we introduce a sequence-based representation of the core biosynthesis of modular natural products, which we call primary sequences, that bridges chemical structures and BGCs. We also present RetroMol, an algorithm that parses either natural product structures or their encoding BGCs into their primary sequences of natural product building blocks. RetroMol allows for similarity scoring between natural products and BGCs, enabling the retrieval of compounds, BGCs, and a combination of the two, based on their biosynthetic similarity. This can, for instance, be used to retrieve biosynthetically similar but structurally dissimilar compounds, or link natural products to candidate coding BGCs in large experimental datasets. We demonstrate the latter by rediscovering the nocardichelin B BGC as a proof of principle. We also exemplify the utility of biosynthetic similarity by showing various pairs of biosynthetically similar compounds with low structural similarity. Together, these results establish primary sequences as a shared biosynthetic encoding for natural product comparison and BGC prioritization.

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04.
arXiv (CS.LG) 2026-06-15

Mitigating Heterogeneity-Induced Drift in Hierarchical Sign-Based Federated Learning

Authors:
Amirreza Kazemi↗Seyed Mohammad Azimi-Abarghouyi↗Gabor Fodor↗Carlo Fischione↗

arXiv:2602.02355v2 Announce Type: replace-cross Abstract: Hierarchical federated learning (HFL) is well suited for large-scale wireless and Internet of Things systems, where devices communicate with nearby edge servers before reaching the cloud. In these environments, uplink bandwidth and latency impose strict communication constraints, making aggressive gradient compression essential. One-bit sign-based stochastic gradient descent methods provide an attractive solution in flat federated settings, but their behavior in hierarchical edge–cloud architectures remains insufficiently understood, especially under inter-cluster data heterogeneity. To address this gap, we develop a sign-based HFL framework in which devices transmit binary stochastic-gradient signs to edge servers, edge servers apply majority voting, and the cloud periodically aggregates edge models. Our analysis reveals that inter-cluster heterogeneity induces a persistent bias term in the convergence bound, reflecting the drift of edge models toward local objectives. This term cannot be removed by increasing the number of training rounds or by tuning standard hyperparameters alone. We therefore propose \(\mathtt{DC-HierSignSGD}\), a drift-corrected sign-based HFL algorithm in which devices apply a cloud-assisted gradient correction before taking the sign. We show that this pre-sign correction mitigates the non-vanishing heterogeneity-induced bias while preserving binary device–edge communication during the repeated local sign-update steps. Experiments under severe inter-cluster heterogeneity demonstrate that \(\mathtt{DC-HierSignSGD}\) improves the stability and accuracy of sign-based HFL and achieves performance comparable to full-precision hierarchical SGD with substantially lower device–edge communication.

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05.
arXiv (CS.LG) 2026-06-12

PLaID++: A Preference Aligned Language Model for Targeted Inorganic Materials Design

Authors:
Andy Xu↗Rohan Desai↗Larry Wang↗Ethan Ritz↗Gabriel Hope↗

arXiv:2509.07150v4 Announce Type: replace Abstract: Reinforcement Learning from Verifiable Rewards (RLVR) has emerged as a promising approach to improve correctness in LLMs, however, in many scientific problems, the objective is not necessarily to produce the correct answer, but instead to produce a diverse array of candidates which satisfy a set of constraints. We study this challenge in the context of materials generation. To this end, we introduce PLaID++, an LLM post-trained for stable and property-guided crystal generation. We find that performance hinges on our crystallographic representation and reward formulation. First, we introduce a compact, symmetry-informed Wyckoff text representation which improves computational efficiency and encourages generalization from physical priors. Second, we demonstrate that temperature scaling acts as an entropy regularizer which counteracts mode collapse and encourages exploration. By encoding symmetry constraints directly into text and guiding model outputs towards desirable chemical space, PLaID++ generates structures that are thermodynamically stable, unique, and novel at a $\sim$50\% greater rate than prior methods and conditionally generates structures with desired space group properties. Our work demonstrates the potential of adapting post-training techniques from natural language processing to materials design, paving the way for targeted and efficient discovery of novel materials.

