GoBERT: Gene Ontology Graph Informed BERT for Universal Gene Function Prediction

Exploring the functions of genes and gene products is crucial to a wide range of fields, including medical research, evolutionary biology, and environmental science. However, discovering new functions largely relies on expensive and exhaustive wet lab experiments. Existing methods of automatic function annotation or prediction mainly focus on protein function prediction with sequence, 3D-structures or protein family information. In this study, we propose to tackle the gene function prediction problem by exploring Gene Ontology graph and annotation with BERT (GoBERT) to decipher the underlying relationships among gene functions. Our proposed novel function prediction task utilizes existing functions as inputs and generalizes the function prediction to gene and gene products. Specifically, two pre-train tasks are designed to jointly train GoBERT to capture both explicit and implicit relations of functions. Neighborhood prediction is a self-supervised multi-label classification task that captures the explicit function relations. Specified masking and recovering task helps GoBERT in finding implicit patterns among functions. The pre-trained GoBERT possess the ability to predict novel functions for various gene and gene products based on known functional annotations. Extensive experiments, biological case studies, and ablation studies are conducted to demonstrate the superiority of our proposed GoBERT.

HELM: Hierarchical Encoding for mRNA Language Modeling

Messenger RNA (mRNA) plays a crucial role in protein synthesis, with its codon structure directly impacting biological properties. While Language Models (LMs) have shown promise in analyzing biological sequences, existing approaches fail to account for the hierarchical nature of mRNA's codon structure. We introduce Hierarchical Encoding for mRNA Language Modeling (HELM), a novel pre-training strategy that incorporates codon-level hierarchical structure into language model training. HELM modulates the loss function based on codon synonymity, aligning the model's learning process with the biological reality of mRNA sequences. We evaluate HELM on diverse mRNA datasets and tasks, demonstrating that HELM outperforms standard language model pre-training as well as existing foundation model baselines on six diverse downstream property prediction tasks and an antibody region annotation tasks on average by around 8\%. Additionally, HELM enhances the generative capabilities of language model, producing diverse mRNA sequences that better align with the underlying true data distribution compared to non-hierarchical baselines.

Beyond Sequence: Impact of Geometric Context for RNA Property Prediction

Accurate prediction of RNA properties, such as stability and interactions, is crucial for advancing our understanding of biological processes and developing RNA-based therapeutics. RNA structures can be represented as 1D sequences, 2D topological graphs, or 3D all-atom models, each offering different insights into its function. Existing works predominantly focus on 1D sequence-based models, which overlook the geometric context provided by 2D and 3D geometries. This study presents the first systematic evaluation of incorporating explicit 2D and 3D geometric information into RNA property prediction, considering not only performance but also real-world challenges such as limited data availability, partial labeling, sequencing noise, and computational efficiency. To this end, we introduce a newly curated set of RNA datasets with enhanced 2D and 3D structural annotations, providing a resource for model evaluation on RNA data. Our findings reveal that models with explicit geometry encoding generally outperform sequence-based models, with an average prediction RMSE reduction of around 12% across all various RNA tasks and excelling in low-data and partial labeling regimes, underscoring the value of explicitly incorporating geometric context. On the other hand, geometry-unaware sequence-based models are more robust under sequencing noise but often require around 2-5x training data to match the performance of geometry-aware models. Our study offers further insights into the trade-offs between different RNA representations in practical applications and addresses a significant gap in evaluating deep learning models for RNA tasks.

SE(3)-Hyena Operator for Scalable Equivariant Learning

Modeling global geometric context while maintaining equivariance is crucial for accurate predictions in many fields such as biology, chemistry, or vision. Yet, this is challenging due to the computational demands of processing high-dimensional data at scale. Existing approaches such as equivariant self-attention or distance-based message passing, suffer from quadratic complexity with respect to sequence length, while localized methods sacrifice global information. Inspired by the recent success of state-space and long-convolutional models, in this work, we introduce SE(3)-Hyena operator, an equivariant long-convolutional model based on the Hyena operator. The SE(3)-Hyena captures global geometric context at sub-quadratic complexity while maintaining equivariance to rotations and translations. Evaluated on equivariant associative recall and n-body modeling, SE(3)-Hyena matches or outperforms equivariant self-attention while requiring significantly less memory and computational resources for long sequences. Our model processes the geometric context of 20k tokens x3.5 times faster than the equivariant transformer and allows x175 longer a context within the same memory budget.

