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Sen Yang

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Neuro-Symbolic Integration Brings Causal and Reliable Reasoning Proofs

Nov 16, 2023
Sen Yang, Xin Li, Leyang Cui, Lidong Bing, Wai Lam

Though prompting LLMs with various reasoning structures produces reasoning proofs along with answers, these proofs are not ensured to be causal and reliable due to the inherent defects of LLMs. Tracking such deficiencies, we present a neuro-symbolic integration method, in which a neural LLM is used to represent the knowledge of the problem while an LLM-free symbolic solver is adopted to do deliberative reasoning using the knowledge. Specifically, our customized meta-interpreters allow the production of reasoning proofs and support flexible search strategies. These reasoning proofs are ensured to be causal and reliable because of the deterministic executing nature of the symbolic solvers. Empirically, on ProofWriter, our method surpasses the CoT baseline by nearly double in accuracy and more than triple in proof similarity. On GSM8K, our method also shows accuracy improvements and nearly doubled proof similarity. Our code is released at https://github.com/DAMO-NLP-SG/CaRing

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Once Upon a $\textit{Time}$ in $\textit{Graph}$: Relative-Time Pretraining for Complex Temporal Reasoning

Oct 23, 2023
Sen Yang, Xin Li, Lidong Bing, Wai Lam

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Our physical world is constantly evolving over time, rendering challenges for pre-trained language models to understand and reason over the temporal contexts of texts. Existing work focuses on strengthening the direct association between a piece of text and its time-stamp. However, the knowledge-time association is usually insufficient for the downstream tasks that require reasoning over temporal dependencies between knowledge. In this work, we make use of the underlying nature of time, all temporally-scoped sentences are strung together through a one-dimensional time axis, and suggest creating a graph structure based on the relative placements of events along the time axis. Inspired by the graph view, we propose RemeMo ($\underline{Re}$lative Ti$\underline{me}$ $\underline{Mo}$deling), which explicitly connects all temporally-scoped facts by modeling the time relations between any two sentences. Experimental results show that RemeMo outperforms the baseline T5 on multiple temporal question answering datasets under various settings. Further analysis suggests that RemeMo is especially good at modeling long-range complex temporal dependencies. We release our code and pre-trained checkpoints at $\href{https://github.com/DAMO-NLP-SG/RemeMo}{\text{this url}}$.

* EMNLP 2023 main 
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Domain generalization across tumor types, laboratories, and species -- insights from the 2022 edition of the Mitosis Domain Generalization Challenge

Sep 27, 2023
Marc Aubreville, Nikolas Stathonikos, Taryn A. Donovan, Robert Klopfleisch, Jonathan Ganz, Jonas Ammeling, Frauke Wilm, Mitko Veta, Samir Jabari, Markus Eckstein, Jonas Annuscheit, Christian Krumnow, Engin Bozaba, Sercan Cayir, Hongyan Gu, Xiang 'Anthony' Chen, Mostafa Jahanifar, Adam Shephard, Satoshi Kondo, Satoshi Kasai, Sujatha Kotte, VG Saipradeep, Maxime W. Lafarge, Viktor H. Koelzer, Ziyue Wang, Yongbing Zhang, Sen Yang, Xiyue Wang, Katharina Breininger, Christof A. Bertram

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Recognition of mitotic figures in histologic tumor specimens is highly relevant to patient outcome assessment. This task is challenging for algorithms and human experts alike, with deterioration of algorithmic performance under shifts in image representations. Considerable covariate shifts occur when assessment is performed on different tumor types, images are acquired using different digitization devices, or specimens are produced in different laboratories. This observation motivated the inception of the 2022 challenge on MItosis Domain Generalization (MIDOG 2022). The challenge provided annotated histologic tumor images from six different domains and evaluated the algorithmic approaches for mitotic figure detection provided by nine challenge participants on ten independent domains. Ground truth for mitotic figure detection was established in two ways: a three-expert consensus and an independent, immunohistochemistry-assisted set of labels. This work represents an overview of the challenge tasks, the algorithmic strategies employed by the participants, and potential factors contributing to their success. With an $F_1$ score of 0.764 for the top-performing team, we summarize that domain generalization across various tumor domains is possible with today's deep learning-based recognition pipelines. When assessed against the immunohistochemistry-assisted reference standard, all methods resulted in reduced recall scores, but with only minor changes in the order of participants in the ranking.

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ADNet: Lane Shape Prediction via Anchor Decomposition

Aug 21, 2023
Lingyu Xiao, Xiang Li, Sen Yang, Wankou Yang

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In this paper, we revisit the limitations of anchor-based lane detection methods, which have predominantly focused on fixed anchors that stem from the edges of the image, disregarding their versatility and quality. To overcome the inflexibility of anchors, we decompose them into learning the heat map of starting points and their associated directions. This decomposition removes the limitations on the starting point of anchors, making our algorithm adaptable to different lane types in various datasets. To enhance the quality of anchors, we introduce the Large Kernel Attention (LKA) for Feature Pyramid Network (FPN). This significantly increases the receptive field, which is crucial in capturing the sufficient context as lane lines typically run throughout the entire image. We have named our proposed system the Anchor Decomposition Network (ADNet). Additionally, we propose the General Lane IoU (GLIoU) loss, which significantly improves the performance of ADNet in complex scenarios. Experimental results on three widely used lane detection benchmarks, VIL-100, CULane, and TuSimple, demonstrate that our approach outperforms the state-of-the-art methods on VIL-100 and exhibits competitive accuracy on CULane and TuSimple. Code and models will be released on https://github.com/ Sephirex-X/ADNet.