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

Toward Accessible Psychotherapy Training Using AI-Driven Interactive Patient Avatars

Authors:
Pascal Riachi↗Sofie Kamber↗Stella Brogna↗Andrew Gloster↗Rafael Wampfler↗

Training psychotherapists in evidence-based interventions such as Acceptance and Commitment Therapy (ACT) requires repeated practice with meaningful feedback, yet opportunities for safe, standardized training are limited by ethical, logistical, and resource constraints. We introduce a system designed to support ACT-oriented psychotherapy training through spoken dialogue with an embodied virtual patient. The system uses large language models to simulate patient behavior conditioned on profiles derived from real therapy sessions and configurable clinical scenarios, while a separate automated evaluator provides turn-by-turn feedback on therapist responses based on established ACT fidelity criteria. Rather than aiming to replace supervision, the system is intended to support deliberate practice by enabling experimentation, reflection, and immediate feedback in low-risk settings. Expert evaluation with practicing psychologists confirmed high realism in patient behavior and demonstrated that immediate turn-by-turn ACT feedback increased therapists' awareness of intervention choices and enabled effective experimentation with alternative responses. Quantitative evaluation across 49 therapy transcripts identified GPT-4o-mini as the optimal feedback model, achieving the lowest mean absolute error (MAE = 6.12) in replicating human supervisor ACT fidelity ratings with statistically significant agreement. This work demonstrates the potential of fidelity-aware simulated patients as a scalable complement to psychotherapy training.

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08.
arXiv (CS.CL) 2026-06-18

ScholarSum: Student-Teacher Abstractive Summarization via Knowledge Graph Reasoning and Reflective Refinement

Authors:
Bohou Zhang↗Xiaoyu Tao↗Mingyue Cheng↗Huijie Liu↗Qi Liu↗

Abstractive summarization plays a crucial role in enabling efficient understanding of scientific literature, yet it inherently demands both linguistic fluency and factual faithfulness. Existing approaches often fail to reconcile these two requirements. Extractive methods rely on rigid sentence splicing that disrupts macro-level logical coherence, while large language model (LLM)-based generative approaches, despite mastering linguistic fluency, exhibit limited factual consistency. In this work, we propose ScholarSum, a hierarchical reflective graph-based framework that emulates a student-teacher writing process for fluent and faithful scientific summarization. ScholarSum first organizes the document into a hierarchical knowledge graph by segmenting it into semantically coherent units, whose multi-layered community structure captures global logic and macro-level themes. Guided by this global structure, the student generates an initial draft, which is subsequently refined through fine-grained evidence retrieval. To ensure factual consistency, a teacher-like reviewer then iteratively examines the draft, identifies unsupported content, and prompts targeted re-retrieval and rewriting until the summary meets rigorous quality standards. Extensive experiments demonstrate that ScholarSum significantly outperforms previous baselines in terms of both completeness and faithfulness. Our code is available at https://github.com/Xiaoyu-Tao/ScholarSum.

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09.
arXiv (CS.CL) 2026-06-17

Learning task-specific subspaces via interventional post-training of speech foundation models

Authors:
Jack Cox↗Jon Barker↗

Speech foundation models, pre-trained on large corpora of unlabelled speech data, produce general-purpose representations which are useful across tasks. However, these representations encode information about salient speech variables in a distributed manner, while downstream speech tasks rely on only some of this variability. In this work, we propose a post-training refinement approach using interventional contrastive learning. By leveraging an interventional dataset and multi-part contrastive loss, we learn a transformation from the entangled representation space of speech foundation models into separate content and speaker subspaces. We evaluate the learnt representations on speaker verification and keyword spotting tasks, showing improved out-of-domain speaker verification performance and evidence that speaker and content information are separated across the learned subspaces.

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10.
arXiv (quant-ph) 2026-06-19

