Physical Consistency Bridges Heterogeneous Data in Molecular Multi-Task Learning

In recent years, machine learning has demonstrated impressive capability in handling molecular science tasks. To support various molecular properties at scale, machine learning models are trained in the multi-task learning paradigm. Nevertheless, data of different molecular properties are often not aligned: some quantities, e.g. equilibrium structure, demand more cost to compute than others, e.g. energy, so their data are often generated by cheaper computational methods at the cost of lower accuracy, which cannot be directly overcome through multi-task learning. Moreover, it is not straightforward to leverage abundant data of other tasks to benefit a particular task. To handle such data heterogeneity challenges, we exploit the specialty of molecular tasks that there are physical laws connecting them, and design consistency training approaches that allow different tasks to exchange information directly so as to improve one another. Particularly, we demonstrate that the more accurate energy data can improve the accuracy of structure prediction. We also find that consistency training can directly leverage force and off-equilibrium structure data to improve structure prediction, demonstrating a broad capability for integrating heterogeneous data.

LIDIA: Precise Liver Tumor Diagnosis on Multi-Phase Contrast-Enhanced CT via Iterative Fusion and Asymmetric Contrastive Learning

The early detection and precise diagnosis of liver tumors are tasks of critical clinical value, yet they pose significant challenges due to the high heterogeneity and variability of liver tumors. In this work, a precise LIver tumor DIAgnosis network on multi-phase contrast-enhance CT, named LIDIA, is proposed for real-world scenario. To fully utilize all available phases in contrast-enhanced CT, LIDIA first employs the iterative fusion module to aggregate variable numbers of image phases, thereby capturing the features of lesions at different phases for better tumor diagnosis. To effectively mitigate the high heterogeneity problem of liver tumors, LIDIA incorporates asymmetric contrastive learning to enhance the discriminability between different classes. To evaluate our method, we constructed a large-scale dataset comprising 1,921 patients and 8,138 lesions. LIDIA has achieved an average AUC of 93.6% across eight different types of lesions, demonstrating its effectiveness. Besides, LIDIA also demonstrated strong generalizability with an average AUC of 89.3% when tested on an external cohort of 828 patients.

Improved Esophageal Varices Assessment from Non-Contrast CT Scans

Esophageal varices (EV), a serious health concern resulting from portal hypertension, are traditionally diagnosed through invasive endoscopic procedures. Despite non-contrast computed tomography (NC-CT) imaging being a less expensive and non-invasive imaging modality, it has yet to gain full acceptance as a primary clinical diagnostic tool for EV evaluation. To overcome existing diagnostic challenges, we present the Multi-Organ-cOhesion-Network (MOON), a novel framework enhancing the analysis of critical organ features in NC-CT scans for effective assessment of EV. Drawing inspiration from the thorough assessment practices of radiologists, MOON establishes a cohesive multiorgan analysis model that unifies the imaging features of the related organs of EV, namely esophagus, liver, and spleen. This integration significantly increases the diagnostic accuracy for EV. We have compiled an extensive NC-CT dataset of 1,255 patients diagnosed with EV, spanning three grades of severity. Each case is corroborated by endoscopic diagnostic results. The efficacy of MOON has been substantiated through a validation process involving multi-fold cross-validation on 1,010 cases and an independent test on 245 cases, exhibiting superior diagnostic performance compared to methods focusing solely on the esophagus (for classifying severe grade: AUC of 0.864 versus 0.803, and for moderate to severe grades: AUC of 0.832 versus 0.793). To our knowledge, MOON is the first work to incorporate a synchronized multi-organ NC-CT analysis for EV assessment, providing a more acceptable and minimally invasive alternative for patients compared to traditional endoscopy.

