new

Get trending papers in your email inbox!

Subscribe

Daily Papers

byAK and the research community

Jun 12

2DNMRGym: An Annotated Experimental Dataset for Atom-Level Molecular Representation Learning in 2D NMR via Surrogate Supervision

Two-dimensional (2D) Nuclear Magnetic Resonance (NMR) spectroscopy, particularly Heteronuclear Single Quantum Coherence (HSQC) spectroscopy, plays a critical role in elucidating molecular structures, interactions, and electronic properties. However, accurately interpreting 2D NMR data remains labor-intensive and error-prone, requiring highly trained domain experts, especially for complex molecules. Machine Learning (ML) holds significant potential in 2D NMR analysis by learning molecular representations and recognizing complex patterns from data. However, progress has been limited by the lack of large-scale and high-quality annotated datasets. In this work, we introduce 2DNMRGym, the first annotated experimental dataset designed for ML-based molecular representation learning in 2D NMR. It includes over 22,000 HSQC spectra, along with the corresponding molecular graphs and SMILES strings. Uniquely, 2DNMRGym adopts a surrogate supervision setup: models are trained using algorithm-generated annotations derived from a previously validated method and evaluated on a held-out set of human-annotated gold-standard labels. This enables rigorous assessment of a model's ability to generalize from imperfect supervision to expert-level interpretation. We provide benchmark results using a series of 2D and 3D GNN and GNN transformer models, establishing a strong foundation for future work. 2DNMRGym supports scalable model training and introduces a chemically meaningful benchmark for evaluating atom-level molecular representations in NMR-guided structural tasks. Our data and code is open-source and available on Huggingface and Github.

  • 3 authors
·
May 16, 2025

Precision measurement of the last bound states in H_2 and determination of the H + H scattering length

The binding energies of the five bound rotational levels J=0-4 in the highest vibrational level v=14 in the X^1Sigma_g^+ ground electronic state of H_2 were measured in a three-step ultraviolet-laser experiment. Two-photon UV-photolysis of H_2S produced population in these high-lying bound states, that were subsequently interrogated at high precision via Doppler-free spectroscopy of the F^1Sigma_g^+ - X^1Sigma_g^+ system. A third UV-laser was used for detection through auto-ionizing resonances. The experimentally determined binding energies were found to be in excellent agreement with calculations based on non-adiabatic perturbation theory, also including relativistic and quantum electrodynamical contributions. The s-wave scattering length of the H + H system is derived from the binding energy of the last bound J=0 level via a direct semi-empirical approach, yielding a value of a_s = 0.2724(5) a_0, in good agreement with a result from a previously followed theoretical approach. The subtle effect of the malpha^4 relativity contribution to a_s was found to be significant. In a similar manner a value for the p-wave scattering volume is determined via the J=1 binding energy yielding a_p = -134.0000(6) a_0^3. The binding energy of the last bound state in H_2, the (v=14, J=4) level, is determined at 0.023(4) cm^{-1}, in good agreement with calculation. The effect of the hyperfine substructure caused by the two hydrogen atoms at large internuclear separation, giving rise to three distinct dissociation limits, is discussed.

  • 3 authors
·
Feb 3, 2025

Nuclear Quadrupole Hyperfine Structure in HC14N/H14NC and DC15N/D15NC Isomerization: A Diagnostic Tool for Characterizing Vibrational Localization

Large-amplitude molecular motions which occur during isomerization can cause significant changes in electronic structure. These variations in electronic properties can be used to identify vibrationally-excited eigenstates which are localized along the potential energy surface. This work demonstrates that nuclear quadrupole hyperfine interactions can be used as a diagnostic marker of progress along the isomerization path in both the HC14N/H14NC and DC15N/D15NC chemical systems. Ab initio calculations at the CCSD(T)/cc-pCVQZ level indicate that the hyperfine interaction is extremely sensitive to the chemical bonding of the quadrupolar 14N nucleus and can therefore be used to determine in which potential well the vibrational wavefunction is localized. A natural bonding orbital analysis along the isomerization path further demonstrates that hyperfine interactions arise from the asphericity of the electron density at the quadrupolar nucleus. Using the CCSD(T) potential surface, the quadrupole coupling constants of highly-excited vibrational states are computed from a one-dimensional internal coordinate path Hamiltonian. The excellent agreement between ab initio calculations and recent measurements demonstrates that nuclear quadrupole hyperfine structure can be used as a diagnostic tool for characterizing localized HCN and HNC vibrational states.

