Anatomy-guided Pathology Segmentation

Pathological structures in medical images are typically deviations from the expected anatomy of a patient. While clinicians consider this interplay between anatomy and pathology, recent deep learning algorithms specialize in recognizing either one of the two, rarely considering the patient's body from such a joint perspective. In this paper, we develop a generalist segmentation model that combines anatomical and pathological information, aiming to enhance the segmentation accuracy of pathological features. Our Anatomy-Pathology Exchange (APEx) training utilizes a query-based segmentation transformer which decodes a joint feature space into query-representations for human anatomy and interleaves them via a mixing strategy into the pathology-decoder for anatomy-informed pathology predictions. In doing so, we are able to report the best results across the board on FDG-PET-CT and Chest X-Ray pathology segmentation tasks with a margin of up to 3.3% as compared to strong baseline methods. Code and models will be publicly available at github.com/alexanderjaus/APEx.

SciEx: Benchmarking Large Language Models on Scientific Exams with Human Expert Grading and Automatic Grading

With the rapid development of Large Language Models (LLMs), it is crucial to have benchmarks which can evaluate the ability of LLMs on different domains. One common use of LLMs is performing tasks on scientific topics, such as writing algorithms, querying databases or giving mathematical proofs. Inspired by the way university students are evaluated on such tasks, in this paper, we propose SciEx - a benchmark consisting of university computer science exam questions, to evaluate LLMs ability on solving scientific tasks. SciEx is (1) multilingual, containing both English and German exams, and (2) multi-modal, containing questions that involve images, and (3) contains various types of freeform questions with different difficulty levels, due to the nature of university exams. We evaluate the performance of various state-of-the-art LLMs on our new benchmark. Since SciEx questions are freeform, it is not straightforward to evaluate LLM performance. Therefore, we provide human expert grading of the LLM outputs on SciEx. We show that the free-form exams in SciEx remain challenging for the current LLMs, where the best LLM only achieves 59.4\% exam grade on average. We also provide detailed comparisons between LLM performance and student performance on SciEx. To enable future evaluation of new LLMs, we propose using LLM-as-a-judge to grade the LLM answers on SciEx. Our experiments show that, although they do not perform perfectly on solving the exams, LLMs are decent as graders, achieving 0.948 Pearson correlation with expert grading.

Accurate Fine-Grained Segmentation of Human Anatomy in Radiographs via Volumetric Pseudo-Labeling

Purpose: Interpreting chest radiographs (CXR) remains challenging due to the ambiguity of overlapping structures such as the lungs, heart, and bones. To address this issue, we propose a novel method for extracting fine-grained anatomical structures in CXR using pseudo-labeling of three-dimensional computed tomography (CT) scans. Methods: We created a large-scale dataset of 10,021 thoracic CTs with 157 labels and applied an ensemble of 3D anatomy segmentation models to extract anatomical pseudo-labels. These labels were projected onto a two-dimensional plane, similar to the CXR, allowing the training of detailed semantic segmentation models for CXR without any manual annotation effort. Results: Our resulting segmentation models demonstrated remarkable performance on CXR, with a high average model-annotator agreement between two radiologists with mIoU scores of 0.93 and 0.85 for frontal and lateral anatomy, while inter-annotator agreement remained at 0.95 and 0.83 mIoU. Our anatomical segmentations allowed for the accurate extraction of relevant explainable medical features such as the cardio-thoracic-ratio. Conclusion: Our method of volumetric pseudo-labeling paired with CT projection offers a promising approach for detailed anatomical segmentation of CXR with a high agreement with human annotators. This technique may have important clinical implications, particularly in the analysis of various thoracic pathologies.

360BEV: Panoramic Semantic Mapping for Indoor Bird's-Eye View

Seeing only a tiny part of the whole is not knowing the full circumstance. Bird's-eye-view (BEV) perception, a process of obtaining allocentric maps from egocentric views, is restricted when using a narrow Field of View (FoV) alone. In this work, mapping from 360{\deg} panoramas to BEV semantics, the 360BEV task, is established for the first time to achieve holistic representations of indoor scenes in a top-down view. Instead of relying on narrow-FoV image sequences, a panoramic image with depth information is sufficient to generate a holistic BEV semantic map. To benchmark 360BEV, we present two indoor datasets, 360BEV-Matterport and 360BEV-Stanford, both of which include egocentric panoramic images and semantic segmentation labels, as well as allocentric semantic maps. Besides delving deep into different mapping paradigms, we propose a dedicated solution for panoramic semantic mapping, namely 360Mapper. Through extensive experiments, our methods achieve 44.32% and 45.78% in mIoU on both datasets respectively, surpassing previous counterparts with gains of +7.60% and +9.70% in mIoU. Code and datasets will be available at: https://jamycheung.github.io/360BEV.html.

Mirror U-Net: Marrying Multimodal Fission with Multi-task Learning for Semantic Segmentation in Medical Imaging

Positron Emission Tomography (PET) and Computer Tomography (CT) are routinely used together to detect tumors. PET/CT segmentation models can automate tumor delineation, however, current multimodal models do not fully exploit the complementary information in each modality, as they either concatenate PET and CT data or fuse them at the decision level. To combat this, we propose Mirror U-Net, which replaces traditional fusion methods with multimodal fission by factorizing the multimodal representation into modality-specific branches and an auxiliary multimodal decoder. At these branches, Mirror U-Net assigns a task tailored to each modality to reinforce unimodal features while preserving multimodal features in the shared representation. In contrast to previous methods that use either fission or multi-task learning, Mirror U-Net combines both paradigms in a unified framework. We explore various task combinations and examine which parameters to share in the model. We evaluate Mirror U-Net on the AutoPET PET/CT and on the multimodal MSD BrainTumor datasets, demonstrating its effectiveness in multimodal segmentation and achieving state-of-the-art performance on both datasets. Our code will be made publicly available.