Thermodynamic Value of XOR-Game-Induced Side Information in a Szilard Engine

Authors:
Piotr \'Cwikli\'nski↗

arXiv:2605.12044v3 Announce Type: replace Abstract: We introduce a Szilard-type thermodynamic valuation of side-information channels induced by Bell-type correlations. In each round, a two-level working system is thermalized with a degenerate Hamiltonian, so that its physical microstate is a uniform classical bit. A trusted referee embeds this bit into a finite two-player XOR game, and a correlation resource produces a compressed controller bit. The controller uses only this compressed bit as side information for feedback. The construction is formulated first for arbitrary finite XOR games. The referee encoding makes the game-winning event equivalent to correct prediction of the physical microstate. Consequently, the induced side-information channel is binary symmetric, with success probability equal to the XOR-game winning probability of the supplied behaviour. The reversible Szilard feedback value is therefore fixed by the mutual information between the microstate and the controller record. Optimizing over local, quantum, and nonsignalling behaviour sets turns the corresponding game values into local, quantum, and nonsignalling thermodynamic ceilings. The construction is an effective-channel valuation, not a claim that Bell nonlocality is thermodynamic fuel. The controller receives only the compressed prediction bit, not the auxiliary variables that define the game. The thermodynamic costs of the referee, the correlation resource, and the preprocessing are not included. When controller-memory reset is included in a full cycle, the net work is non-positive, consistently with the second law.

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11.
medRxiv (Medicine) 2026-06-22

A Drug-Specific, Half-Life-Adjusted Framework for Classifying CNS-Active Systemic Therapy Exposure During and After Radiotherapy

Authors:
Pari Mitre↗Drapkin↗Dohopolski↗

Clinical oncology datasets often store systemic therapy as a regimen label with a start date and an end date. Those records are clinically recognizable but can be analytically incomplete when the research question concerns whether a patient was exposed to a concurrent CNS-active drug (cCNS-aD) or an adjuvant CNS-active drug (aCNS-aD) around radiotherapy. Contemporary CNS-oncology studies usually define CNS activity by empiric drug lists and define concurrency by fixed calendar windows, although the literature shows substantial heterogeneity across both concepts. This paper proposes a generalizable framework for converting raw systemic therapy records into reproducible cCNS-aD and aCNS-aD variables, useful in subgrouping for clinical studies. The framework uses a transparent CNS scoring model based on three clinical evidence components: intracranial objective response rate, consensus CNS endorsement, and intrathecal route of administration. It then defines a pharmacokinetic exposure proxy as the recorded end date plus five half-lives. Concurrent exposure is classified by overlap with the radiotherapy interval, while post-radiotherapy exposure is classified by overlap with a prespecified post-RT attribution window. The framework separately identifies post-RT pharmacokinetic persistence and post-RT treatment initiation, allowing investigators to distinguish continued exposure from true adjuvant initiation. This is a methodological framework and reference implementation. Implementation audits and endpoint-specific sensitivity analyses remain necessary before use as a definitive exposure classifier

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

TokenPilot: Cache-Efficient Context Management for LLM Agents

Authors:
Buqiang Xu↗Zirui Xue↗Dianmou Chen↗Chenyang Fu↗Chiyu Wu↗Caiying Huang↗Chen Jiang↗Jizhan Fang↗Xinle Deng↗Yijun Chen↗Yunzhi Yao↗Xuehai Wang↗…

As LLM agents are deployed in long-horizon sessions, context accumulation drives up inference costs. Existing approaches utilize text pruning or dynamic memory eviction to minimize token footprints; however, their unconstrained sequence mutations alter layouts, introducing prefix mismatches and cache invalidation. This reveals a critical trade-off between text sparsity and prompt cache continuity. To address this, we present TokenPilot, a dual-granularity context management framework. Globally, Ingestion-Aware Compaction acts as a framework harness to stabilize prompt prefixes and eliminate open-world environmental noise at the ingestion gate. Locally, Lifecycle-Aware Eviction monitors the ongoing residual utility of context segments, enforcing a conservative batch-turn schedule to offload content segments only when task relevance expires. Experiments on PinchBench and Claw-Eval under both isolated and continuous modes demonstrate that TokenPilot reduces costs by 61% and 56% in isolated mode, and 61% and 87% in continuous mode, while maintaining competitive performance compared to prior systems. TokenPilot has been integrated into LightMem2 at https://github.com/zjunlp/LightMem2.