  • 1 authors
·
Dec 20, 2010

A Retrospective Systematic Study on Hierarchical Sparse Query Transformer-assisted Ultrasound Screening for Early Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC), ranking as the third leading cause of cancer-related mortality worldwide, demands urgent improvements in early detection to enhance patient survival. While ultrasound remains the preferred screening modality due to its cost-effectiveness and real-time capabilities, its sensitivity (59%-78%) heavily relies on radiologists' expertise, leading to inconsistent diagnostic outcomes and operational inefficiencies. Recent advancements in AI technology offer promising solutions to bridge this gap. This study introduces the Hierarchical Sparse Query Transformer (HSQformer), a novel hybrid architecture that synergizes CNNs' local feature extraction with Vision Transformers' global contextual awareness through latent space representation and sparse learning. By dynamically activating task-specific experts via a Mixture-of-Experts (MoE) framework, HSQformer achieves hierarchical feature integration without structural redundancy. Evaluated across three clinical scenarios: single-center, multi-center, and high-risk patient cohorts, HSQformer outperforms state-of-the-art models (e.g., 95.38% AUC in multi-center testing) and matches senior radiologists' diagnostic accuracy while significantly surpassing junior counterparts. These results highlight the potential of AI-assisted tools to standardize HCC screening, reduce dependency on human expertise, and improve early diagnosis rates. The full code is available at https://github.com/Asunatan/HSQformer.

  • 11 authors
·
Feb 5, 2025

HSIGene: A Foundation Model For Hyperspectral Image Generation

Hyperspectral image (HSI) plays a vital role in various fields such as agriculture and environmental monitoring. However, due to the expensive acquisition cost, the number of hyperspectral images is limited, degenerating the performance of downstream tasks. Although some recent studies have attempted to employ diffusion models to synthesize HSIs, they still struggle with the scarcity of HSIs, affecting the reliability and diversity of the generated images. Some studies propose to incorporate multi-modal data to enhance spatial diversity, but the spectral fidelity cannot be ensured. In addition, existing HSI synthesis models are typically uncontrollable or only support single-condition control, limiting their ability to generate accurate and reliable HSIs. To alleviate these issues, we propose HSIGene, a novel HSI generation foundation model which is based on latent diffusion and supports multi-condition control, allowing for more precise and reliable HSI generation. To enhance the spatial diversity of the training data while preserving spectral fidelity, we propose a new data augmentation method based on spatial super-resolution, in which HSIs are upscaled first, and thus abundant training patches could be obtained by cropping the high-resolution HSIs. In addition, to improve the perceptual quality of the augmented data, we introduce a novel two-stage HSI super-resolution framework, which first applies RGB bands super-resolution and then utilizes our proposed Rectangular Guided Attention Network (RGAN) for guided HSI super-resolution. Experiments demonstrate that the proposed model is capable of generating a vast quantity of realistic HSIs for downstream tasks such as denoising and super-resolution. The code and models are available at https://github.com/LiPang/HSIGene.

  • 7 authors
·
Sep 19, 2024

HyperSIGMA: Hyperspectral Intelligence Comprehension Foundation Model

Accurate hyperspectral image (HSI) interpretation is critical for providing valuable insights into various earth observation-related applications such as urban planning, precision agriculture, and environmental monitoring. However, existing HSI processing methods are predominantly task-specific and scene-dependent, which severely limits their ability to transfer knowledge across tasks and scenes, thereby reducing the practicality in real-world applications. To address these challenges, we present HyperSIGMA, a vision transformer-based foundation model that unifies HSI interpretation across tasks and scenes, scalable to over one billion parameters. To overcome the spectral and spatial redundancy inherent in HSIs, we introduce a novel sparse sampling attention (SSA) mechanism, which effectively promotes the learning of diverse contextual features and serves as the basic block of HyperSIGMA. HyperSIGMA integrates spatial and spectral features using a specially designed spectral enhancement module. In addition, we construct a large-scale hyperspectral dataset, HyperGlobal-450K, for pre-training, which contains about 450K hyperspectral images, significantly surpassing existing datasets in scale. Extensive experiments on various high-level and low-level HSI tasks demonstrate HyperSIGMA's versatility and superior representational capability compared to current state-of-the-art methods. Moreover, HyperSIGMA shows significant advantages in scalability, robustness, cross-modal transferring capability, real-world applicability, and computational efficiency. The code and models will be released at https://github.com/WHU-Sigma/HyperSIGMA.

  • 22 authors
·
Jun 17, 2024

Auger Spectroscopy via Generative Quantum Eigensolver: A Quantum Approach to Molecular Excitations

Auger electron spectroscopy, a way of characterizing electronic structure through core-level decay processes, is widely used in materials characterization; however direct calculation from molecular geometry requires accurate treatment of many excited states, posing a challenge for classical methods. We present a hybrid quantum-classical workflow for calculating Auger spectra that combines the generative quantum eigensolver (GQE) for ground-state preparation, the quantum self-consistent equation-of-motion method for excited-state calculations, and the one-centre approximation for Auger transition rates. GQE uses a GPT-2 model to generate quantum circuits for ground-state optimization, allowing our workflow to benefit from HPC parallelization and GPU-acceleration for favourable scaling with system size. We demonstrate the validity of our workflow by calculating the Auger spectrum of water with the STO-3G basis set and demonstrating qualitative and quantitative agreement with spectra obtained using completely classical full configuration interaction calculations, from the computational literature, and from the experimental literature. We also find that for water, substituting the variational quantum eigensolver (VQE) for GQE results in near-identical spectra, but that the ground state estimator generated by GQE contains about half the total gate count as that generated by VQE.