Cardiac ultrasound simulation for autonomous ultrasound navigation

Ultrasound is well-established as an imaging modality for diagnostic and interventional purposes. However, the image quality varies with operator skills as acquiring and interpreting ultrasound images requires extensive training due to the imaging artefacts, the range of acquisition parameters and the variability of patient anatomies. Automating the image acquisition task could improve acquisition reproducibility and quality but training such an algorithm requires large amounts of navigation data, not saved in routine examinations. Thus, we propose a method to generate large amounts of ultrasound images from other modalities and from arbitrary positions, such that this pipeline can later be used by learning algorithms for navigation. We present a novel simulation pipeline which uses segmentations from other modalities, an optimized volumetric data representation and GPU-accelerated Monte Carlo path tracing to generate view-dependent and patient-specific ultrasound images. We extensively validate the correctness of our pipeline with a phantom experiment, where structures' sizes, contrast and speckle noise properties are assessed. Furthermore, we demonstrate its usability to train neural networks for navigation in an echocardiography view classification experiment by generating synthetic images from more than 1000 patients. Networks pre-trained with our simulations achieve significantly superior performance in settings where large real datasets are not available, especially for under-represented classes. The proposed approach allows for fast and accurate patient-specific ultrasound image generation, and its usability for training networks for navigation-related tasks is demonstrated.

MB-DECTNet: A Model-Based Unrolled Network for Accurate 3D DECT Reconstruction

Numerous dual-energy CT (DECT) techniques have been developed in the past few decades. Dual-energy CT (DECT) statistical iterative reconstruction (SIR) has demonstrated its potential for reducing noise and increasing accuracy. Our lab proposed a joint statistical DECT algorithm for stopping power estimation and showed that it outperforms competing image-based material-decomposition methods. However, due to its slow convergence and the high computational cost of projections, the elapsed time of 3D DECT SIR is often not clinically acceptable. Therefore, to improve its convergence, we have embedded DECT SIR into a deep learning model-based unrolled network for 3D DECT reconstruction (MB-DECTNet) that can be trained in an end-to-end fashion. This deep learning-based method is trained to learn the shortcuts between the initial conditions and the stationary points of iterative algorithms while preserving the unbiased estimation property of model-based algorithms. MB-DECTNet is formed by stacking multiple update blocks, each of which consists of a data consistency layer (DC) and a spatial mixer layer, where the spatial mixer layer is the shrunken U-Net, and the DC layer is a one-step update of an arbitrary traditional iterative method. Although the proposed network can be combined with numerous iterative DECT algorithms, we demonstrate its performance with the dual-energy alternating minimization (DEAM). The qualitative result shows that MB-DECTNet with DEAM significantly reduces noise while increasing the resolution of the test image. The quantitative result shows that MB-DECTNet has the potential to estimate attenuation coefficients accurately as traditional statistical algorithms but with a much lower computational cost.

A Metal Artifact Reduction Scheme For Accurate Iterative Dual-Energy CT Algorithms

CT images have been used to generate radiation therapy treatment plans for more than two decades. Dual-energy CT (DECT) has shown high accuracy in estimating electronic density or proton stopping-power maps used in treatment planning. However, the presence of metal implants introduces severe streaking artifacts in the reconstructed images, affecting the diagnostic accuracy and treatment performance. In order to reduce the metal artifacts in DECT, we introduce a metal-artifact reduction scheme for iterative DECT algorithms. An estimate is substituted for the corrupt data in each iteration. We utilize normalized metal-artifact reduction (NMAR) composed with image-domain decomposition to initialize the algorithm and speed up the convergence. A fully 3D joint statistical DECT algorithm, dual-energy alternating minimization (DEAM), with the proposed scheme is tested on experimental and clinical helical data acquired on a Philips Brilliance Big Bore scanner. We compared DEAM with the proposed method to the original DEAM and vendor reconstructions with and without metal-artifact reduction for orthopedic implants (O-MAR). The visualization and quantitative analysis show that DEAM with the proposed method has the best performance in reducing streaking artifacts caused by metallic objects.