* ICCV2023 accepted 
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SNR-based beaconless multi-scan link acquisition model with vibration for LEO-to-ground laser communication

Aug 06, 2023
Sen Yang, Xiaofeng Li

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We propose a link acquisition time model deeply involving the process from the transmitted power to received signal-to-noise ratio (SNR) for LEO-to-ground laser communication for the first time. Compared with the conventional acquisition models founded on geometry analysis with divergence angle threshold, utilizing SNR as the decision criterion is more appropriate for practical engineering requirements. Specially, under the combined effects of platform vibration and turbulence, we decouple the parameters of beam divergence angle, spiral pitch, and coverage factor at a fixed transmitted power for a given average received SNR threshold. Then the single-scan acquisition probability is obtained by integrating the field of uncertainty (FOU), probability distribution of coverage factor, and receiver field angle. Consequently, the closed-form analytical expression of acquisition time expectation adopting multi-scan, which ensures acquisition success, with essential reset time between single-scan is derived. The optimizations concerning the beam divergence angle, spiral pitch, and FOU are presented. Moreover, the influence of platform vibration is investigated. All the analytical derivations are confirmed by Monte Carlo simulations. Notably, we provide a theoretical method for designing the minimum divergence angle modulated by the laser, which not only improves the acquisition performance within a certain vibration range, but also achieves a good trade-off with the system complexity.

* 15 pages, 7 figures 
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Enhancing Grammatical Error Correction Systems with Explanations

May 25, 2023
Yuejiao Fei, Leyang Cui, Sen Yang, Wai Lam, Zhenzhong Lan, Shuming Shi

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Grammatical error correction systems improve written communication by detecting and correcting language mistakes. To help language learners better understand why the GEC system makes a certain correction, the causes of errors (evidence words) and the corresponding error types are two key factors. To enhance GEC systems with explanations, we introduce EXPECT, a large dataset annotated with evidence words and grammatical error types. We propose several baselines and anlysis to understand this task. Furthermore, human evaluation verifies our explainable GEC system's explanations can assist second-language learners in determining whether to accept a correction suggestion and in understanding the associated grammar rule.

* 9 pages, 7 figures, accepted to the main conference of ACL 2023 
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MedGPTEval: A Dataset and Benchmark to Evaluate Responses of Large Language Models in Medicine

May 12, 2023
Jie Xu, Lu Lu, Sen Yang, Bilin Liang, Xinwei Peng, Jiali Pang, Jinru Ding, Xiaoming Shi, Lingrui Yang, Huan Song, Kang Li, Xin Sun, Shaoting Zhang

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METHODS: First, a set of evaluation criteria is designed based on a comprehensive literature review. Second, existing candidate criteria are optimized for using a Delphi method by five experts in medicine and engineering. Third, three clinical experts design a set of medical datasets to interact with LLMs. Finally, benchmarking experiments are conducted on the datasets. The responses generated by chatbots based on LLMs are recorded for blind evaluations by five licensed medical experts. RESULTS: The obtained evaluation criteria cover medical professional capabilities, social comprehensive capabilities, contextual capabilities, and computational robustness, with sixteen detailed indicators. The medical datasets include twenty-seven medical dialogues and seven case reports in Chinese. Three chatbots are evaluated, ChatGPT by OpenAI, ERNIE Bot by Baidu Inc., and Doctor PuJiang (Dr. PJ) by Shanghai Artificial Intelligence Laboratory. Experimental results show that Dr. PJ outperforms ChatGPT and ERNIE Bot in both multiple-turn medical dialogue and case report scenarios.

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Why is the winner the best?

