HVTSurv: Hierarchical Vision Transformer for Patient-Level Survival Prediction from Whole Slide Image

Survival prediction based on whole slide images (WSIs) is a challenging task for patient-level multiple instance learning (MIL). Due to the vast amount of data for a patient (one or multiple gigapixels WSIs) and the irregularly shaped property of WSI, it is difficult to fully explore spatial, contextual, and hierarchical interaction in the patient-level bag. Many studies adopt random sampling pre-processing strategy and WSI-level aggregation models, which inevitably lose critical prognostic information in the patient-level bag. In this work, we propose a hierarchical vision Transformer framework named HVTSurv, which can encode the local-level relative spatial information, strengthen WSI-level context-aware communication, and establish patient-level hierarchical interaction. Firstly, we design a feature pre-processing strategy, including feature rearrangement and random window masking. Then, we devise three layers to progressively obtain patient-level representation, including a local-level interaction layer adopting Manhattan distance, a WSI-level interaction layer employing spatial shuffle, and a patient-level interaction layer using attention pooling. Moreover, the design of hierarchical network helps the model become more computationally efficient. Finally, we validate HVTSurv with 3,104 patients and 3,752 WSIs across 6 cancer types from The Cancer Genome Atlas (TCGA). The average C-Index is 2.50-11.30% higher than all the prior weakly supervised methods over 6 TCGA datasets. Ablation study and attention visualization further verify the superiority of the proposed HVTSurv. Implementation is available at: https://github.com/szc19990412/HVTSurv.

Lightweight wood panel defect detection method incorporating attention mechanism and feature fusion network

In recent years, deep learning has made significant progress in wood panel defect detection. However, there are still challenges such as low detection , slow detection speed, and difficulties in deploying embedded devices on wood panel surfaces. To overcome these issues, we propose a lightweight wood panel defect detection method called YOLOv5-LW, which incorporates attention mechanisms and a feature fusion network.Firstly, to enhance the detection capability of acceptable defects, we introduce the Multi-scale Bi-directional Feature Pyramid Network (MBiFPN) as a feature fusion network. The MBiFPN reduces feature loss, enriches local and detailed features, and improves the model's detection capability for acceptable defects.Secondly, to achieve a lightweight design, we reconstruct the ShuffleNetv2 network model as the backbone network. This reconstruction reduces the number of parameters and computational requirements while maintaining performance. We also introduce the Stem Block and Spatial Pyramid Pooling Fast (SPPF) models to compensate for any accuracy loss resulting from the lightweight design, ensuring the model's detection capabilities remain intact while being computationally efficient.Thirdly, we enhance the backbone network by incorporating Efficient Channel Attention (ECA), which improves the network's focus on key information relevant to defect detection. By attending to essential features, the model becomes more proficient in accurately identifying and localizing defects.We validate the proposed method using a self-developed wood panel defect dataset.The experimental results demonstrate the effectiveness of the improved YOLOv5-LW method. Compared to the original model, our approach achieves a 92.8\% accuracy rate, reduces the number of parameters by 27.78\%, compresses computational volume by 41.25\%, improves detection inference speed by 10.16\%

PDS-MAR: a fine-grained Projection-Domain Segmentation-based Metal Artifact Reduction method for intraoperative CBCT images with guidewires

Since the invention of modern CT systems, metal artifacts have been a persistent problem. Due to increased scattering, amplified noise, and insufficient data collection, it is more difficult to suppress metal artifacts in cone-beam CT, limiting its use in human- and robot-assisted spine surgeries where metallic guidewires and screws are commonly used. In this paper, we demonstrate that conventional image-domain segmentation-based MAR methods are unable to eliminate metal artifacts for intraoperative CBCT images with guidewires. To solve this problem, we present a fine-grained projection-domain segmentation-based MAR method termed PDS-MAR, in which metal traces are augmented and segmented in the projection domain before being inpainted using triangular interpolation. In addition, a metal reconstruction phase is proposed to restore metal areas in the image domain. The digital phantom study and real CBCT data study demonstrate that the proposed algorithm achieves significantly better artifact suppression than other comparing methods and has the potential to advance the use of intraoperative CBCT imaging in clinical spine surgeries.

Meerkat Behaviour Recognition Dataset

Recording animal behaviour is an important step in evaluating the well-being of animals and further understanding the natural world. Current methods for documenting animal behaviour within a zoo setting, such as scan sampling, require excessive human effort, are unfit for around-the-clock monitoring, and may produce human-biased results. Several animal datasets already exist that focus predominantly on wildlife interactions, with some extending to action or behaviour recognition. However, there is limited data in a zoo setting or data focusing on the group behaviours of social animals. We introduce a large meerkat (Suricata Suricatta) behaviour recognition video dataset with diverse annotated behaviours, including group social interactions, tracking of individuals within the camera view, skewed class distribution, and varying illumination conditions. This dataset includes videos from two positions within the meerkat enclosure at the Wellington Zoo (Wellington, New Zealand), with 848,400 annotated frames across 20 videos and 15 unannotated videos.

JCCS-PFGM: A Novel Circle-Supervision based Poisson Flow Generative Model for Multiphase CECT Progressive Low-Dose Reconstruction with Joint Condition

Multiphase contrast-enhanced computed tomography (CECT) scan is clinically significant to demonstrate the anatomy at different phases. In practice, such a multiphase CECT scan inherently takes longer time and deposits much more radiation dose into a patient body than a regular CT scan, and reduction of the radiation dose typically compromise the CECT image quality and its diagnostic value. With Joint Condition and Circle-Supervision, here we propose a novel Poisson Flow Generative Model (JCCS-PFGM) to promote the progressive low-dose reconstruction for multiphase CECT. JCCS-PFGM is characterized by the following three aspects: a progressive low-dose reconstruction scheme, a circle-supervision strategy, and a joint condition mechanism. Our extensive experiments are performed on a clinical dataset consisting of 11436 images. The results show that our JCCS-PFGM achieves promising PSNR up to 46.3dB, SSIM up to 98.5%, and MAE down to 9.67 HU averagely on phases I, II and III, in quantitative evaluations, as well as gains high-quality readable visualizations in qualitative assessments. All of these findings reveal our method a great potential to be adapted for clinical CECT scans at a much-reduced radiation dose.

