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Whole slide image (WSI) assessment is a challenging and crucial step in cancer diagnosis and treatment planning. WSIs require high magnifications to facilitate sub-cellular analysis. Precise annotations for patch- or even pixel-level classifications in the context of gigapixel WSIs are tedious to acquire and require domain experts. Coarse-grained labels, on the other hand, are easily accessible, which makes WSI classification an ideal use case for multiple instance learning (MIL). In our work, we propose a novel embedding-based Dual-Query MIL pipeline (DQ-MIL). We contribute to both the embedding and aggregation steps. Since all-purpose visual feature representations are not yet available, embedding models are currently limited in terms of generalizability. With our work, we explore the potential of dynamic meta-embedding based on cutting-edge self-supervised pre-trained models in the context of MIL. Moreover, we propose a new MIL architecture capable of combining MIL-attention with correlated self-attention. The Dual-Query Perceiver design of our approach allows us to leverage the concept of self-distillation and to combine the advantages of a small model in the context of a low data regime with the rich feature representation of a larger model. We demonstrate the superior performance of our approach on three histopathological datasets, where we show improvement of up to 10% over state-of-the-art approaches.

Pathological alterations in the human vascular system underlie many chronic diseases, such as atherosclerosis and aneurysms. However, manually analyzing diagnostic images of the vascular system, such as computed tomographic angiograms (CTAs) is a time-consuming and tedious process. To address this issue, we propose a deep learning model to segment the vascular system in CTA images of patients undergoing surgery for peripheral arterial disease (PAD). Our study focused on accurately segmenting the vascular system (1) from the descending thoracic aorta to the iliac bifurcation and (2) from the descending thoracic aorta to the knees in CTA images using deep learning techniques. Our approach achieved average Dice accuracies of 93.5% and 80.64% in test dataset for (1) and (2), respectively, highlighting its high accuracy and potential clinical utility. These findings demonstrate the use of deep learning techniques as a valuable tool for medical professionals to analyze the health of the vascular system efficiently and accurately. Please visit the GitHub page for this paper at //github.com/pip-alireza/TransOnet.

Complete resection of malignant gliomas is hampered by the difficulty in distinguishing tumor cells at the infiltration zone. Fluorescence guidance with 5-ALA assists in reaching this goal. Using hyperspectral imaging, previous work characterized five fluorophores' emission spectra in most human brain tumors. In this paper, the effectiveness of these five spectra was explored for different tumor and tissue classification tasks in 184 patients (891 hyperspectral measurements) harboring low- (n=30) and high-grade gliomas (n=115), non-glial primary brain tumors (n=19), radiation necrosis (n=2), miscellaneous (n=10) and metastases (n=8). Four machine learning models were trained to classify tumor type, grade, glioma margins and IDH mutation. Using random forests and multi-layer perceptrons, the classifiers achieved average test accuracies of 74-82%, 79%, 81%, and 93% respectively. All five fluorophore abundances varied between tumor margin types and tumor grades (p < 0.01). For tissue type, at least four of the five fluorophore abundances were found to be significantly different (p < 0.01) between all classes. These results demonstrate the fluorophores' differing abundances in different tissue classes, as well as the value of the five fluorophores as potential optical biomarkers, opening new opportunities for intraoperative classification systems in fluorescence-guided neurosurgery.

Accurately predicting the lifespan of lithium-ion batteries (LIBs) is pivotal for optimizing usage and preventing accidents. Previous studies in constructing prediction models often relied on inputs challenging to measure in real-time operations and failed to capture intra-cycle and inter-cycle data patterns, essential features for accurate predictions, comprehensively. In this study, we employ attention mechanisms (AM) to develop data-driven models for predicting LIB lifespan using easily measurable inputs such as voltage, current, temperature, and capacity data. The developed model integrates recurrent neural network (RNN) and convolutional neural network (CNN) components, featuring two types of attention mechanisms: temporal attention (TA) and cyclic attention (CA). The inclusion of TA aims to identify important time steps within each cycle by scoring the hidden states of the RNN, whereas CA strives to capture key features of inter-cycle correlations through self-attention (SA). This enhances model accuracy and elucidates critical features in the input data. To validate our method, we apply it to publicly available cycling data consisting of three batches of cycling modes. The calculated TA scores highlight the rest phase as a key characteristic distinguishing LIB data among different batches. Additionally, CA scores reveal variations in the importance of cycles across batches. By leveraging CA scores, we explore the potential to reduce the number of cycles in the input data. The single-head and multi-head attentions enable us to decrease the input dimension from 100 to 50 and 30 cycles, respectively.