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

Text-Vision Co-Instructed Image Editing

Authors:
Chenxi Xie↗Yuhui Wu↗Qiaosi Yi↗Lei Zhang↗

Existing image editing methods can be generally categorized into textual instruction-based and visual prompt-based ones. Textual instructions are semantically expressive, but are limited by the coarse granularity of spatial control of the editing results. In contrast, visual prompts such as drag and point can provide precise spatial guidance, but are limited by the inherent ambiguity in semantic intent. To unify the strength of textual and visual prompts, we present Text-Vision Co-Instructed Image Editing, which jointly models textual instructions as semantic intent and sparse visual instructions as spatial guidance, aiming to achieve precise and intent-faithful image manipulation. To this end, we first construct a textual-visual instruction paired dataset with more than 23K samples derived from dynamic videos, enabling aligned supervision for cross-modal instruction. We then propose TV-Edit, a Textual-Visual instruction unified Editing framework to contextualize drag or point-based visual instructions with image-text semantics and lift them into semantic-aware control representations for pretrained editing backbones. By integrating semantic intent and spatial constraints, TV-Edit leads to more precise spatial control, less instruction ambiguity, and stronger structural consistency than text-only or drag-based alternatives. Finally, we establish TV-Edit-Bench, a deliberately designed benchmark to evaluate semantic faithfulness, spatial alignment, and visual consistency with ground-truth references and controlled textual-visual variations for reliable assessment. Our experiments across multiple editing backbones demonstrate that TV-Edit consistently yields more precise and intent-faithful edits, significantly outperforming state-of-the-art instruction-based and drag-based baselines.

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

Slots, Transitions, Loops: Learning Composable World Models for ARC

Authors:
Gege Gao↗Bernhard Sch\"olkopf↗Andreas Geiger↗

ARC tests in-context rule induction: given a few input-output demonstrations, a model must infer the hidden rule and apply it to a new query. While many approaches express ARC rules through language, code, or symbolic programs, ARC itself is visual-symbolic: rules appear as grid transitions over objects, colors, shapes, and spatial relations. We introduce Loop-OWM, an object-centric world-modeling architecture that learns these rules as composable transitions over structured states. It combines color-prototype slots, demonstration-conditioned task summaries, and a looped transition model with dense propagation and slot-conditioned correction. On both ARC-1 and ARC-2, Loop-OWM outperforms non-looped and looped baselines with comparable or fewer parameters. These results suggest that ARC rules can be learned not only as language descriptions or searched programs, but also as transitions over visual-symbolic world states.

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

Generalizing Beyond Suboptimality: Offline Reinforcement Learning Learns Effective Scheduling through Random Solutions

Authors:
Jesse van Remmerden↗Zaharah Bukhsh↗Yingqian Zhang↗

arXiv:2509.10303v2 Announce Type: replace-cross Abstract: Online reinforcement learning (RL) approaches have demonstrated strong performance on Job Shop Scheduling (JSP) and Flexible JSP (FJSP) problems by learning scheduling policies through direct interaction with simulated environments. However, these methods often require extensive training interactions, limiting their sample efficiency and practical applicability. Motivated by this challenge, we introduce Conservative Discrete Quantile Actor-Critic (CDQAC), an offline RL algorithm that learns effective scheduling policies directly from static, suboptimal datasets. CDQAC couples a quantile-based critic with delayed policy updates to estimate the return distribution of machine-operation pairs. Extensive experiments on JSP and FJSP benchmarks demonstrate that CDQAC consistently outperforms the data-generating heuristics, surpasses state-of-the-art offline and online RL baselines, and is highly sample efficient, requiring only 1 to 5% of the original dataset to learn high-quality policies. Our analysis suggests that, in scheduling, offline RL performance is governed mainly by state-action coverage rather than the quality of individual trajectories. Scheduling couples a dense reward aligned with the makespan objective with equal-length trajectories across heuristics, enabling effective learning from a broad range of behaviors. Consistent with this observation, datasets generated by a simple random heuristic with broader coverage let it outperform policies trained on datasets produced by stronger heuristics such as Genetic Algorithms.

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

Improving Human-Robot Teamwork in Urban Search and Rescue Through Episodic Memory of Prior Collaboration

Authors:
Taewoon Kim↗Emma van Zoelen↗Mark Neerincx↗

arXiv:2606.18836v1 Announce Type: cross Abstract: Effective human-robot teamwork requires robots to adapt to partners, situations, and task dynamics from the start of an interaction. In the MATRX Urban Search and Rescue (USAR) environment, people can externalize collaboration patterns (CPs) they discover during teamwork through a chat and reflection interface. We study whether a robot can use such prior team experience to become a better teammate in future interactions. To this end, we represent historical CPs as knowledge-graph episodic memories and use graph representation learning with a node-classification objective to identify a representative and effective memory for reuse. We then initialize the robot with this memory before a new collaboration episode begins. Across 20 participants and 160 round-level observations, initializing the robot with a single automatically selected prior CP increases rescue success from 25.7% to 41.3% and reduces average task time by 283 seconds. The strongest gains appear at the beginning of interaction, suggesting that reusable episodic memory can help robots enter collaboration with more effective task knowledge and support smoother early teamwork.

