Qin Ren

Qin Ren, Yifan Wang, Ruogu Fang et al.

Survival prediction using whole slide images (WSIs) can be formulated as a multiple instance learning (MIL) problem. However, existing MIL methods often fail to explicitly capture pathological heterogeneity within WSIs, both globally -- through long-tailed morphological distributions, and locally through -- tile-level prediction uncertainty. Optimal transport (OT) provides a principled way of modeling such heterogeneity by incorporating marginal distribution constraints. Building on this insight, we propose OTSurv, a novel MIL framework from an optimal transport perspective. Specifically, OTSurv formulates survival predictions as a heterogeneity-aware OT problem with two constraints: (1) global long-tail constraint that models prior morphological distributions to avert both mode collapse and excessive uniformity by regulating transport mass allocation, and (2) local uncertainty-aware constraint that prioritizes high-confidence patches while suppressing noise by progressively raising the total transport mass. We then recast the initial OT problem, augmented by these constraints, into an unbalanced OT formulation that can be solved with an efficient, hardware-friendly matrix scaling algorithm. Empirically, OTSurv sets new state-of-the-art results across six popular benchmarks, achieving an absolute 3.6% improvement in average C-index. In addition, OTSurv achieves statistical significance in log-rank tests and offers high interpretability, making it a powerful tool for survival prediction in digital pathology. Our codes are available at https://github.com/Y-Research-SBU/OTSurv.

Wen Zhang, Qin Ren, Wenjing Liu et al.

Accurate nuclear instance segmentation is a pivotal task in computational pathology, supporting data-driven clinical insights and facilitating downstream translational applications. While large vision foundation models have shown promise for zero-shot biomedical segmentation, most existing approaches still depend on dense supervision and computationally expensive fine-tuning. Consequently, training-free methods present a compelling research direction, yet remain largely unexplored. In this work, we introduce SPROUT, a fully training- and annotation-free prompting framework for nuclear instance segmentation. SPROUT leverages histology-informed priors to construct slide-specific reference prototypes that mitigate domain gaps. These prototypes progressively guide feature alignment through a partial optimal transport scheme. The resulting foreground and background features are transformed into positive and negative point prompts, enabling the Segment Anything Model (SAM) to produce precise nuclear delineations without any parameter updates. Extensive experiments across multiple histopathology benchmarks demonstrate that SPROUT achieves competitive performance without supervision or retraining, establishing a novel paradigm for scalable, training-free nuclear instance segmentation in pathology.

Weihong Lin, Qifang Gao, Lei Sun et al.

Recent grid-based document representations like BERTgrid allow the simultaneous encoding of the textual and layout information of a document in a 2D feature map so that state-of-the-art image segmentation and/or object detection models can be straightforwardly leveraged to extract key information from documents. However, such methods have not achieved comparable performance to state-of-the-art sequence- and graph-based methods such as LayoutLM and PICK yet. In this paper, we propose a new multi-modal backbone network by concatenating a BERTgrid to an intermediate layer of a CNN model, where the input of CNN is a document image and the BERTgrid is a grid of word embeddings, to generate a more powerful grid-based document representation, named ViBERTgrid. Unlike BERTgrid, the parameters of BERT and CNN in our multimodal backbone network are trained jointly. Our experimental results demonstrate that this joint training strategy improves significantly the representation ability of ViBERTgrid. Consequently, our ViBERTgrid-based key information extraction approach has achieved state-of-the-art performance on real-world datasets.

Ramanpreet S Pahwa, Soon Wee Ho, Ren Qin et al.

For over 40 years lithographic silicon scaling has driven circuit integration and performance improvement in the semiconductor industry. As silicon scaling slows down, the industry is increasingly dependent on IC package technologies to contribute to further circuit integration and performance improvements. This is a paradigm shift and requires the IC package industry to reduce the size and increase the density of internal interconnects on a scale which has never been done before. Traditional package characterization and process optimization relies on destructive techniques such as physical cross-sections and delayering to extract data from internal package features. These destructive techniques are not practical with today's advanced packages. In this paper we will demonstrate how data acquired non-destructively with a 3D X-ray microscope can be enhanced and optimized using machine learning, and can then be used to measure, characterize and optimize the design and production of buried interconnects in advanced IC packages. Test vehicles replicating 2.5D and HBM construction were designed and fabricated, and digital data was extracted from these test vehicles using 3D X-ray and machine learning techniques. The extracted digital data was used to characterize and optimize the design and production of the interconnects and demonstrates a superior alternative to destructive physical analysis. We report an mAP of 0.96 for 3D object detection, a dice score of 0.92 for 3D segmentation, and an average of 2.1um error for 3D metrology on the test dataset. This paper is the first part of a multi-part report.