Delivering Arbitrary-Modal Semantic Segmentation

Multimodal fusion can make semantic segmentation more robust. However, fusing an arbitrary number of modalities remains underexplored. To delve into this problem, we create the DeLiVER arbitrary-modal segmentation benchmark, covering Depth, LiDAR, multiple Views, Events, and RGB. Aside from this, we provide this dataset in four severe weather conditions as well as five sensor failure cases to exploit modal complementarity and resolve partial outages. To make this possible, we present the arbitrary cross-modal segmentation model CMNeXt. It encompasses a Self-Query Hub (SQ-Hub) designed to extract effective information from any modality for subsequent fusion with the RGB representation and adds only negligible amounts of parameters (~0.01M) per additional modality. On top, to efficiently and flexibly harvest discriminative cues from the auxiliary modalities, we introduce the simple Parallel Pooling Mixer (PPX). With extensive experiments on a total of six benchmarks, our CMNeXt achieves state-of-the-art performance on the DeLiVER, KITTI-360, MFNet, NYU Depth V2, UrbanLF, and MCubeS datasets, allowing to scale from 1 to 81 modalities. On the freshly collected DeLiVER, the quad-modal CMNeXt reaches up to 66.30% in mIoU with a +9.10% gain as compared to the mono-modal baseline. The DeLiVER dataset and our code are at: https://jamycheung.github.io/DELIVER.html.

Detailed Annotations of Chest X-Rays via CT Projection for Report Understanding

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

Behind Every Domain There is a Shift: Adapting Distortion-aware Vision Transformers for Panoramic Semantic Segmentation

In this paper, we address panoramic semantic segmentation, which provides a full-view and dense-pixel understanding of surroundings in a holistic way. Panoramic segmentation is under-explored due to two critical challenges: (1) image distortions and object deformations on panoramas; (2) lack of annotations for training panoramic segmenters. To tackle these problems, we propose a Transformer for Panoramic Semantic Segmentation (Trans4PASS) architecture. First, to enhance distortion awareness, Trans4PASS, equipped with Deformable Patch Embedding (DPE) and Deformable MLP (DMLP) modules, is capable of handling object deformations and image distortions whenever (before or after adaptation) and wherever (shallow or deep levels) by design. We further introduce the upgraded Trans4PASS+ model, featuring DMLPv2 with parallel token mixing to improve the flexibility and generalizability in modeling discriminative cues. Second, we propose a Mutual Prototypical Adaptation (MPA) strategy for unsupervised domain adaptation. Third, aside from Pinhole-to-Panoramic (Pin2Pan) adaptation, we create a new dataset (SynPASS) with 9,080 panoramic images to explore a Synthetic-to-Real (Syn2Real) adaptation scheme in 360{\deg} imagery. Extensive experiments are conducted, which cover indoor and outdoor scenarios, and each of them is investigated with Pin2Pan and Syn2Real regimens. Trans4PASS+ achieves state-of-the-art performances on four domain adaptive panoramic semantic segmentation benchmarks. Code is available at https://github.com/jamycheung/Trans4PASS.

Breaking with Fixed Set Pathology Recognition through Report-Guided Contrastive Training

When reading images, radiologists generate text reports describing the findings therein. Current state-of-the-art computer-aided diagnosis tools utilize a fixed set of predefined categories automatically extracted from these medical reports for training. This form of supervision limits the potential usage of models as they are unable to pick up on anomalies outside of their predefined set, thus, making it a necessity to retrain the classifier with additional data when faced with novel classes. In contrast, we investigate direct text supervision to break away from this closed set assumption. By doing so, we avoid noisy label extraction via text classifiers and incorporate more contextual information. We employ a contrastive global-local dual-encoder architecture to learn concepts directly from unstructured medical reports while maintaining its ability to perform free form classification. We investigate relevant properties of open set recognition for radiological data and propose a method to employ currently weakly annotated data into training. We evaluate our approach on the large-scale chest X-Ray datasets MIMIC-CXR, CheXpert, and ChestX-Ray14 for disease classification. We show that despite using unstructured medical report supervision, we perform on par with direct label supervision through a sophisticated inference setting.

Bending Reality: Distortion-aware Transformers for Adapting to Panoramic Semantic Segmentation

Panoramic images with their 360-degree directional view encompass exhaustive information about the surrounding space, providing a rich foundation for scene understanding. To unfold this potential in the form of robust panoramic segmentation models, large quantities of expensive, pixel-wise annotations are crucial for success. Such annotations are available, but predominantly for narrow-angle, pinhole-camera images which, off the shelf, serve as sub-optimal resources for training panoramic models. Distortions and the distinct image-feature distribution in 360-degree panoramas impede the transfer from the annotation-rich pinhole domain and therefore come with a big dent in performance. To get around this domain difference and bring together semantic annotations from pinhole- and 360-degree surround-visuals, we propose to learn object deformations and panoramic image distortions in the Deformable Patch Embedding (DPE) and Deformable MLP (DMLP) components which blend into our Transformer for PAnoramic Semantic Segmentation (Trans4PASS) model. Finally, we tie together shared semantics in pinhole- and panoramic feature embeddings by generating multi-scale prototype features and aligning them in our Mutual Prototypical Adaptation (MPA) for unsupervised domain adaptation. On the indoor Stanford2D3D dataset, our Trans4PASS with MPA maintains comparable performance to fully-supervised state-of-the-arts, cutting the need for over 1,400 labeled panoramas. On the outdoor DensePASS dataset, we break state-of-the-art by 14.39% mIoU and set the new bar at 56.38%. Code will be made publicly available at https://github.com/jamycheung/Trans4PASS.