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

ATV-Net: Adaptive Triple-View Network with Dynamic Feature Fusion

Authors:
Sheng-Wei Chan↗Hsin-Jui Pan↗Chun-Po Shen↗Chia-Min Lin↗Yung-Che Wang↗Jen-Shiun Chiang↗

Recent advances in semantic segmentation rely heavily on attention-based and transformer-style architectures that, while accurate, introduce considerable architectural complexity and computational cost. This paper asks whether a compact CNN-based segmentation head can remain competitive by adaptively selecting useful receptive-field evidence. We propose ATV-Net, an Adaptive Triple-View Network that attaches a lightweight head to a conventional backbone. The head organizes three complementary views – point-wise, neighborhood-level, and enlarged context – and fuses them through an Adaptive Decision Gate that generates image-dependent weights from global feature statistics. This allows the model to emphasize different receptive-field responses according to scene content, without dense attention or multi-scale aggregation. Experiments on Cityscapes and Pascal VOC 2012 show that ATV-Net achieves 80.31% mIoU on Cityscapes with ResNet-101 and 80.90% with ConvNeXt-Tiny, and 86.7% and 88.5% mIoU on Pascal VOC 2012, respectively, while requiring fewer GFLOPs than representative context-aggregation and attention-based heads. The results indicate that adaptive receptive-field selection remains a practical and effective design choice for CNN-based semantic segmentation.

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

AuAu: A Benchmark for Auditing Authoritarian Alignment in Large Language Models

Authors:
Andreas Einwiller↗Max Klabunde↗Florian Lemmerich↗

The worldwide surge of authoritarianism, combined with the increasing central role in users' everyday lives, raises the question of to what extent specific models exhibit or promote authoritarian attitudes and characteristics. We introduce AuAu, a comprehensive benchmark that aims to assess the risk of LLMs generating responses with authoritarian tendencies. This benchmark combines three evaluation approaches: (i) psychometric questions from an extensive pool of 15 human validated instruments; (ii) contextual behavior vignettes probing intended actions in concrete situations; and (iii) responses to realistic user prompts. Unlike prior work, AuAu evaluates not only a general closeness towards authoritarianism but also the established sub-concepts Authoritarian Aggression, Authoritarian Submission, and Conventionalism. Evaluating 17 models from China, the EU, Russia, and the USA, we find that all tested models exhibit substantial authoritarian response rates under the psychometric evaluation, though rates drop significantly in increasingly more realistic downstream task. We further find that an authoritarian system prompt easily manipulates 15 out of 17 models to promote increased authoritarianism. Our results underscore the need for continued, systematic auditing of LLM-based AI systems to detect and ultimately mitigate undesired authoritarian tendencies in generated output. Our code and data are available at: https://github.com/andreaseinwiller/AuAu

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

Damage Adaptation in Seconds for Architected Materials

Authors:
James Avtges↗Jake Ketchum↗Helena Young↗Taekyoung Kim↗Ryan Truby↗Todd Murphey↗

arXiv:2606.17394v1 Announce Type: cross Abstract: Adaptation to damages and in-situ physical repairs is essential for long-term robot autonomy, yet challenging outside of narrowly defined and well-anticipated bounds. In this work we proprioceptively adapt to catastrophic damage in soft-actuated systems in under one minute. Architected materials are well equipped for adaptation: actuator failure occurs gradually rather than acutely, and damage can be described in a low-dimensional, discrete coordinate space. Surprisingly, latent damage representations plus a simple yet robust ensemble method is sufficient for adapting to unseen damage in real-time. Moreover, we identify conditions under which exponential sample complexity collapses to linear sample complexity for learned representations of architected materials, a concrete advantage over rigid components or continuum soft mechanisms. We demonstrate LEAP, our method for adaptive proprioception, via a tracing task for a 6DoF soft wrist based on Handed Shearing Auxetic (HSA) actuators. Our algorithm is able to adapt to cuts, burns, and actuator repairs, enabling simulation-free real-time adaptation that is critical for realizing the promise of soft robots outside the lab. Videos and more information are available at https://murpheylab.github.io/leap.