Test-Time Training on Graphs with Large Language Models

Graph Neural Networks have demonstrated great success in various fields of multimedia. However, the distribution shift between the training and test data challenges the effectiveness of GNNs. To mitigate this challenge, Test-Time Training (TTT) has been proposed as a promising approach. Traditional TTT methods require a demanding unsupervised training strategy to capture the information from test to benefit the main task. Inspired by the great annotation ability of Large Language Models (LLMs) on Text-Attributed Graphs (TAGs), we propose to enhance the test-time training on graphs with LLMs as annotators. In this paper, we design a novel Test-Time Training pipeline, LLMTTT, which conducts the test-time adaptation under the annotations by LLMs on a carefully-selected node set. Specifically, LLMTTT introduces a hybrid active node selection strategy that considers not only node diversity and representativeness, but also prediction signals from the pre-trained model. Given annotations from LLMs, a two-stage training strategy is designed to tailor the test-time model with the limited and noisy labels. A theoretical analysis ensures the validity of our method and extensive experiments demonstrate that the proposed LLMTTT can achieve a significant performance improvement compared to existing Out-of-Distribution (OOD) generalization methods.

Modality-Agnostic Structural Image Representation Learning for Deformable Multi-Modality Medical Image Registration

Establishing dense anatomical correspondence across distinct imaging modalities is a foundational yet challenging procedure for numerous medical image analysis studies and image-guided radiotherapy. Existing multi-modality image registration algorithms rely on statistical-based similarity measures or local structural image representations. However, the former is sensitive to locally varying noise, while the latter is not discriminative enough to cope with complex anatomical structures in multimodal scans, causing ambiguity in determining the anatomical correspondence across scans with different modalities. In this paper, we propose a modality-agnostic structural representation learning method, which leverages Deep Neighbourhood Self-similarity (DNS) and anatomy-aware contrastive learning to learn discriminative and contrast-invariance deep structural image representations (DSIR) without the need for anatomical delineations or pre-aligned training images. We evaluate our method on multiphase CT, abdomen MR-CT, and brain MR T1w-T2w registration. Comprehensive results demonstrate that our method is superior to the conventional local structural representation and statistical-based similarity measures in terms of discriminability and accuracy.

Actions Speak Louder than Words: Trillion-Parameter Sequential Transducers for Generative Recommendations

Large-scale recommendation systems are characterized by their reliance on high cardinality, heterogeneous features and the need to handle tens of billions of user actions on a daily basis. Despite being trained on huge volume of data with thousands of features, most Deep Learning Recommendation Models (DLRMs) in industry fail to scale with compute. Inspired by success achieved by Transformers in language and vision domains, we revisit fundamental design choices in recommendation systems. We reformulate recommendation problems as sequential transduction tasks within a generative modeling framework (``Generative Recommenders''), and propose a new architecture, HSTU, designed for high cardinality, non-stationary streaming recommendation data. HSTU outperforms baselines over synthetic and public datasets by up to 65.8\% in NDCG, and is 5.3x to 15.2x faster than FlashAttention2-based Transformers on 8192 length sequences. HSTU-based Generative Recommenders, with 1.5 trillion parameters, improve metrics in online A/B tests by 12.4\% and have been deployed on multiple surfaces of a large internet platform with billions of users. More importantly, the model quality of Generative Recommenders empirically scales as a power-law of training compute across three orders of magnitude, up to GPT-3/LLaMa-2 scale, which reduces carbon footprint needed for future model developments, and further paves the way for the first foundational models in recommendations.

3DGAUnet: 3D generative adversarial networks with a 3D U-Net based generator to achieve the accurate and effective synthesis of clinical tumor image data for pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) presents a critical global health challenge, and early detection is crucial for improving the 5-year survival rate. Recent medical imaging and computational algorithm advances offer potential solutions for early diagnosis. Deep learning, particularly in the form of convolutional neural networks (CNNs), has demonstrated success in medical image analysis tasks, including classification and segmentation. However, the limited availability of clinical data for training purposes continues to provide a significant obstacle. Data augmentation, generative adversarial networks (GANs), and cross-validation are potential techniques to address this limitation and improve model performance, but effective solutions are still rare for 3D PDAC, where contrast is especially poor owing to the high heterogeneity in both tumor and background tissues. In this study, we developed a new GAN-based model, named 3DGAUnet, for generating realistic 3D CT images of PDAC tumors and pancreatic tissue, which can generate the interslice connection data that the existing 2D CT image synthesis models lack. Our innovation is to develop a 3D U-Net architecture for the generator to improve shape and texture learning for PDAC tumors and pancreatic tissue. Our approach offers a promising path to tackle the urgent requirement for creative and synergistic methods to combat PDAC. The development of this GAN-based model has the potential to alleviate data scarcity issues, elevate the quality of synthesized data, and thereby facilitate the progression of deep learning models to enhance the accuracy and early detection of PDAC tumors, which could profoundly impact patient outcomes. Furthermore, this model has the potential to be adapted to other types of solid tumors, hence making significant contributions to the field of medical imaging in terms of image processing models.

