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01.
arXiv (quant-ph) 2026-06-19

Operator Learning for efficient Quantum Computation

arXiv:2606.20184v1 Announce Type: new Abstract: An efficient implementation of quantum algorithms is often hindered by the lack of efficient primitives for operators and state preparation. This limits both the ability of near-term quantum hardware to simulate complex problems and the potential of fault-tolerant algorithms to achieve practical quantum advantage. To address this, we propose a full-stack variational framework that transforms arbitrary operators to compact quantum circuits. The resulting variational circuits can be tailored to the connectivity and long-range interaction of the target hardware. The learning process employs backpropagation together with a cost function that efficiently optimizes unitary operators and non-unitary – dense or sparse – operators using only a single ancilla qubit for block encoding. Additionally, we introduce a regularization term that reduces the approximation error. The approach is validated for both quantum mechanical and engineering applications. In the former case, we learn propagators that arise in native quantum problems – such as quantum simulation and quantum chemistry – and achieve improved resource scaling in comparison to standard Suzuki-Trotter expansions. In the latter case, we demonstrate the approach's ability to implement the second-order central finite difference approximation of the Laplace operator – relevant for solving partial differential equations – while improving upon current error metrics. The final example deals with learning a dense, non-unitary operator that arises in the analysis of inviscid potential flow around an airfoil. This universality of the framework opens the door for solving general problems beyond prototypical engineering and quantum applications.

02.
arXiv (CS.LG) 2026-06-11

JGRA: Jacobian Geometry Robustness Assessment in NISQ Noise-Aware Quantum Neural Networks

arXiv:2606.09964v2 Announce Type: replace-cross Abstract: The NISQ era places stringent constraints on quantum computation, where noise and decoherence fundamentally limit performance. In classical deep learning, model robustness and resilience to perturbations are well studied: deep neural networks (DNNs) maintain high performance despite pruning, noise injection, and structural perturbations due to inherent redundancy in their representations. A central challenge in quantum machine learning is to transfer this notion of robustness to quantum neural networks (QNNs) under realistic NISQ noise. While classical deep learning exhibits robustness through structural redundancy, analogous principles for QNNs remain underdeveloped. We propose JGRA: a framework for assessing robustness in noise-aware QNNs via Jacobian geometry, capturing model sensitivity to parameter perturbations induced by noise. Our method includes entropy-matched noise calibration, noise-aware training, and noise-conditioned Jacobian extraction, yielding geometric descriptors that link clean-regime structure to noisy inference behaviour. We also empirically demonstrate that these descriptors encode predictive information about robustness under unseen noise.

03.
arXiv (CS.CL) 2026-06-11

AI4SLT: Empirical Processes in Lean 4 for Formal Statistical Learning Theory

We present the first comprehensive Lean 4 formalization of statistical learning theory (SLT) grounded in empirical process theory. Our en-to-end formal infrastructure implement the missing contents in latest Lean library, including a complete development of Gaussian Lipschitz concentration, Dudley's entropy integral theorem for sub-Gaussian processes, and an application to least-squares (sparse) regression with a sharp rate. The project was carried out using a human-AI collaborative workflow, in which humans design proof strategies and AI agents execute tactical proof construction, leading to the human-verified Lean 4 toolbox for SLT. Beyond implementation, the formalization process exposes and resolves implicit assumptions and missing details in standard SLT textbooks, enforcing a granular, line-by-line understanding of the theory. This work establishes a reusable formal foundation and opens the door for future developments in machine learning theory. The code is provided in https://github.com/YuanheZ/lean-stat-learning-theory.

04.
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.