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

SciText2Eq: Assessing LLMs for Explainable Equation Generation for Scientific Creativity

Authors:
Yifan Mo↗Xiao Fu↗Yue Su↗Qingyu Meng↗Koen Hindriks↗Qingzhi Liu↗Jiahuan Pei↗

arXiv:2606.16003v1 Announce Type: new Abstract: This work investigates the ability of large language models (LLMs) to generate mathematical equations from scientific texts. Prior work faces challenges in unstructured grounding, multi-equation dependency, and humanaligned evaluation. To this end, we construct a dataset of AI research papers, pairing contextual passages with ground-truth equations and variable descriptions. We develop an explainable equation generation workflow and evaluate it across diverse open- and closed-source LLM backbones. We introduce an evaluation protocol combining automatic metrics, LLM-based rubrics, and human judgments to assess accuracy, explainability, and human-LLM alignment. Results indicate that LLMs perform moderately on lexical- and syntactic-based similarity, while struggling with semantic accuracy. Comparisons between LLM-based evaluations and human judgments reveal limited alignment, highlighting challenges in using LLMs to assess equation quality. These findings offer insights for improving equation generation models and developing more reliable evaluation methods for scientific text. We provide code and data for reproducibility.

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21.
bioRxiv (Bioinfo) 2026-06-12

PeptiDIA: A Machine Learning Framework for Enhanced Peptide Identification in Fast-Gradient Data-Independent Acquisition Proteomics

Authors:
Ortona↗Leclercq↗Roux-Dalvai↗Routy↗Bonnet↗Droit↗

Data-independent acquisition (DIA) mass spectrometry has become increasingly prevalent in proteomics as advances in instrumentation, chromatography, and computational analysis have enabled robust proteome identification across complex biological samples. However, analytical depth achieved with fast chromatographic gradients remains lower than that obtained using long-gradients, reflecting a throughput-depth trade-off. Here, we present PeptiDIA, a machine learning framework that enhances peptide identification in fast-gradient DIA data by leveraging paired fast and long-gradient acquisitions from identical samples. PeptiDIA processes DIA-NN outputs generated at relaxed false discovery rate thresholds to obtain expanded candidate peptide pools and trains gradient-boosted decision tree models using long-gradient identifications as reference labels. The model integrates DIA-NN features with engineered peptide descriptors and applies isotonic regression to calibrate probabilities, enabling controlled peptide recovery relative to the long-gradient reference. Applied to human and murine datasets spanning six tissues acquired on an Orbitrap Exploris 480, PeptiDIA increased peptide identifications by 25-34% at 1% target reference-discordance rate (RDR) and increased the number of protein groups containing at least one rescued peptide by 15-17%. Overall, PeptiDIA improves the identification depth of fast-gradient DIA-NN workflows without altering acquisition strategies. The framework is available as a web application and command-line tool at https://github.com/Jordano700/PeptiDIA.

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22.
arXiv (CS.AI) 2026-06-17

FoundCause: Causal Discovery with Latent Confounders from Observational Data

Authors:
Patrick Bl\"obaum↗Krishnakumar Balasubramanian↗Shiva Prasad Kasiviswanathan↗

arXiv:2606.17516v1 Announce Type: cross Abstract: Causal discovery from observational data remains challenging due to the need to recover directed structure and latent confounding without interventions. We propose FoundCause, an amortized causal discovery model trained entirely on synthetic data that maps datasets directly to causal graphs in a single forward pass. By learning from large collections of simulated structural causal models, FoundCause captures transferable statistical patterns that generalize beyond individual datasets. The architecture incorporates several key inductive biases for causal discovery. It uses a permutation-invariant transformer encoder with alternating attention over samples and variables to jointly model cross-variable dependence and per-variable distributions. Pairwise statistical features derived from classical asymmetry measures are injected through statistics-conditioned attention, guiding the model toward known causal signals. A factorized decoder separates edge existence from direction, while a triangular refinement module enables reasoning over higher-order causal motifs such as chains and colliders. In addition, a dedicated confounder module based on learnable latent tokens explicitly models hidden common causes, and the model explicitly handles missing data via its masked input representation. To our knowledge, FoundCause is the first amortized causal discovery approach to explicitly model latent confounding. FoundCause outperforms 11 classical non-amortized methods (e.g., PC, GES, NOTEARS-style optimization) and 4 amortized causal discovery methods on 15 real-world datasets, achieving +9.6% improvement in $F_1$, +1.2% in AUROC, and an 18.9% reduction in structural Hamming distance relative to the strongest non-amortized methods, while performing inference in a single forward pass.

