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Automatic surgical phase recognition is a challenging and crucial task with the potential to improve patient safety and become an integral part of intra-operative decision-support systems. In this paper, we propose, for the first time in workflow analysis, a Multi-Stage Temporal Convolutional Network (MS-TCN) that performs hierarchical prediction refinement for surgical phase recognition. Causal, dilated convolutions allow for a large receptive field and online inference with smooth predictions even during ambiguous transitions. Our method is thoroughly evaluated on two datasets of laparoscopic cholecystectomy videos with and without the use of additional surgical tool information. Outperforming various state-of-the-art LSTM approaches, we verify the suitability of the proposed causal MS-TCN for surgical phase recognition.
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Farm parcel delineation provides cadastral data that is important in developing and managing climate change policies. Specifically, farm parcel delineation informs applications in downstream governmental policies of land allocation, irrigation, fertilization, green-house gases (GHGs), etc. This data can also be useful for the agricultural insurance sector for assessing compensations following damages associated with extreme weather events - a growing trend related to climate change. Using satellite imaging can be a scalable and cost effective manner to perform the task of farm parcel delineation to collect this valuable data. In this paper, we break down this task using satellite imaging into two approaches: 1) Segmentation of parcel boundaries, and 2) Segmentation of parcel areas. We implemented variations of UNets, one of which takes into account temporal information, which achieved the best results on our dataset on farmland parcels in France in 2017.
A cascaded multi-planar scheme with a modified residual U-Net architecture was used to segment thalamic nuclei on conventional and white-matter-nulled (WMn) magnetization prepared rapid gradient echo (MPRAGE) data. A single network was optimized to work with images from healthy controls and patients with multiple sclerosis (MS) and essential tremor (ET), acquired at both 3T and 7T field strengths. Dice similarity coefficient and volume similarity index (VSI) were used to evaluate performance. Clinical utility was demonstrated by applying this method to study the effect of MS on thalamic nuclei atrophy. Segmentation of each thalamus into twelve nuclei was achieved in under a minute. For 7T WMn-MPRAGE, the proposed method outperforms current state-of-the-art on patients with ET with statistically significant improvements in Dice for five nuclei (increase in the range of 0.05-0.18) and VSI for four nuclei (increase in the range of 0.05-0.19), while performing comparably for healthy and MS subjects. Dice and VSI achieved using 7T WMn-MPRAGE data are comparable to those using 3T WMn-MPRAGE data. For conventional MPRAGE, the proposed method shows a statistically significant Dice improvement in the range of 0.14-0.63 over FreeSurfer for all nuclei and disease types. Effect of noise on network performance shows robustness to images with SNR as low as half the baseline SNR. Atrophy of four thalamic nuclei and whole thalamus was observed for MS patients compared to healthy control subjects, after controlling for the effect of parallel imaging, intracranial volume, gender, and age (p<0.004). The proposed segmentation method is fast, accurate, performs well across disease types and field strengths, and shows great potential for improving our understanding of thalamic nuclei involvement in neurological diseases.
Multi-stage learning is an effective technique to invoke multiple deep-learning modules sequentially. This paper applies multi-stage learning to speech enhancement by using a multi-stage structure, where each stage comprises a self-attention (SA) block followed by stacks of temporal convolutional network (TCN) blocks with doubling dilation factors. Each stage generates a prediction that is refined in a subsequent stage. A fusion block is inserted at the input of later stages to re-inject original information. The resulting multi-stage speech enhancement system, in short, multi-stage SA-TCN, is compared with state-of-the-art deep-learning speech enhancement methods using the LibriSpeech and VCTK data sets. The multi-stage SA-TCN systems hyper-parameters are fine-tuned, and the impact of the SA block, the fusion block and the number of stages are determined. The use of a multi-stage SA-TCN system as a front-end for automatic speech recognition systems is investigated as well. It is shown that the multi-stage SA-TCN systems perform well relative to other state-of-the-art systems in terms of speech enhancement and speech recognition scores.
Surgical phase recognition is of particular interest to computer assisted surgery systems, in which the goal is to predict what phase is occurring at each frame for a surgery video. Networks with multi-stage architecture have been widely applied in many computer vision tasks with rich patterns, where a predictor stage first outputs initial predictions and an additional refinement stage operates on the initial predictions to perform further refinement. Existing works show that surgical video contents are well ordered and contain rich temporal patterns, making the multi-stage architecture well suited for the surgical phase recognition task. However, we observe that when simply applying the multi-stage architecture to the surgical phase recognition task, the end-to-end training manner will make the refinement ability fall short of its wishes. To address the problem, we propose a new non end-to-end training strategy and explore different designs of multi-stage architecture for surgical phase recognition task. For the non end-to-end training strategy, the refinement stage is trained separately with proposed two types of disturbed sequences. Meanwhile, we evaluate three different choices of refinement models to show that our analysis and solution are robust to the choices of specific multi-stage models. We conduct experiments on two public benchmarks, the M2CAI16 Workflow Challenge, and the Cholec80 dataset. Results show that multi-stage architecture trained with our strategy largely boosts the performance of the current state-of-the-art single-stage model. Code is available at url{https://github.com/ChinaYi/casual_tcn}.
We propose HookNet, a semantic segmentation model for histopathology whole-slide images, which combines context and details via multiple branches of encoder-decoder convolutional neural networks. Concentricpatches at multiple resolutions with different fields of view are used to feed different branches of HookNet, and intermediate representations are combined via a hooking mechanism. We describe a framework to design and train HookNet for achieving high-resolution semantic segmentation and introduce constraints to guarantee pixel-wise alignment in feature maps during hooking. We show the advantages of using HookNet in two histopathology image segmentation tasks where tissue type prediction accuracy strongly depends on contextual information, namely (1) multi-class tissue segmentation in breast cancer and, (2) segmentation of tertiary lymphoid structures and germinal centers in lung cancer. Weshow the superiority of HookNet when compared with single-resolution U-Net models working at different resolutions as well as with a recently published multi-resolution model for histopathology image segmentation
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