Integrating the different data modalities of cancer patients can significantly improve the predictive performance of patient survival. However, most existing methods ignore the simultaneous utilization of rich semantic features at different scales in pathology images. When collecting multimodal data and extracting features, there is a likelihood of encountering intra-modality missing data, introducing noise into the multimodal data. To address these challenges, this paper proposes a new end-to-end framework, FORESEE, for robustly predicting patient survival by mining multimodal information. Specifically, the cross-fusion transformer effectively utilizes features at the cellular level, tissue level, and tumor heterogeneity level to correlate prognosis through a cross-scale feature cross-fusion method. This enhances the ability of pathological image feature representation. Secondly, the hybrid attention encoder (HAE) uses the denoising contextual attention module to obtain the contextual relationship features and local detail features of the molecular data. HAE's channel attention module obtains global features of molecular data. Furthermore, to address the issue of missing information within modalities, we propose an asymmetrically masked triplet masked autoencoder to reconstruct lost information within modalities. Extensive experiments demonstrate the superiority of our method over state-of-the-art methods on four benchmark datasets in both complete and missing settings.
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AI-based diagnoses have demonstrated dermatologist-level performance in classifying skin cancer. However, such systems are prone to under-performing when tested on data from minority groups that lack sufficient representation in the training sets. Although data collection and annotation offer the best means for promoting minority groups, these processes are costly and time-consuming. Prior works have suggested that data from majority groups may serve as a valuable information source to supplement the training of diagnosis tools for minority groups. In this work, we propose an effective diffusion-based augmentation framework that maximizes the use of rich information from majority groups to benefit minority groups. Using groups with different skin types as a case study, our results show that the proposed framework can generate synthetic images that improve diagnostic results for the minority groups, even when there is little or no reference data from these target groups. The practical value of our work is evident in medical imaging analysis, where under-diagnosis persists as a problem for certain groups due to insufficient representation.
The exploration of biomarkers, which are clinically useful biomolecules, and the development of prediction models using them are important problems in biomedical research. Biomarkers are widely used for disease screening, and some are related not only to the presence or absence of a disease but also to its severity. These biomarkers can be useful for prioritization of treatment and clinical decision-making. Considering a model helpful for both disease screening and severity prediction, this paper focuses on regression modeling for an ordinal response equipped with a hierarchical structure. If the response variable is a combination of the presence of disease and severity such as \{{\it healthy, mild, intermediate, severe}\}, for example, the simplest method would be to apply the conventional ordinal regression model. However, the conventional model has flexibility issues and may not be suitable for the problems addressed in this paper, where the levels of the response variable might be heterogeneous. Therefore, this paper proposes a model assuming screening and severity prediction as different tasks, and an estimation method based on structural sparse regularization that leverages any common structure between the tasks when such commonality exists. In numerical experiments, the proposed method demonstrated stable performance across many scenarios compared to existing ordinal regression methods.
The spatial composition and cellular heterogeneity of the tumor microenvironment plays a critical role in cancer development and progression. High-definition pathology imaging of tumor biopsies provide a high-resolution view of the spatial organization of different types of cells. This allows for systematic assessment of intra- and inter-patient spatial cellular interactions and heterogeneity by integrating accompanying patient-level genomics data. However, joint modeling across tumor biopsies presents unique challenges due to non-conformability (lack of a common spatial domain across biopsies) as well as high-dimensionality. To address this problem, we propose the Dual random effect and main effect selection model for Spatially structured regression model (DreameSpase). DreameSpase employs a Bayesian variable selection framework that facilitates the assessment of spatial heterogeneity with respect to covariates both within (through fixed effects) and between spaces (through spatial random effects) for non-conformable spatial domains. We demonstrate the efficacy of DreameSpase via simulations and integrative analyses of pathology imaging and gene expression data obtained from $335$ melanoma biopsies. Our findings confirm several existing relationships, e.g. neutrophil genes being associated with both inter- and intra-patient spatial heterogeneity, as well as discovering novel associations. We also provide freely available and computationally efficient software for implementing DreameSpase.
We propose a fresh take on understanding the mechanisms of neural networks by analyzing the rich directional structure of optimization trajectories, represented by their pointwise parameters. Towards this end, we introduce some natural notions of the complexity of optimization trajectories, both qualitative and quantitative, which hallmark the directional nature of optimization in neural networks: when is there redundancy, and when exploration. We use them to reveal the inherent nuance and interplay involved between various optimization choices, such as momentum and weight decay. Further, the trajectory perspective helps us see the effect of scale on regularizing the directional nature of trajectories, and as a by-product, we also observe an intriguing heterogeneity of Q,K,V dynamics in the middle attention layers in LLMs and which is homogenized by scale. Importantly, we put the significant directional redundancy observed to the test by demonstrating that training only scalar batchnorm parameters some while into training matches the performance of training the entire network, which thus exhibits the potential of hybrid optimization schemes that are geared towards efficiency.