05.
medRxiv (Medicine) 2026-06-17

Frequency-dependent cognitive effects of Deep Brain Stimulation in Parkinson's Disease: A Systematic Review and Meta-Analysis

Background: Subthalamic nucleus deep brain stimulation (STN-DBS) improves levodopa-induced motor complications and cardinal motor symptoms of Parkinson's disease (PD), but stimulation frequency may differentially shape outcomes. This is evident for axial and gait symptoms, which may respond differently to lower-frequency stimulation. Whether frequency-dependent effects extend to cognition remains unclear. Objective: To investigate the cognitive effects of DBS at distinct frequencies in PD. Methods: We conducted a systematic review and meta-analysis (PROSPERO - CRD42024618253). PubMed, Web of Science, and EMBASE were searched for studies assessing cognitive outcomes under different stimulation frequencies. Eight cognitive domains were defined: verbal fluency, cognitive flexibility, executive control, working memory, attention, processing speed, episodic memory, and time processing. Multilevel random-effects meta-analyses were performed, with effect sizes expressed as Hedges' g. Results: Forty-three studies met the inclusion criteria, the majority (n = 31) involving STN-DBS. Twenty-one STN-DBS studies, including 355 patients, were included in the meta-analysis. Compared with HFS ([≥] 130 Hz), lower frequencies (4-80 Hz) were associated with better verbal fluency (g = 0.27) and cognitive flexibility (g = 0.38), with consistent effects across sensitivity and leave-one-out analyses. Accuracy-based executive control measures also favored lower-frequency stimulation. OFF-stimulation comparisons showed a concordant pattern. Evidence for other targets (PPN and NBM) was limited. Conclusions: Lower-frequency STN-DBS was associated with modest benefits in specific cognitive domains compared with HFS. These findings highlight the need for future research to determine how frequency interacts with stimulation location and symptom-specific networks to shape cognitive and cognitive-motor outcomes in PD.

07.
arXiv (quant-ph) 2026-06-12

Hamiltonian-Aware ADAPT Variational Quantum Eigensolver for Molecular Ground-State Simulation

arXiv:2606.13118v1 Announce Type: new Abstract: Designing compact ansätze in Variational Quantum Eigensolver (VQE) is crucial for solving energetic problems of practical molecules on near-term quantum devices. However, existing Adaptive Derivative-Assembled Pseudo-Trotter (ADAPT) ansätze face two challenges: improper operator selection and accumulation of degraded operators. In this paper, we propose the Hamiltonian-Aware (HA) ADAPT-VQE algorithm to address these issues. First, we establish a novel excitation operator selection criterion. It breaks the local constraint of existing criteria by incorporating Hamiltonian information, prioritizes physically meaningful excitation operators, and incurs no extra classical or quantum computational overhead. Furthermore, we develop a problem-adaptive method for discriminating and pruning redundant excitation operators stemming from improper selection and inevitable degradation. This method balances redundant operator pruning and convergence guarantee, and is applicable to ansätze with arbitrary scales. Systematic numerical experiments on typical strongly correlated molecular systems demonstrate that our HA-ADAPT-VQE avoids energy plateaus and outperforms baseline algorithms in terms of energy error, ansatz size, and measurement cost. This work offers an efficient, robust ansatz construction paradigm, facilitating the development and practical deployment of large-scale VQE in quantum chemistry.

08.
arXiv (CS.LG) 2026-06-11

CP4SBI: Local Conformal Calibration of Credible Sets in Simulation-Based Inference

arXiv:2508.17077v3 Announce Type: replace-cross Abstract: Current experimental scientists have been increasingly relying on simulation-based inference (SBI) to invert complex non-linear models with intractable likelihoods. However, posterior approximations obtained with SBI are often miscalibrated, causing credible regions to undercover true parameters. We develop $\texttt{CP4SBI}$, a model-agnostic conformal calibration framework that constructs credible sets with local Bayesian coverage. Our two proposed variants, namely local calibration via regression trees and CDF-based calibration, enable finite-sample local coverage guarantees for any scoring function, including HPD, symmetric, and quantile-based regions. Experiments on widely used SBI benchmarks demonstrate that our approach improves the quality of uncertainty quantification for neural posterior estimators using both normalizing flows and score-diffusion modeling.