Diagnosis of breast cancer malignancy at the early stages is a crucial step for controlling its side effects. Histopathological analysis provides a unique opportunity for malignant breast cancer detection. However, such a task would be tedious and time-consuming for the histopathologists. Deep Neural Networks enable us to learn informative features directly from raw histopathological images without manual feature extraction. Although Convolutional Neural Networks (CNNs) have been the dominant architectures in the computer vision realm, Transformer-based architectures have shown promising results in different computer vision tasks. Although harnessing the capability of Transformer-based architectures for medical image analysis seems interesting, these architectures are large, have a significant number of trainable parameters, and require large datasets to be trained on, which are usually rare in the medical domain. It has been claimed and empirically proved that at least part of the superior performance of Transformer-based architectures in Computer Vision domain originates from patch embedding operation. In this paper, we borrowed the previously introduced idea of integrating a fully Convolutional Neural Network architecture with Patch Embedding operation and presented an efficient CNN architecture for breast cancer malignancy detection from histopathological images. Despite the number of parameters that is significantly smaller than other methods, the accuracy performance metrics achieved 97.65%, 98.92%, 99.21%, and 98.01% for 40x, 100x, 200x, and 400x magnifications respectively. We took a step forward and modified the architecture using Group Convolution and Channel Shuffling ideas and reduced the number of trainable parameters even more with a negligible decline in performance and achieved 95.42%, 98.16%, 96.05%, and 97.92% accuracy for the mentioned magnifications respectively.

Decades of research indicate that emotion recognition is more effective when drawing information from multiple modalities. But what if some modalities are sometimes missing? To address this problem, we propose a novel Transformer-based architecture for recognizing valence and arousal in a time-continuous manner even with missing input modalities. We use a coupling of cross-attention and self-attention mechanisms to emphasize relationships between modalities during time and enhance the learning process on weak salient inputs. Experimental results on the Ulm-TSST dataset show that our model exhibits an improvement of the concordance correlation coefficient evaluation of 37% when predicting arousal values and 30% when predicting valence values, compared to a late-fusion baseline approach.

Physical inactivity remains a major public health concern, having associations with adverse health outcomes such as cardiovascular disease and type-2 diabetes. Mobile health applications present a promising avenue for low-cost, scalable physical activity promotion, yet often suffer from small effect sizes and low adherence rates, particularly in comparison to human coaching. Goal-setting is a critical component of health coaching that has been underutilized in adaptive algorithms for mobile health interventions. This paper introduces a modification to the Thompson sampling algorithm that places emphasis on individualized goal-setting by optimizing personalized reward functions. As a step towards supporting goal-setting, this paper offers a balanced approach that can leverage shared structure while optimizing individual preferences and goals. We prove that our modification incurs only a constant penalty on the cumulative regret while preserving the sample complexity benefits of data sharing. In a physical activity simulator, we demonstrate that our algorithm achieves substantial improvements in cumulative regret compared to baselines that do not share data or do not optimize for individualized rewards.

The notion of group invariance helps neural networks in recognizing patterns and features under geometric transformations. Indeed, it has been shown that group invariance can largely improve deep learning performances in practice, where such transformations are very common. This research studies affine invariance on continuous-domain convolutional neural networks. Despite other research considering isometric invariance or similarity invariance, we focus on the full structure of affine transforms generated by the generalized linear group $\mathrm{GL}_2(\mathbb{R})$. We introduce a new criterion to assess the similarity of two input signals under affine transformations. Then, unlike conventional methods that involve solving complex optimization problems on the Lie group $G_2$, we analyze the convolution of lifted signals and compute the corresponding integration over $G_2$. In sum, our research could eventually extend the scope of geometrical transformations that practical deep-learning pipelines can handle.

Recent artificial intelligence (AI) systems have reached milestones in "grand challenges" ranging from Go to protein-folding. The capability to retrieve medical knowledge, reason over it, and answer medical questions comparably to physicians has long been viewed as one such grand challenge. Large language models (LLMs) have catalyzed significant progress in medical question answering; Med-PaLM was the first model to exceed a "passing" score in US Medical Licensing Examination (USMLE) style questions with a score of 67.2% on the MedQA dataset. However, this and other prior work suggested significant room for improvement, especially when models' answers were compared to clinicians' answers. Here we present Med-PaLM 2, which bridges these gaps by leveraging a combination of base LLM improvements (PaLM 2), medical domain finetuning, and prompting strategies including a novel ensemble refinement approach. Med-PaLM 2 scored up to 86.5% on the MedQA dataset, improving upon Med-PaLM by over 19% and setting a new state-of-the-art. We also observed performance approaching or exceeding state-of-the-art across MedMCQA, PubMedQA, and MMLU clinical topics datasets. We performed detailed human evaluations on long-form questions along multiple axes relevant to clinical applications. In pairwise comparative ranking of 1066 consumer medical questions, physicians preferred Med-PaLM 2 answers to those produced by physicians on eight of nine axes pertaining to clinical utility (p < 0.001). We also observed significant improvements compared to Med-PaLM on every evaluation axis (p < 0.001) on newly introduced datasets of 240 long-form "adversarial" questions to probe LLM limitations. While further studies are necessary to validate the efficacy of these models in real-world settings, these results highlight rapid progress towards physician-level performance in medical question answering.