Recent advancements in machine learning have significantly improved the identification of disease-associated genes from gene expression datasets. However, these processes often require extensive expertise and manual effort, limiting their scalability. Large Language Model (LLM)-based agents have shown promise in automating these tasks due to their increasing problem-solving abilities. To support the evaluation and development of such methods, we introduce GenoTEX, a benchmark dataset for the automatic exploration of gene expression data, involving the tasks of dataset selection, preprocessing, and statistical analysis. GenoTEX provides annotated code and results for solving a wide range of gene identification problems, in a full analysis pipeline that follows the standard of computational genomics. These annotations are curated by human bioinformaticians who carefully analyze the datasets to ensure accuracy and reliability. To provide baselines for these tasks, we present GenoAgents, a team of LLM-based agents designed with context-aware planning, iterative correction, and domain expert consultation to collaboratively explore gene datasets. Our experiments with GenoAgents demonstrate the potential of LLM-based approaches in genomics data analysis, while error analysis highlights the challenges and areas for future improvement. We propose GenoTEX as a promising resource for benchmarking and enhancing AI-driven methods for genomics data analysis. We make our benchmark publicly available at \url{//github.com/Liu-Hy/GenoTex}.
Remote proctoring technology, a cheating-preventive measure, often raises privacy and fairness concerns that may affect test-takers' experiences and the validity of test results. Our study explores how selectively obfuscating information in video recordings can protect test-takers' privacy while ensuring effective and fair cheating detection. Interviews with experts (N=9) identified four key video regions indicative of potential cheating behaviors: the test-taker's face, body, background and the presence of individuals in the background. Experts recommended specific obfuscation methods for each region based on privacy significance and cheating behavior frequency, ranging from conventional blurring to advanced methods like replacement with deepfake, 3D avatars and silhouetting. We then conducted a vignette experiment with potential test-takers (N=259, non-experts) to evaluate their perceptions of cheating detection, visual privacy and fairness, using descriptions and examples of still images for each expert-recommended combination of video regions and obfuscation methods. Our results indicate that the effectiveness of obfuscation methods varies by region. Tailoring remote proctoring with region-specific advanced obfuscation methods can improve the perceptions of privacy and fairness compared to the conventional methods, though it may decrease perceived information sufficiency for detecting cheating. However, non-experts preferred conventional blurring for videos they were more willing to share, highlighting a gap between the perceived effectiveness of the advanced obfuscation methods and their practical acceptance. This study contributes to the field of user-centered privacy by suggesting promising directions to address current remote proctoring challenges and guiding future research.
Modern machine learning models are sensitive to the manipulation of both the training data (poisoning attacks) and inference data (adversarial examples). Recognizing this issue, the community has developed many empirical defenses against both attacks and, more recently, provable certification methods against inference-time attacks. However, such guarantees are still largely lacking for training-time attacks. In this work, we present FullCert, the first end-to-end certifier with sound, deterministic bounds, which proves robustness against both training-time and inference-time attacks. We first bound all possible perturbations an adversary can make to the training data under the considered threat model. Using these constraints, we bound the perturbations' influence on the model's parameters. Finally, we bound the impact of these parameter changes on the model's prediction, resulting in joint robustness guarantees against poisoning and adversarial examples. To facilitate this novel certification paradigm, we combine our theoretical work with a new open-source library BoundFlow, which enables model training on bounded datasets. We experimentally demonstrate FullCert's feasibility on two different datasets.
Bayesian predictive probabilities are commonly used for interim monitoring of clinical trials through efficacy and futility stopping rules. Despite their usefulness, calculation of predictive probabilities, particularly in pre-experiment trial simulation, can be a significant challenge. We introduce an approximation for computing predictive probabilities using either a p-value or a posterior probability that significantly reduces this burden. We show the approximation has a high degree of concordance with standard Monte Carlo imputation methods for computing predictive probabilities, and present five simulation studies comparing the approximation to the full predictive probability for a range of primary analysis strategies: dichotomous, time-to-event, and ordinal endpoints, as well as historical borrowing and longitudinal modeling. We find that this faster method of predictive probability approximation works well in all five applications, thus significantly reducing the computational burden of trial simulation, allowing more virtual trials to be simulated to achieve greater precision in estimating trial operating characteristics.
Despite advances in areas such as the personalization of robots, sustaining adoption of robots for long-term use in families remains a challenge. Recent studies have identified integrating robots into families' routines and rituals as a promising approach to support long-term adoption. However, few studies explored the integration of robots into family routines and there is a gap in systematic measures to capture family preferences for robot integration. Building upon existing routine inventories, we developed Family-Robot Routines Inventory (FRRI), with 24 family routines and 24 child routine items, to capture parents' attitudes toward and expectations from the integration of robotic technology into their family routines. Using this inventory, we collected data from 150 parents through an online survey. Our analysis indicates that parents had varying perceptions for the utility of integrating robots into their routines. For example, parents found robot integration to be more helpful in children's individual routines, than to the collective routines of their families. We discuss the design implications of these preliminary findings, and how they may serve as a first step toward understanding the diverse challenges and demands of designing and integrating household robots for families.
Understanding causality helps to structure interventions to achieve specific goals and enables predictions under interventions. With the growing importance of learning causal relationships, causal discovery tasks have transitioned from using traditional methods to infer potential causal structures from observational data to the field of pattern recognition involved in deep learning. The rapid accumulation of massive data promotes the emergence of causal search methods with brilliant scalability. Existing summaries of causal discovery methods mainly focus on traditional methods based on constraints, scores and FCMs, there is a lack of perfect sorting and elaboration for deep learning-based methods, also lacking some considers and exploration of causal discovery methods from the perspective of variable paradigms. Therefore, we divide the possible causal discovery tasks into three types according to the variable paradigm and give the definitions of the three tasks respectively, define and instantiate the relevant datasets for each task and the final causal model constructed at the same time, then reviews the main existing causal discovery methods for different tasks. Finally, we propose some roadmaps from different perspectives for the current research gaps in the field of causal discovery and point out future research directions.
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