09.
arXiv (CS.CV) 2026-06-12

CACR:Reinforcing Temporal Answer Grounding in Instructional Video via Candidate-Aware Causal Reasoning

The task of temporal answer grounding in instructional video (TAGV), which aims to locate precise video segments that respond to natural language queries, is increasingly important for direct video answer retrieval. This task remains challenging due to the need to comprehend semantically complex questions and to address the significant length mismatch between untrimmed videos and short target moments. Existing methods often suffer from sensitivity to irrelevant content or insufficient visual reasoning capabilities. To tackle these limitations, we propose a Candidate-Aware Causal Reasoning (CACR) framework. Our approach first employs a Visual-Language Pre-training based Candidate Selection (VBCS) algorithm to efficiently generate K candidate segments, then applies a temporal logic reasoning module enhanced by a rejection reward mechanism and optimized via Group Relative Policy Optimization (GRPO) for robust inference. Extensive experiments on six benchmarks demonstrate that our method achieves state-of-the-art performance in terms of mean Intersection-over-Union (mIoU), providing a new perspective for reasoning-based retrieval in long videos.

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

Single-Step Phase-Engineered Pulse for Active Readout Cavity Reset in Superconducting Circuits

arXiv:2512.08393v2 Announce Type: replace Abstract: In a circuit QED architecture, we experimentally demonstrate a hardware-efficient and qubit-state-dependent Single-Step Phase-Engineered (SSPE) pulse scheme for actively depopulating a readout cavity. The protocol appends a reset segment with tailored amplitude and phase to a standard square readout pulse. Within the linear-response regime, the optimal reset amplitude scales proportionally with the readout amplitude, while the optimal reset phase remains invariant, significantly simplifying the experimental calibration procedure. Time-resolved measurements of the cavity photon number dynamics demonstrate that the SSPE scheme significantly outperforms the CLEAR protocol in terms of reset speed. Crucially, this approach enables arbitrarily fast, overshoot-free depletion of the cavity photon population, with the ultimate reset rate constrained by the finite analog bandwidth of the measurement chain. Furthermore, a comprehensive evaluation of the QND nature demonstrates that the SSPE scheme introduces no additional non-QND measurement errors. It exhibits non-QNDness comparable to both the free-decay and CLEAR protocols, with residual errors predominantly governed by state switching induced by qubit relaxation during the readout process. Thses results establish the SSPE scheme as a practical and scalable approach for achieving rapid and smooth cavity reset in superconducting quantum circuits.

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

High-efficiency telecom conversion of heralded atomic biphoton wavepackets

arXiv:2603.09824v2 Announce Type: replace Abstract: We demonstrate high-efficiency telecom frequency conversion of heralded atomic biphoton wavepackets using a diamond-type atomic ensemble. By placing a 2.5 MHz heralded-photon spectrum within the high-efficiency region of the converter response, we achieve a conversion efficiency of 79.4(2.6)% while maintaining strong time-resolved correlations and well-defined temporal wavepackets. For a broader 17.4 MHz input bandwidth, the conversion efficiency is reduced to about 55%, whereas the temporal waveform remains largely preserved. This behavior reflects the nearly flat central response of the converter, which mainly causes spectral-edge loss rather than temporal-mode distortion. These results identify spectral matching as an effective route to efficient and low-distortion telecom conversion of narrowband quantum light from atomic systems.

12.
arXiv (quant-ph) 2026-06-17

Tripartite entanglement of remote atomic qubits

arXiv:2606.17173v1 Announce Type: new Abstract: Distributed entanglement across multi-node quantum networks is essential for a wide range of quantum technologies, including modular quantum computers, distributed sensing and metrology, and multi-party secure communication protocols. Such large-scale quantum networks will require photonic interconnects to generate and sustain entangled states across localized nodes. Previously, three-node distributed Greenberger-Horne-Zeilinger (GHZ) states have been generated between solid-state qubits and atomic ensembles, but not yet in the platform of individual atomic qubits, which can be replicated, detected, and individually controlled with high fidelity. Here we report the first fully-distributed GHZ state of qubits across a three-node quantum network of single atomic memories, using photonic interconnects. We achieve a bounded fidelity of $0.841(17) \leq \mathcal{F} \leq 0.881(17)$ at an entanglement generation rate of 0.095(5)/sec and measure a clear violation of Mermin's inequality while closing the detection loophole for the first time in a fully-distributed multipartite entangled state.