  • 19 authors
·
Mar 13

Protein Chemical Shift Prediction

The protein chemical shifts holds a large amount of information about the 3-dimensional structure of the protein. A number of chemical shift predictors based on the relationship between structures resolved with X-ray crystallography and the corresponding experimental chemical shifts have been developed. These empirical predictors are very accurate on X-ray structures but tends to be insensitive to small structural changes. To overcome this limitation it has been suggested to make chemical shift predictors based on quantum mechanical(QM) calculations. In this thesis the development of the QM derived chemical shift predictor Procs14 is presented. Procs14 is based on 2.35 million density functional theory(DFT) calculations on tripeptides and contains corrections for hydrogen bonding, ring current and the effect of the previous and following residue. Procs14 is capable at performing predictions for the 13CA, 13CB, 13CO, 15NH, 1HN and 1HA backbone atoms. In order to benchmark Procs14, a number of QM NMR calculations are performed on full protein structures. Of the tested empirical and QM derived predictors, Procs14 reproduced the QM chemical shifts with the highest accuracy. A comparison with the QM derived predictor CheShift-2 on X-ray structures and NMR ensembles with experimental chemical shift data, showed that Procs14 predicted the chemical shifts with the best accuracy. The predictions on the NMR ensembles exhibited the best performance. This suggests that future work might benefit from using ensemble sampling when performing simulations of protein folding with chemical shifts. Procs14 is implemented in the markov chain monte carlo protein folding framework PHAISTOS. The computational efficient implementation of Procs14 allows for rapid predictions and therefore potential use in refinement and folding of protein structures.

  • 1 authors
·
Sep 23, 2014

Deciphering the "chemical" nature of the exotic isotopes of Hydrogen by the MC-QTAIM analysis: The positively charged Muon and the Muonic Helium as new members of the Periodic Table

This report is a primarily survey on the chemical nature of some exotic species containing the positively charged muon and the muonic Helium, i.e., the negatively charged muon plus helium nucleus, as exotic isotopes of hydrogen, using the newly developed multi-component quantum theory of atoms in molecules (MC-QTAIM) analysis, employing ab initio non-Born-Oppenhiemer wavefunctions. Accordingly, the "atoms in molecules" analysis performed on various asymmetric exotic isotopomers of hydrogen molecule, recently detected experimentally [Science 331, 448 (2011)], demonstrates that both the exotic isotopes are capable of forming atoms in molecules and retaining the identity of hydrogen atom. Various derived properties of atomic basins containing muonic helium cast no doubt that apart from its short life time, it is a heavier isotope of hydrogen while the properties of basins containing the positively charged muon are more remote from those of the orthodox hydrogen basins, capable of appreciable donation of electrons as well as large charge polarization; however, with some tolerance, they may be categorized also as hydrogen basins though with a smaller electronegativity. All in all, present study also clearly demonstrates that the MC-QTAIM analysis is an efficient approach to decipher the chemical nature of species containing exotic constituents, hard to be elucidated by experimental and/or alternative theoretical schemes.

  • 2 authors
·
Nov 25, 2013

hqQUBO: A Hybrid-querying Quantum Optimization Model Validated with 16-qubits on an Ion Trap Quantum Computer for Life Science Applications

AlphaFold has achieved groundbreaking advancements in protein structure prediction, exerting profound influence across biology, medicine, and drug discovery. However, its reliance on multiple sequence alignment (MSA) is inherently time-consuming due to the NP-hard nature of constructing MSAs. Quantum computing emerges as a promising alternative, compared to classical computers, offering the potentials for exponential speedup and improved accuracy on such complex optimization challenges. This work bridges the gap between quantum computing and MSA task efficiently and successfully, where we compared classical and quantum computational scaling as the number of qubits increases, and assessed the role of quantum entanglement in model performance. Furthermore, we proposed an innovative hybrid query encoding approach hyQUBO to avoid redundancy, and thereby the quantum resources significantly reduced to a scaling of O(NL). Additionally, coupling of VQE and the quenched CVaR scheme was utilized to enhance the robustness and convergence. The integration of multiple strategies facilitates the robust deployment of the quantum algorithm from idealized simulators (on CPU and GPU) to real-world, noisy quantum devices (HYQ-A37). To the best of our knowledge, our work represented the largest-scale implementation of digital simulation using up to 16 qubits on a trapped-ion quantum computer for life science problem, which achieved state of the art performance in both simulation and experimental results. Our work paves the way towards large-scale simulations of life science tasks on real quantum processors.

