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Successful treatment of solid cancers relies on complete surgical excision of the tumor either for definitive treatment or before adjuvant therapy. Intraoperative and postoperative radial sectioning, the most common form of margin assessment, can lead to incomplete excision and increase the risk of recurrence and repeat procedures. Mohs Micrographic Surgery is associated with complete removal of basal cell and squamous cell carcinoma through real-time margin assessment of 100% of the peripheral and deep margins. Real-time assessment in many tumor types is constrained by tissue size, complexity, and specimen processing / assessment time during general anesthesia. We developed an artificial intelligence platform to reduce the tissue preprocessing and histological assessment time through automated grossing recommendations, mapping and orientation of tumor to the surgical specimen. Using basal cell carcinoma as a model system, results demonstrate that this approach can address surgical laboratory efficiency bottlenecks for rapid and complete intraoperative margin assessment.

The problem of optimally measuring an analytic function of unknown local parameters each linearly coupled to a qubit sensor is well understood, with applications ranging from field interpolation to noise characterization. Here, we resolve a number of open questions that arise when extending this framework to Mach-Zehnder interferometers and quadrature displacement sensing. In particular, we derive lower bounds on the achievable mean square error in estimating a linear function of either local phase shifts or quadrature displacements. In the case of local phase shifts, these results prove, and somewhat generalize, a conjecture by Proctor et al. [arXiv:1702.04271 (2017)]. For quadrature displacements, we extend proofs of lower bounds to the case of arbitrary linear functions. We provide optimal protocols achieving these bounds up to small (multiplicative) constants and describe an algebraic approach to deriving new optimal protocols, possibly subject to additional constraints. Using this approach, we prove necessary conditions for the amount of entanglement needed for any optimal protocol for both local phase and displacement sensing.

The attention mechanism in Transformers is an important primitive for accurate and scalable sequence modeling. Its quadratic-compute and linear-memory complexity however remain significant bottlenecks. Linear attention and state-space models enable linear-time, constant-memory sequence modeling and can moreover be trained efficiently through matmul-rich parallelization across sequence length. However, at their core these models are still RNNs, and thus their use of a fixed-size hidden state to model the context is a fundamental limitation. This paper develops log-linear attention, an attention mechanism that balances linear attention's efficiency and the expressiveness of softmax attention. Log-linear attention replaces the fixed-size hidden state with a logarithmically growing set of hidden states. We show that with a particular growth function, log-linear attention admits a similarly matmul-rich parallel form whose compute cost is log-linear in sequence length. Log-linear attention is a general framework and can be applied on top of existing linear attention variants. As case studies, we instantiate log-linear variants of two recent architectures -- Mamba-2 and Gated DeltaNet -- and find they perform well compared to their linear-time variants.

The attention mechanism in Transformers is an important primitive for accurate and scalable sequence modeling. Its quadratic-compute and linear-memory complexity however remain significant bottlenecks. Linear attention and state-space models enable linear-time, constant-memory sequence modeling and can moreover be trained efficiently through matmul-rich parallelization across sequence length. However, at their core these models are still RNNs, and thus their use of a fixed-size hidden state to model the context is a fundamental limitation. This paper develops log-linear attention, an attention mechanism that balances linear attention's efficiency and the expressiveness of softmax attention. Log-linear attention replaces the fixed-size hidden state with a logarithmically growing set of hidden states. We show that with a particular growth function, log-linear attention admits a similarly matmul-rich parallel form whose compute cost is log-linear in sequence length. Log-linear attention is a general framework and can be applied on top of existing linear attention variants. As case studies, we instantiate log-linear variants of two recent architectures -- Mamba-2 and Gated DeltaNet -- and find they perform well compared to their linear-time variants.

Over 150,000 Americans are diagnosed with colorectal cancer (CRC) every year, and annually over 50,000 individuals will die from CRC, necessitating improvements in screening, prognostication, disease management, and therapeutic options. Tumor metastasis is the primary factor related to the risk of recurrence and mortality. Yet, screening for nodal and distant metastasis is costly, and invasive and incomplete resection may hamper adequate assessment. Signatures of the tumor-immune microenvironment (TIME) at the primary site can provide valuable insights into the aggressiveness of the tumor and the effectiveness of various treatment options. Spatially-resolved transcriptomics technologies offer an unprecedented characterization of TIME through high multiplexing, yet their scope is constrained by cost. Meanwhile, it has long been suspected that histological, cytological and macroarchitectural tissue characteristics correlate well with molecular information (e.g., gene expression). Thus, a method for predicting transcriptomics data through inference of RNA patterns from whole slide images (WSI) is a key step in studying metastasis at scale. In this work, we collected and preprocessed Visium spatial transcriptomics data (17,943 genes at up to 5,000 spots per patient sampled in a honeycomb pattern) from tissue across four stage-III matched colorectal cancer patients. We compare and prototype several convolutional, Transformer, and graph convolutional neural networks to predict spatial RNA patterns under the hypothesis that the transformer and graph-based approaches better capture relevant spatial tissue architecture. We further analyzed the model's ability to recapitulate spatial autocorrelation statistics using SPARK and SpatialDE. Overall, results indicate that the transformer and graph-based approaches were unable to outperform the convolutional neural network architecture, though they exhibited optimal performance for relevant disease-associated genes. Initial findings suggest that different neural networks that operate on different scales are relevant for capturing distinct disease pathways (e.g., epithelial to mesenchymal transition). We add further evidence that deep learning models can accurately predict gene expression in whole slide images and comment on understudied factors which may increase its external applicability (e.g., tissue context). Our preliminary work will motivate further investigation of inference for molecular patterns from whole slide images as metastasis predictors and in other applications.Competing Interest StatementThe authors have declared no competing interest.