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

Selecting Samples on Graphs: A Unified Dataset Pruning Framework for Lossless Training Acceleration

The rapid growth of modern training datasets has significantly increased computational cost, motivating dataset pruning~(DP) methods which retain only a subset of informative samples to reduce training cost. Existing pruning criteria typically rely on either intrinsic signals that assess samples independently or extrinsic signals that promote diversity via pairwise relations. While effective in their own specific regimes, each captures only one aspect of sample utility and lacks robustness across different pruning ratios or data distribution. In this work, we present a unified graph-based DP framework. By modeling the dataset as a weighted graph, where node weights encode intrinsic value and edge weights encode extrinsic value, DP can be cast as a Maximum Weight Clique Problem (MWCP). Although MWCP is NP-hard, its structure admits a principled greedy solution based on sample-wise marginal gains. Under a few mild conditions, we further prove that this unified objective enjoys a formal approximation guarantee, which applies to a broad family of importance metrics and provides practical design guidelines. Extensive experiments show that our method outperforms existing DP methods while substantially reducing training cost, reducing training time by over 40\% without sacrificing accuracy on ImageNet-1k with ResNet-50.

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

Amortized mean-shift interacting particles

arXiv:2606.15871v1 Announce Type: cross Abstract: Bayesian inference for inverse problems is run to evaluate integrals – posterior expectations, tail probabilities, and risks – across a stream of observations. The standard estimate averages the integrand over posterior samples, a Monte-Carlo average whose error decays only as the square root of the sample size, so accuracy demands many samples – prohibitive when each one calls a partial-differential-equation forward model. Mean-shift interacting particles need far fewer: they return a small set of signed-weight nodes – a deterministic quadrature whose weighted averages estimate those integrals. Finding the nodes, however, is a per-observation optimization that, in its most accurate form, reads the posterior score at every step – returning the cost it meant to save. We introduce amortized mean-shift interacting particles, a learned map that emits the weighted nodes from an observation and a few posterior samples in a single forward pass. Training asks only for joint parameter-observation samples and a posterior to draw from – a conditional normalizing flow, an empirical conditional, or any reference the user can sample – and the map learns to integrate that posterior from samples alone, evaluating neither its density nor its score. Once trained, it generalizes to unseen observations and integrands at any node budget and improves on independent samples in two ways: by reweighting them, provably no worse than the equal weights of Monte-Carlo; and by moving them, which empirically lowers it further. Across closed-form, sampled, learned, and physics-based posteriors – up to a thousand-coefficient groundwater field – it integrates more accurately than the same number of samples at every budget, and a posterior-whitened, dimension-aware kernel removes the high-dimensional wall. The result is a Pareto improvement on Monte-Carlo integration, not a competitor to drawing more samples.

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

From Awareness to Action: Understanding and Overcoming the Research-Practice Gap in Algorithmic Fairness for Public Health

arXiv:2606.11214v1 Announce Type: cross Abstract: Algorithmic fairness is essential for responsible ML-driven public health research, yet its practical implementation remains limited. To investigate this awareness-action gap, we conducted a sequential mixed-methods study comprising expert interviews, an online survey, and systematic mapping. The expert interviews informed the design of the survey, which in turn revealed fragmented definitions of fairness, limited training and guidance, reliance on external sources, and rare use of formal assessment, mitigation, or monitoring. These findings were subsequently mapped onto three established research-practice gap lenses: the Knowledge-Practice Gap, the Knowledge-to-Action Cycle, and the Knowing-Doing Gap, each offering complementary perspectives. Building on this synthesis, we introduce the Fairness-to-Action framework, which integrates methodological, organizational, and systemic dimensions to identify where translation of algorithmic fairness knowledge stalls. Our analysis shows that fairness remains weakly institutionalized, translation mechanisms are externally driven, and system-level priorities continue to emphasize accuracy over fairness. These insights suggest critical leverage points for advancing safe, fair, and ethical ML-driven public health research practice.