  • 8 authors
·
Jun 1, 2025

Synthetic stellar spectra to study multiple populations in globular clusters: an extended grid and the effects on the integrated light

Most Galactic Globular Clusters (GCs) harbour multiple populations of stars (MPs), composed of at least two generations: the first characterized by a "standard" α-enhanced metal mixture, as observed in field halo stars of the Milky Way, and the second displaying anti-correlated CN--ONa chemical abundance pattern in combination with an enhanced helium fraction. Adequate collections of stellar spectra are needed to characterize the effect of such stellar abundance changes on the integrated light of GCs. We present a grid of synthetic stellar spectra covering the atmospheric parameters relevant to old stellar populations at four subsolar metallicities and two abundance patterns, representative of first- and second-generations of stars in GCs. Integrated spectra of populations were computed using our stellar grid and empirical stellar populations, namely, colour-magnitude diagrams from literature for Galactic GCs. The spectra range from 290 to 1000nm, where we measured the effect on several spectrophotometric indices due to the surface abundance variations attributed to MPs. We find non-negligible effects of the MPs on spectroscopic indices sensitive to C, N, Ca, or Na, and on Balmer indices; we also describe how MPs modify specific regions in the near-UV and near-IR that can be measured with narrow or medium photometric passbands. The effects vary with metallicity. A number of these changes remain detectable even when accounting for the stochastic fluctuations due to the finite nature of the stellar population cluster.

  • 5 authors
·
Apr 22, 2024

Low-Light Hyperspectral Image Enhancement

Due to inadequate energy captured by the hyperspectral camera sensor in poor illumination conditions, low-light hyperspectral images (HSIs) usually suffer from low visibility, spectral distortion, and various noises. A range of HSI restoration methods have been developed, yet their effectiveness in enhancing low-light HSIs is constrained. This work focuses on the low-light HSI enhancement task, which aims to reveal the spatial-spectral information hidden in darkened areas. To facilitate the development of low-light HSI processing, we collect a low-light HSI (LHSI) dataset of both indoor and outdoor scenes. Based on Laplacian pyramid decomposition and reconstruction, we developed an end-to-end data-driven low-light HSI enhancement (HSIE) approach trained on the LHSI dataset. With the observation that illumination is related to the low-frequency component of HSI, while textural details are closely correlated to the high-frequency component, the proposed HSIE is designed to have two branches. The illumination enhancement branch is adopted to enlighten the low-frequency component with reduced resolution. The high-frequency refinement branch is utilized for refining the high-frequency component via a predicted mask. In addition, to improve information flow and boost performance, we introduce an effective channel attention block (CAB) with residual dense connection, which served as the basic block of the illumination enhancement branch. The effectiveness and efficiency of HSIE both in quantitative assessment measures and visual effects are demonstrated by experimental results on the LHSI dataset. According to the classification performance on the remote sensing Indian Pines dataset, downstream tasks benefit from the enhanced HSI. Datasets and codes are available: https://github.com/guanguanboy/HSIE{https://github.com/guanguanboy/HSIE}.

  • 3 authors
·
Aug 5, 2022

Generative Quantum-inspired Kolmogorov-Arnold Eigensolver

High-performance computing (HPC) is increasingly important for scalable quantum chemistry workflows that couple classical generative models, quantum circuit simulation, and selected configuration interaction postprocessing. We present the generative quantum-inspired Kolmogorov-Arnold eigensolver (GQKAE), a parameter-efficient extension of the generative quantum eigensolver (GQE) for quantum chemistry. GQKAE replaces the parameter-heavy feed-forward network components in GPT-style generative eigensolvers with hybrid quantum-inspired Kolmogorov-Arnold network modules, forming a compact HQKANsformer backbone. The method preserves autoregressive operator selection and the quantum-selected configuration interaction evaluation pipeline, while using single-qubit DatA Re-Uploading ActivatioN modules to provide expressive nonlinear mappings. Numerical benchmarks on H4, N2, LiH, C2H6, H2O, and the H2O dimer show that GQKAE achieves chemical accuracy comparable to the GPT-based GQE architecture, while reducing trainable parameters and memory by approximately 66% and improving wall-time performance. For strongly correlated systems such as N2 and LiH, GQKAE also improves convergence behavior and final energy errors. These results indicate that quantum-inspired Kolmogorov-Arnold networks can reduce classical-side overhead while preserving circuit-generation quality, offering a scalable route for HPC-quantum co-design on near-term quantum platforms.

  • 12 authors
·
May 5 2