A Machine-learning Based Initialization for Joint Statistical Iterative Dual-energy CT with Application to Proton Therapy

Dual-energy CT (DECT) has been widely investigated to generate more informative and more accurate images in the past decades. For example, Dual-Energy Alternating Minimization (DEAM) algorithm achieves sub-percentage uncertainty in estimating proton stopping-power mappings from experimental 3-mm collimated phantom data. However, elapsed time of iterative DECT algorithms is not clinically acceptable, due to their low convergence rate and the tremendous geometry of modern helical CT scanners. A CNN-based initialization method is introduced to reduce the computational time of iterative DECT algorithms. DEAM is used as an example of iterative DECT algorithms in this work. The simulation results show that our method generates denoised images with greatly improved estimation accuracy for adipose, tonsils, and muscle tissue. Also, it reduces elapsed time by approximately 5-fold for DEAM to reach the same objective function value for both simulated and real data.

Unsupervised Deformable Registration for Multi-Modal Images via Disentangled Representations

We propose a fully unsupervised multi-modal deformable image registration method (UMDIR), which does not require any ground truth deformation fields or any aligned multi-modal image pairs during training. Multi-modal registration is a key problem in many medical image analysis applications. It is very challenging due to complicated and unknown relationships between different modalities. In this paper, we propose an unsupervised learning approach to reduce the multi-modal registration problem to a mono-modal one through image disentangling. In particular, we decompose images of both modalities into a common latent shape space and separate latent appearance spaces via an unsupervised multi-modal image-to-image translation approach. The proposed registration approach is then built on the factorized latent shape code, with the assumption that the intrinsic shape deformation existing in original image domain is preserved in this latent space. Specifically, two metrics have been proposed for training the proposed network: a latent similarity metric defined in the common shape space and a learningbased image similarity metric based on an adversarial loss. We examined different variations of our proposed approach and compared them with conventional state-of-the-art multi-modal registration methods. Results show that our proposed methods achieve competitive performance against other methods at substantially reduced computation time.

Task Driven Generative Modeling for Unsupervised Domain Adaptation: Application to X-ray Image Segmentation

Automatic parsing of anatomical objects in X-ray images is critical to many clinical applications in particular towards image-guided invention and workflow automation. Existing deep network models require a large amount of labeled data. However, obtaining accurate pixel-wise labeling in X-ray images relies heavily on skilled clinicians due to the large overlaps of anatomy and the complex texture patterns. On the other hand, organs in 3D CT scans preserve clearer structures as well as sharper boundaries and thus can be easily delineated. In this paper, we propose a novel model framework for learning automatic X-ray image parsing from labeled CT scans. Specifically, a Dense Image-to-Image network (DI2I) for multi-organ segmentation is first trained on X-ray like Digitally Reconstructed Radiographs (DRRs) rendered from 3D CT volumes. Then we introduce a Task Driven Generative Adversarial Network (TD-GAN) architecture to achieve simultaneous style transfer and parsing for unseen real X-ray images. TD-GAN consists of a modified cycle-GAN substructure for pixel-to-pixel translation between DRRs and X-ray images and an added module leveraging the pre-trained DI2I to enforce segmentation consistency. The TD-GAN framework is general and can be easily adapted to other learning tasks. In the numerical experiments, we validate the proposed model on 815 DRRs and 153 topograms. While the vanilla DI2I without any adaptation fails completely on segmenting the topograms, the proposed model does not require any topogram labels and is able to provide a promising average dice of 85% which achieves the same level accuracy of supervised training (88%).