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

Phys-JEPA: Physics-Informed Latent World Models for Multivariate Time-Series Forecasting

arXiv:2606.16076v1 Announce Type: cross Abstract: Multivariate forecasting in physical systems requires models that predict coupled temporal variables while preserving meaningful state evolution. Deep forecasters can fit temporal correlations, and physics-informed models can regularize predictions with scientific constraints, but these directions are often connected only at the decoded-output level. As a result, the hidden predictive state that generates future trajectories may remain statistically useful but physically unstructured. We introduce Phys-JEPA, a physics-informed joint-embedding predictive architecture for multivariate time-series forecasting. Phys-JEPA learns a latent world model in which predictive states are decomposed into physical and residual components, and physical consistency is imposed directly on latent states and latent transitions rather than only on decoded forecasts. This formulation uses known physical variables to organize the representation space while retaining residual capacity for unresolved dynamics. On Jena Climate 2009–2016, Phys-JEPA reduces aggregate MSE from 0.12482 to 0.12273 and temperature MSE from 0.01892 to 0.01831 at H=24. On Traffic, full Phys-JEPA improves aggregate MSE over the supervised baseline across all tested horizons, reducing H=192 MSE from 0.800784 to 0.773873. On Electricity, the best variant depends on horizon: static latent consistency is strongest at H=24 and H=48, while full Phys-JEPA gives the best aggregate and target-variable MSE at H=192. These initial results suggest that moving physics-informed learning from output space to latent predictive state space is a promising direction for interpretable temporal world models.

17.
arXiv (CS.AI) 2026-06-18

Searching for Synergy in Shared Workspace Human-AI Collaboration

arXiv:2606.18413v1 Announce Type: new Abstract: Automated AI agents are increasingly capable, yet many scientific and professional tasks require human judgment and contextual expertise. We study shared-workspace human-AI teams, where AI agents and human collaborators must coordinate responsibilities before submitting a final answer. Using the Collaborative Gym environment with DiscoveryBench tasks, we examine when adding simulated human collaborators improves performance and when process loss turns additional collaborators into coordination overhead. Across 1,482 sessions, adding relevant collaborators can lower performance when teams lack structure to coordinate their contributions. We then evaluate scaffolding that combines shared group memory with simulated human-in-the-loop (HITL) gates, where selected actions require approval from a designated simulated participant. This scaffolding yields higher mean performance, most clearly in three-person teams, with clearer responsibility signals and stronger routing of expertise to team actions. Overall, how human-AI teams coordinate and integrate expertise matters as much as the capability available to them.

18.
arXiv (math.PR) 2026-06-15

Mixing Times for the Facilitated Exclusion Process

arXiv:2402.18999v2 Announce Type: replace Abstract: The facilitated simple exclusion process (FEP) is a one-dimensional exclusion process with a dynamical constraint. We establish bounds on the mixing time of the FEP on the segment, with closed boundaries, and the circle. The FEP on these spaces exhibits transient states that, if the macroscopic density of particles is at least $1/2$, the process will eventually exit to reach an ergodic component. If the macroscopic density is less than $1/2$ the process will hit an absorbing state. We show that the symmetric FEP (SFEP) on the segment $\{1,\ldots,N\}$, with $k>N/2$ particles, has mixing time of order $N^{2}\log(N-k)$ and exhibits the pre-cutoff phenomenon. For the asymmetric FEP (AFEP) on the segment, we show that there exists initial conditions for which the hitting time of the ergodic component is exponentially slow in the number of holes $N-k$. In particular, when $N-k$ is large enough, the hitting time of the ergodic component determines the mixing time. For the SFEP on the circle of size $N$, and macroscopic particle density $\rho \in(1/2,1)$, we establish bounds on the mixing time of order $N^{2}\log N$ for the process restricted to its ergodic component. We also give an upper bound on the hitting time of the ergodic component of order $N^{2}\log N$ for a large class of initial conditions. The proofs rely on couplings with exclusion processes (both open and closed boundaries) via a novel lattice path (height function) construction of the FEP.

