Multimodal Data Integration for Precision Oncology: Challenges and Future Directions

The essence of precision oncology lies in its commitment to tailor targeted treatments and care measures to each patient based on the individual characteristics of the tumor. The inherent heterogeneity of tumors necessitates gathering information from diverse data sources to provide valuable insights from various perspectives, fostering a holistic comprehension of the tumor. Over the past decade, multimodal data integration technology for precision oncology has made significant strides, showcasing remarkable progress in understanding the intricate details within heterogeneous data modalities. These strides have exhibited tremendous potential for improving clinical decision-making and model interpretation, contributing to the advancement of cancer care and treatment. Given the rapid progress that has been achieved, we provide a comprehensive overview of about 300 papers detailing cutting-edge multimodal data integration techniques in precision oncology. In addition, we conclude the primary clinical applications that have reaped significant benefits, including early assessment, diagnosis, prognosis, and biomarker discovery. Finally, derived from the findings of this survey, we present an in-depth analysis that explores the pivotal challenges and reveals essential pathways for future research in the field of multimodal data integration for precision oncology.

Cohort-Individual Cooperative Learning for Multimodal Cancer Survival Analysis

Recently, we have witnessed impressive achievements in cancer survival analysis by integrating multimodal data, e.g., pathology images and genomic profiles. However, the heterogeneity and high dimensionality of these modalities pose significant challenges for extracting discriminative representations while maintaining good generalization. In this paper, we propose a Cohort-individual Cooperative Learning (CCL) framework to advance cancer survival analysis by collaborating knowledge decomposition and cohort guidance. Specifically, first, we propose a Multimodal Knowledge Decomposition (MKD) module to explicitly decompose multimodal knowledge into four distinct components: redundancy, synergy and uniqueness of the two modalities. Such a comprehensive decomposition can enlighten the models to perceive easily overlooked yet important information, facilitating an effective multimodal fusion. Second, we propose a Cohort Guidance Modeling (CGM) to mitigate the risk of overfitting task-irrelevant information. It can promote a more comprehensive and robust understanding of the underlying multimodal data, while avoiding the pitfalls of overfitting and enhancing the generalization ability of the model. By cooperating the knowledge decomposition and cohort guidance methods, we develop a robust multimodal survival analysis model with enhanced discrimination and generalization abilities. Extensive experimental results on five cancer datasets demonstrate the effectiveness of our model in integrating multimodal data for survival analysis.

Anatomy-guided fiber trajectory distribution estimation for cranial nerves tractography

Diffusion MRI tractography is an important tool for identifying and analyzing the intracranial course of cranial nerves (CNs). However, the complex environment of the skull base leads to ambiguous spatial correspondence between diffusion directions and fiber geometry, and existing diffusion tractography methods of CNs identification are prone to producing erroneous trajectories and missing true positive connections. To overcome the above challenge, we propose a novel CNs identification framework with anatomy-guided fiber trajectory distribution, which incorporates anatomical shape prior knowledge during the process of CNs tracing to build diffusion tensor vector fields. We introduce higher-order streamline differential equations for continuous flow field representations to directly characterize the fiber trajectory distribution of CNs from the tract-based level. The experimental results on the vivo HCP dataset and the clinical MDM dataset demonstrate that the proposed method reduces false-positive fiber production compared to competing methods and produces reconstructed CNs (i.e. CN II, CN III, CN V, and CN VII/VIII) that are judged to better correspond to the known anatomy.

Appearance-guided Attentive Self-Paced Learning for Unsupervised Salient Object Detection

Existing Deep-Learning-based (DL-based) Unsupervised Salient Object Detection (USOD) methods learn saliency information in images based on the prior knowledge of traditional saliency methods and pretrained deep networks. However, these methods employ a simple learning strategy to train deep networks and therefore cannot properly incorporate the "hidden" information of the training samples into the learning process. Moreover, appearance information, which is crucial for segmenting objects, is only used as post-process after the network training process. To address these two issues, we propose a novel appearance-guided attentive self-paced learning framework for unsupervised salient object detection. The proposed framework integrates both self-paced learning (SPL) and appearance guidance into a unified learning framework. Specifically, for the first issue, we propose an Attentive Self-Paced Learning (ASPL) paradigm that organizes the training samples in a meaningful order to excavate gradually more detailed saliency information. Our ASPL facilitates our framework capable of automatically producing soft attention weights that measure the learning difficulty of training samples in a purely self-learning way. For the second issue, we propose an Appearance Guidance Module (AGM), which formulates the local appearance contrast of each pixel as the probability of saliency boundary and finds the potential boundary of the target objects by maximizing the probability. Furthermore, we further extend our framework to other multi-modality SOD tasks by aggregating the appearance vectors of other modality data, such as depth map, thermal image or optical flow. Extensive experiments on RGB, RGB-D, RGB-T and video SOD benchmarks prove that our framework achieves state-of-the-art performance against existing USOD methods and is comparable to the latest supervised SOD methods.