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

Short-Term-to-Long-Term Memory Transfer for Knowledge Graphs under Partial Observability

Authors:
Taewoon Kim↗Vincent Fran\c{c}ois-Lavet↗Michael Cochez↗

arXiv:2605.22142v2 Announce Type: replace-cross Abstract: Reinforcement learning under partial observability requires deciding what information to retain, yet most memory-based approaches do not explicitly model short-term-to-long-term transfer of symbolic observations. We study this transfer process in a temporal knowledge-graph memory setting and cast it as a neuro-symbolic value-based decision problem: for each observed triple, the agent chooses whether to keep or drop it before long-term insertion. To handle variable-sized short-term buffers, we use a per-item Q-learning design with shared parameters and a practical temporal-difference update over matched items across consecutive steps. On the RoomKG benchmark at long-term memory capacity 128, learned transfer decisions outperform symbolic and neural baselines, including symbolic baselines with temporal annotations and history-based LSTM/Transformer baselines. Across transfer-policy ablations, a lightweight local short-term-only variant performs best, and step-level behavior shows that the policy keeps navigation- and query-relevant facts while discarding lower-value candidate facts, supporting explicit and interpretable memory decisions under memory constraints.

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24.
arXiv (CS.CL) 2026-06-12

NTS-CoT: Mitigating Hallucinations in LLM-based News Timeline Summarization with Chain-of-Thought Reasoning

Authors:
Feng Lyu↗Huiqin Yan↗Sijing Duan↗Hao Wu↗Shuang Gu↗Xue Qiao↗Weixu Zhang↗Haolun Wu↗

The rapid updates of online news make tracking event developments challenging, highlighting the need for timeline summarization (TLS). Hallucinations, where LLM-generated content deviates from source news, still remain a critical issue in LLM-based TLS and are not well studied in existing works. To bridge this gap, we identify two primary types of hallucinations: unfaithful content during news summarization and information omission in date-event summarization. Then, we propose NTS-CoT, a novel framework that leverages Chain-of-Thought (CoT) reasoning to mitigate hallucinations in TLS. The framework consists of three key modules: i) Element-CoT to capture essential news elements for faithful summarization, ii) Date Selection to combine temporal saliency and event prominence for timestamp selection, and iii) Causal-CoT to infer causal relationships and reduce omissions in date-event summarization. Extensive experiments, including quantitative analysis on three TLS benchmarks and human evaluation, demonstrate that NTS-CoT outperforms state-of-the-art baselines, effectively mitigating hallucinations and improving LLM-based TLS performance. Our source code is available at https://anonymous.4open.science/r/NTS-CoT .

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25.
arXiv (CS.AI) 2026-06-18

Externalizing Research Synthesis and Validation in AI Scientists through a Research Harness

Authors:
Zijian Wang↗Hanqi Li↗Ziyue Yang↗Zijian Hu↗Shenghan Zuo↗Yunzhe Zhang↗Da Ma↗Danyu Luo↗Chenrun Wang↗Jing Peng↗Tiancheng Huang↗Sijia Guo↗…

arXiv:2606.18874v1 Announce Type: new Abstract: AI systems can increasingly automate scientific workflows, but the reasoning that links prior evidence, generated ideas, experiments and final claims often remains implicit inside model inference. Here we introduce Xcientist, a research harness that externalizes research synthesis and experimental validation into inspectable, contract-governed processes. Xcientist organizes literature evidence, idea states, implementation plans, ablation records and repair traces as persistent research artifacts, so that generated mechanisms can be grounded, executed, tested and revised without losing their evidential basis. We identify claim drift as a failure mode of automated research, where runnable artifacts no longer support the mechanism originally claimed. Across training-free memory systems, graph-structured traffic forecasting and multi-scale physics-informed neural networks, Xcientist preserves traceable trajectories from problem formulation to mechanism design, validation and bounded revision. These results suggest that AI scientists should be evaluated not only by their final artifacts, but by whether their synthesis and validation processes remain attributable, inspectable and scientifically accountable.

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