19.
arXiv (CS.LG) 2026-06-12

Plan, Don't Pose: Long Composite Motion Generation with Text-Aligned BFM

arXiv:2605.29906v2 Announce Type: replace Abstract: Text-to-motion (T2M) generation has broad applications in character animation, virtual avatars, and human-robot interaction. Existing methods typically generate pose trajectories or motion tokens directly from language, forcing a single model to handle semantic interpretation, long-horizon structure, and low-level physical realization. This coupling makes them costly and often unreliable for long, compositional, or semantically dense prompts. We propose Text2BFM, the first framework that aligns natural language with pretrained Behavioral Foundation Models (BFMs) for T2M generation without relying on heavy end-to-end motion generators. Text2BFM operates in the latent policy space of a frozen BFM, using it as an executable motion prior. A text-aligned variational behavioral bottleneck compresses BFM policy-latent sequences into compact motion representations that are compatible with language and preserve long-horizon behavioral structure. Generation is performed in this compact behavioral manifold with a lightweight conditional generator, and the resulting latent encoded behaviors are decoded into policy latents that drive the pretrained frozen BFM. By decoupling semantic planning from motion execution, Text2BFM achieves efficient, robust T2M generation and strong performance on long, compositional textual descriptions.

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

MortarBench: Evaluating Mortgage Loan Origination Agents

arXiv:2606.19416v1 Announce Type: new Abstract: Loan origination is the process by which a lender creates a new loan, from application and underwriting through approval and funding. This process serves a critical role in evaluating the eligibility and level of risk posed by an applicant. Recently, firms have begun using mortgage loan agents to augment human loan officers, despite a lack of any public benchmark. To fill this gap, we present MortarBench, a loan origination agent benchmark. MortarBench uses a financial data synthesis and mutation pipeline to generate examples with broad edge case coverage that match real-world distributions and questions. We find that state-of-the-art large language models (LLMs) perform poorly, with closed-source models achieving at most 77.1\% exact match accuracy. We also discover systematic biases in LLM perception of foreignness related to non-English names. Noting these weaknesses, we introduce CRIT, a confidence calibration framework. Our method increases accuracy to 80.5\% while improving risk management steering and reducing bias.

21.
arXiv (CS.CV) 2026-06-11

SHERPA: Seam-aware Harmonized ERP Adaptation for Open-Domain 360$^\circ$ Panorama Generation

Panoramic imagery is increasingly used in world-generation, games, and simulation, where users may need not only photorealistic scenes but also stylized and non-photorealistic environments. Large-scale text-to-image diffusion and flow models provide broad style and semantic priors for this goal, but planar image training misaligns them with the wrap-around topology and polar regions of $360^\circ$ panoramas represented in equirectangular projection (ERP). We present SHERPA, a lightweight adaptation framework that combines frequency-selective Circular RoPE, Circular Latent Encoding/Decoding, image-side FFN adapters, and a Dual-Path Training Scheme. Circular RoPE replaces only the seam-sensitive high-frequency horizontal RoPE band with integer-periodic harmonics while preserving the pretrained lower-frequency spectrum. The Paired Panorama Path supervises geometry, while the Unpaired Style Path uses self-supervised yaw consistency for target-free stylized prompts. As a result, SHERPA generates $360^\circ$ panoramas across both photorealistic panorama domains and open-domain stylized prompts.

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

CisTransCell: Single-Cell Perturbation Prediction via Gene Function, Regulatory Control, and Cellular Context

arXiv:2606.13713v1 Announce Type: cross Abstract: Predicting cellular transcriptional responses to genetic perturbations is a central problem in single-cell biology, especially in the zero-shot setting where the perturbed gene or gene combination is unseen during training. A major difficulty is that perturbation effects are not determined by expression state alone: they depend on how the perturbed gene product influences other genes and proteins, how those downstream factors act on cis-regulatory elements, and which regulatory programs are active in the current cell state. To better capture this biological complexity, we propose CisTransCell, a cell-conditioned multi-modal framework for single-cell perturbation prediction that augments each gene with two complementary priors: a regulatory-sequence prior that captures how the gene is controlled, and a coding-sequence prior that captures what the gene product does. By integrating these priors with cellular expression state, CisTransCell models perturbation response as a cascade from gene function to regulatory control to downstream transcriptional change. Experiments on benchmark single-cell perturbation datasets show that CisTransCell achieves strong performance in zero-shot perturbation prediction.