Out-of-distribution forgetting: vulnerability of continual learning to intra-class distribution shift

Continual learning (CL) is an important technique to allow artificial neural networks to work in open environments. CL enables a system to learn new tasks without severe interference to its performance on old tasks, i.e., overcome the problems of catastrophic forgetting. In joint learning, it is well known that the out-of-distribution (OOD) problem caused by intentional attacks or environmental perturbations will severely impair the ability of networks to generalize. In this work, we reported a special form of catastrophic forgetting raised by the OOD problem in continual learning settings, and we named it out-of-distribution forgetting (OODF). In continual image classification tasks, we found that for a given category, introducing an intra-class distribution shift significantly impaired the recognition accuracy of CL methods for that category during subsequent learning. Interestingly, this phenomenon is special for CL as the same level of distribution shift had only negligible effects in the joint learning scenario. We verified that CL methods without dedicating subnetworks for individual tasks are all vulnerable to OODF. Moreover, OODF does not depend on any specific way of shifting the distribution, suggesting it is a risk for CL in a wide range of circumstances. Taken together, our work identified an under-attended risk during CL, highlighting the importance of developing approaches that can overcome OODF.

Channelized analog microwave short-time Fourier transform in the optical domain with improved measurement performance

In this article, analog microwave short-time Fourier transform (STFT) with improved measurement performance is implemented in the optical domain by employing stimulated Brillouin scattering (SBS) and channelization. By jointly using three optical frequency combs and filter- and SBS-based frequency-to-time mapping (FTTM), the time-frequency information of the signal under test (SUT) in different frequency intervals is measured in different channels. Then, by using the channel label introduced through subcarriers after photodetection, the obtained low-speed electrical pulses in different channels mixed in the time domain are distinguished and the time-frequency information of the SUT in different channels is respectively obtained and spliced to implement the STFT. For the first time, channelization measurement technology is introduced in the STFT system based on frequency sweeping and FTTM, greatly reducing the frequency-sweep range of the required frequency-sweep signal to the analysis bandwidth divided by the number of channels. In addition, channelization can also be used to improve the time and frequency resolution of the STFT system. A proof-of-concept experiment is performed. 12-GHz and 10-GHz analysis bandwidth is implemented by using a 4-GHz frequency-sweep signal and 3 channels and a 2-GHz frequency-sweep signal and 5 channels. Measurement performance improvement is also demonstrated.

Better Low-Resource Entity Recognition Through Translation and Annotation Fusion

Pre-trained multilingual language models have enabled significant advancements in cross-lingual transfer. However, these models often exhibit a performance disparity when transferring from high-resource languages to low-resource languages, especially for languages that are underrepresented or not in the pre-training data. Motivated by the superior performance of these models on high-resource languages compared to low-resource languages, we introduce a Translation-and-fusion framework, which translates low-resource language text into a high-resource language for annotation using fully supervised models before fusing the annotations back into the low-resource language. Based on this framework, we present TransFusion, a model trained to fuse predictions from a high-resource language to make robust predictions on low-resource languages. We evaluate our methods on two low-resource named entity recognition (NER) datasets, MasakhaNER2.0 and LORELEI NER, covering 25 languages, and show consistent improvement up to +16 F$_1$ over English fine-tuning systems, achieving state-of-the-art performance compared to Translate-train systems. Our analysis depicts the unique advantages of the TransFusion method which is robust to translation errors and source language prediction errors, and complimentary to adapted multilingual language models.

Contrastive Learning with Logic-driven Data Augmentation for Logical Reasoning over Text

Pre-trained large language model (LLM) is under exploration to perform NLP tasks that may require logical reasoning. Logic-driven data augmentation for representation learning has been shown to improve the performance of tasks requiring logical reasoning, but most of these data rely on designed templates and therefore lack generalization. In this regard, we propose an AMR-based logical equivalence-driven data augmentation method (AMR-LE) for generating logically equivalent data. Specifically, we first parse a text into the form of an AMR graph, next apply four logical equivalence laws (contraposition, double negation, commutative and implication laws) on the AMR graph to construct a logically equivalent/inequivalent AMR graph, and then convert it into a logically equivalent/inequivalent sentence. To help the model to better learn these logical equivalence laws, we propose a logical equivalence-driven contrastive learning training paradigm, which aims to distinguish the difference between logical equivalence and inequivalence. Our AMR-LE (Ensemble) achieves #2 on the ReClor leaderboard https://eval.ai/web/challenges/challenge-page/503/leaderboard/1347 . Our model shows better performance on seven downstream tasks, including ReClor, LogiQA, MNLI, MRPC, RTE, QNLI, and QQP. The source code and dataset are public at https://github.com/Strong-AI-Lab/Logical-Equivalence-driven-AMR-Data-Augmentation-for-Representation-Learning .

Neuromodulation Gated Transformer

We introduce a novel architecture, the Neuromodulation Gated Transformer (NGT), which is a simple implementation of neuromodulation in transformers via a multiplicative effect. We compare it to baselines and show that it results in the best average performance on the SuperGLUE benchmark validation sets.