Robust Representation Learning for Unreliable Partial Label Learning

Partial Label Learning (PLL) is a type of weakly supervised learning where each training instance is assigned a set of candidate labels, but only one label is the ground-truth. However, this idealistic assumption may not always hold due to potential annotation inaccuracies, meaning the ground-truth may not be present in the candidate label set. This is known as Unreliable Partial Label Learning (UPLL) that introduces an additional complexity due to the inherent unreliability and ambiguity of partial labels, often resulting in a sub-optimal performance with existing methods. To address this challenge, we propose the Unreliability-Robust Representation Learning framework (URRL) that leverages unreliability-robust contrastive learning to help the model fortify against unreliable partial labels effectively. Concurrently, we propose a dual strategy that combines KNN-based candidate label set correction and consistency-regularization-based label disambiguation to refine label quality and enhance the ability of representation learning within the URRL framework. Extensive experiments demonstrate that the proposed method outperforms state-of-the-art PLL methods on various datasets with diverse degrees of unreliability and ambiguity. Furthermore, we provide a theoretical analysis of our approach from the perspective of the expectation maximization (EM) algorithm. Upon acceptance, we pledge to make the code publicly accessible.

SLPT: Selective Labeling Meets Prompt Tuning on Label-Limited Lesion Segmentation

Medical image analysis using deep learning is often challenged by limited labeled data and high annotation costs. Fine-tuning the entire network in label-limited scenarios can lead to overfitting and suboptimal performance. Recently, prompt tuning has emerged as a more promising technique that introduces a few additional tunable parameters as prompts to a task-agnostic pre-trained model, and updates only these parameters using supervision from limited labeled data while keeping the pre-trained model unchanged. However, previous work has overlooked the importance of selective labeling in downstream tasks, which aims to select the most valuable downstream samples for annotation to achieve the best performance with minimum annotation cost. To address this, we propose a framework that combines selective labeling with prompt tuning (SLPT) to boost performance in limited labels. Specifically, we introduce a feature-aware prompt updater to guide prompt tuning and a TandEm Selective LAbeling (TESLA) strategy. TESLA includes unsupervised diversity selection and supervised selection using prompt-based uncertainty. In addition, we propose a diversified visual prompt tuning strategy to provide multi-prompt-based discrepant predictions for TESLA. We evaluate our method on liver tumor segmentation and achieve state-of-the-art performance, outperforming traditional fine-tuning with only 6% of tunable parameters, also achieving 94% of full-data performance by labeling only 5% of the data.

Improved Prognostic Prediction of Pancreatic Cancer Using Multi-Phase CT by Integrating Neural Distance and Texture-Aware Transformer

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer in which the tumor-vascular involvement greatly affects the resectability and, thus, overall survival of patients. However, current prognostic prediction methods fail to explicitly and accurately investigate relationships between the tumor and nearby important vessels. This paper proposes a novel learnable neural distance that describes the precise relationship between the tumor and vessels in CT images of different patients, adopting it as a major feature for prognosis prediction. Besides, different from existing models that used CNNs or LSTMs to exploit tumor enhancement patterns on dynamic contrast-enhanced CT imaging, we improved the extraction of dynamic tumor-related texture features in multi-phase contrast-enhanced CT by fusing local and global features using CNN and transformer modules, further enhancing the features extracted across multi-phase CT images. We extensively evaluated and compared the proposed method with existing methods in the multi-center (n=4) dataset with 1,070 patients with PDAC, and statistical analysis confirmed its clinical effectiveness in the external test set consisting of three centers. The developed risk marker was the strongest predictor of overall survival among preoperative factors and it has the potential to be combined with established clinical factors to select patients at higher risk who might benefit from neoadjuvant therapy.