23.
arXiv (CS.CL) 2026-06-12

sebis at CRF Filling 2026: A Two-Stage Local LLM Pipeline for Medical CRF Filling

The extraction of structured clinical information from unstructured EHR notes is a persistent bottleneck in healthcare informatics. While large language models (LLMs) offer high performance, their deployment in clinical settings is hindered by privacy risks, inference costs, and the tendency to hallucinate beyond textual evidence. We address these challenges for the CL4Health 2026 Case Report Form (CRF) filling task by proposing a fully local, domain-adapted pipeline using the MedGemma-27B model. Our two-stage architecture, which separates binary presence classification from value extraction, enforces strict adherence to textual evidence and ensures deterministic outputs for negated, uncertain, or unknown states. By leveraging item-specific, few-shot in-context learning without external API calls or fine-tuning, our approach achieves a macro-F1 score of 0.55 on the official English test track. This result secures second place among all locally-hosted, open-source submissions. Our work demonstrates that privacy-preserving, on-premise LLM pipelines can achieve near-competitive performance with proprietary frontier models, providing a practical, data-sovereign framework for clinical NLP.

24.
bioRxiv (Bioinfo) 2026-06-13

ADMETron: An AI-driven SaaS platform for comprehensive ADMET prediction and compound prioritisation

ONTOSIGHT(R) ADMETron is an AI-driven platform designed for rapid prediction and visualization of Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties to support modern drug discovery. The platform integrates an interactive web interface with a scalable predictive engine, enabling high-throughput virtual screening and batch analysis of chemical compounds. Its core architecture combines recurrent neural network (RNN)-derived molecular embeddings from SMILES representations with physicochemical descriptors, which are subsequently modeled using gradient boosting machines (GBMs). This framework provides predictions across 34 ADMET endpoints, including physicochemical properties, absorption, CYP450 interactions, hERG liability, and mutagenicity. The predictive performance of ADMETron was evaluated using benchmark datasets from the Therapeutics Data Commons (TDC), demonstrating strong performance and generalizability across both classification and regression tasks. Beyond predictive modeling, the platform introduces an interactive radar graph-based structure-activity relationship (SAR) visualization framework that enables real-time comparison of multiple compounds and reference drugs across selected ADMET parameters. This feature facilitates intuitive interpretation of multidimensional molecular profiles and supports lead optimization and compound prioritization. Comparative assessment against widely used online ADMET tools further demonstrated broad endpoint coverage spanning pharmacokinetic, physicochemical, toxicity, and medicinal chemistry properties within a unified environment. Together, these capabilities establish ADMETron as a comprehensive platform for ADMET assessment and data-driven decision-making in drug discovery. (https://admetron.partex.ai/).

25.
arXiv (CS.LG) 2026-06-11

Neuro-Relational Programs: Unifying Queries and Neural Computation over Structured Data

arXiv:2606.11946v1 Announce Type: cross Abstract: The conventional approach to deep learning over relational databases applies neural models, such as Graph Neural Networks (GNNs), to a graph representation of the database. Recent approaches instead operate on databases directly, associating tuples with embeddings and extending query mechanisms to jointly process embeddings and relational content. Inspired by these developments, we introduce Neuro-Relational Programs (NRPs), a declarative query language for relational databases whose facts carry numeric vector embeddings. NRPs extend Datalog-style rules with operations that combine, aggregate, and transform embeddings, thereby interleaving relational reasoning and learnable neural components within a single formalism. This yields a general approach to neural computation over relational data: an NRP can be read both as a query plan with trainable components and as a neural architecture with relational structure built in. Natural syntactic fragments of NRPs recover existing architectures and query formalisms. Zero-ary NRPs correspond to non-adaptive query algorithms; monadic NRPs generalize GNN-style message passing and precisely capture Deep Homomorphism Networks, a connection that we extend to frontier-guarded NRPs over databases with row-ids. We characterize the expressive power of unrestricted NRPs with ReLU-FFN transformations by FOCQ, an extension of first-order logic with counting interpreted over real-weighted structures, yielding a precise connection with uniform TC$^0$ over ordered databases. Together, these results establish NRPs as a broad declarative framework for querying and neural computation over relational data.