Benchmarking Deep Models for Salient Object Detection

In recent years, deep network-based methods have continuously refreshed state-of-the-art performance on Salient Object Detection (SOD) task. However, the performance discrepancy caused by different implementation details may conceal the real progress in this task. Making an impartial comparison is required for future researches. To meet this need, we construct a general SALient Object Detection (SALOD) benchmark to conduct a comprehensive comparison among several representative SOD methods. Specifically, we re-implement 14 representative SOD methods by using consistent settings for training. Moreover, two additional protocols are set up in our benchmark to investigate the robustness of existing methods in some limited conditions. In the first protocol, we enlarge the difference between objectness distributions of train and test sets to evaluate the robustness of these SOD methods. In the second protocol, we build multiple train subsets with different scales to validate whether these methods can extract discriminative features from only a few samples. In the above experiments, we find that existing loss functions usually specialized in some metrics but reported inferior results on the others. Therefore, we propose a novel Edge-Aware (EA) loss that promotes deep networks to learn more discriminative features by integrating both pixel- and image-level supervision signals. Experiments prove that our EA loss reports more robust performances compared to existing losses.

Activation to Saliency: Forming High-Quality Labels for Completely Unsupervised Salient Object Detection

Existing deep learning-based Unsupervised Salient Object Detection (USOD) methods rely on supervised pre-trained deep models. Moreover, they generate pseudo labels based on hand-crafted features, which lack high-level semantic information. In order to overcome these shortcomings, we propose a new two-stage Activation-to-Saliency (A2S) framework that effectively excavates high-quality saliency cues to train a robust saliency detector. It is worth noting that our method does not require any manual annotation, even in the pre-training phase. In the first stage, we transform an unsupervisedly pre-trained network to aggregate multi-level features to a single activation map, where an Adaptive Decision Boundary (ADB) is proposed to assist the training of the transformed network. Moreover, a new loss function is proposed to facilitate the generation of high-quality pseudo labels. In the second stage, a self-rectification learning paradigm strategy is developed to train a saliency detector and refine the pseudo labels online. In addition, we construct a lightweight saliency detector using two Residual Attention Modules (RAMs) to largely reduce the risk of overfitting. Extensive experiments on several SOD benchmarks prove that our framework reports significant performance compared with existing USOD methods. Moreover, training our framework on 3,000 images consumes about 1 hour, which is over 30$\times$ faster than previous state-of-the-art methods.

Confidence-guided Adaptive Gate and Dual Differential Enhancement for Video Salient Object Detection

Video salient object detection (VSOD) aims to locate and segment the most attractive object by exploiting both spatial cues and temporal cues hidden in video sequences. However, spatial and temporal cues are often unreliable in real-world scenarios, such as low-contrast foreground, fast motion, and multiple moving objects. To address these problems, we propose a new framework to adaptively capture available information from spatial and temporal cues, which contains Confidence-guided Adaptive Gate (CAG) modules and Dual Differential Enhancement (DDE) modules. For both RGB features and optical flow features, CAG estimates confidence scores supervised by the IoU between predictions and the ground truths to re-calibrate the information with a gate mechanism. DDE captures the differential feature representation to enrich the spatial and temporal information and generate the fused features. Experimental results on four widely used datasets demonstrate the effectiveness of the proposed method against thirteen state-of-the-art methods.

Contour Loss: Boundary-Aware Learning for Salient Object Segmentation

We present a learning model that makes full use of boundary information for salient object segmentation. Specifically, we come up with a novel loss function, i.e., Contour Loss, which leverages object contours to guide models to perceive salient object boundaries. Such a boundary-aware network can learn boundary-wise distinctions between salient objects and background, hence effectively facilitating the saliency detection. Yet the Contour Loss emphasizes on the local saliency. We further propose the hierarchical global attention module (HGAM), which forces the model hierarchically attend to global contexts, thus captures the global visual saliency. Comprehensive experiments on six benchmark datasets show that our method achieves superior performance over state-of-the-art ones. Moreover, our model has a real-time speed of 26 fps on a TITAN X GPU.