Mar 30, 2023
Matthias Eisenmann, Annika Reinke, Vivienn Weru, Minu Dietlinde Tizabi, Fabian Isensee, Tim J. Adler, Sharib Ali, Vincent Andrearczyk, Marc Aubreville, Ujjwal Baid, Spyridon Bakas, Niranjan Balu, Sophia Bano, Jorge Bernal, Sebastian Bodenstedt, Alessandro Casella, Veronika Cheplygina, Marie Daum, Marleen de Bruijne, Adrien Depeursinge, Reuben Dorent, Jan Egger, David G. Ellis, Sandy Engelhardt, Melanie Ganz, Noha Ghatwary, Gabriel Girard, Patrick Godau, Anubha Gupta, Lasse Hansen, Kanako Harada, Mattias Heinrich, Nicholas Heller, Alessa Hering, Arnaud Huaulmé, Pierre Jannin, Ali Emre Kavur, Oldřich Kodym, Michal Kozubek, Jianning Li, Hongwei Li, Jun Ma, Carlos Martín-Isla, Bjoern Menze, Alison Noble, Valentin Oreiller, Nicolas Padoy, Sarthak Pati, Kelly Payette, Tim Rädsch, Jonathan Rafael-Patiño, Vivek Singh Bawa, Stefanie Speidel, Carole H. Sudre, Kimberlin van Wijnen, Martin Wagner, Donglai Wei, Amine Yamlahi, Moi Hoon Yap, Chun Yuan, Maximilian Zenk, Aneeq Zia, David Zimmerer, Dogu Baran Aydogan, Binod Bhattarai, Louise Bloch, Raphael Brüngel, Jihoon Cho, Chanyeol Choi, Qi Dou, Ivan Ezhov, Christoph M. Friedrich, Clifton Fuller, Rebati Raman Gaire, Adrian Galdran, Álvaro García Faura, Maria Grammatikopoulou, SeulGi Hong, Mostafa Jahanifar, Ikbeom Jang, Abdolrahim Kadkhodamohammadi, Inha Kang, Florian Kofler, Satoshi Kondo, Hugo Kuijf, Mingxing Li, Minh Huan Luu, Tomaž Martinčič, Pedro Morais, Mohamed A. Naser, Bruno Oliveira, David Owen, Subeen Pang, Jinah Park, Sung-Hong Park, Szymon Płotka, Elodie Puybareau, Nasir Rajpoot, Kanghyun Ryu, Numan Saeed, Adam Shephard, Pengcheng Shi, Dejan Štepec, Ronast Subedi, Guillaume Tochon, Helena R. Torres, Helene Urien, João L. Vilaça, Kareem Abdul Wahid, Haojie Wang, Jiacheng Wang, Liansheng Wang, Xiyue Wang, Benedikt Wiestler, Marek Wodzinski, Fangfang Xia, Juanying Xie, Zhiwei Xiong, Sen Yang, Yanwu Yang, Zixuan Zhao, Klaus Maier-Hein, Paul F. Jäger, Annette Kopp-Schneider, Lena Maier-Hein

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International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi-center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

* accepted to CVPR 2023 
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CoNIC Challenge: Pushing the Frontiers of Nuclear Detection, Segmentation, Classification and Counting

Mar 14, 2023
Simon Graham, Quoc Dang Vu, Mostafa Jahanifar, Martin Weigert, Uwe Schmidt, Wenhua Zhang, Jun Zhang, Sen Yang, Jinxi Xiang, Xiyue Wang, Josef Lorenz Rumberger, Elias Baumann, Peter Hirsch, Lihao Liu, Chenyang Hong, Angelica I. Aviles-Rivero, Ayushi Jain, Heeyoung Ahn, Yiyu Hong, Hussam Azzuni, Min Xu, Mohammad Yaqub, Marie-Claire Blache, Benoît Piégu, Bertrand Vernay, Tim Scherr, Moritz Böhland, Katharina Löffler, Jiachen Li, Weiqin Ying, Chixin Wang, Dagmar Kainmueller, Carola-Bibiane Schönlieb, Shuolin Liu, Dhairya Talsania, Yughender Meda, Prakash Mishra, Muhammad Ridzuan, Oliver Neumann, Marcel P. Schilling, Markus Reischl, Ralf Mikut, Banban Huang, Hsiang-Chin Chien, Ching-Ping Wang, Chia-Yen Lee, Hong-Kun Lin, Zaiyi Liu, Xipeng Pan, Chu Han, Jijun Cheng, Muhammad Dawood, Srijay Deshpande, Raja Muhammad Saad Bashir, Adam Shephard, Pedro Costa, João D. Nunes, Aurélio Campilho, Jaime S. Cardoso, Hrishikesh P S, Densen Puthussery, Devika R G, Jiji C V, Ye Zhang, Zijie Fang, Zhifan Lin, Yongbing Zhang, Chunhui Lin, Liukun Zhang, Lijian Mao, Min Wu, Vi Thi-Tuong Vo, Soo-Hyung Kim, Taebum Lee, Satoshi Kondo, Satoshi Kasai, Pranay Dumbhare, Vedant Phuse, Yash Dubey, Ankush Jamthikar, Trinh Thi Le Vuong, Jin Tae Kwak, Dorsa Ziaei, Hyun Jung, Tianyi Miao, David Snead, Shan E Ahmed Raza, Fayyaz Minhas, Nasir M. Rajpoot

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Nuclear detection, segmentation and morphometric profiling are essential in helping us further understand the relationship between histology and patient outcome. To drive innovation in this area, we setup a community-wide challenge using the largest available dataset of its kind to assess nuclear segmentation and cellular composition. Our challenge, named CoNIC, stimulated the development of reproducible algorithms for cellular recognition with real-time result inspection on public leaderboards. We conducted an extensive post-challenge analysis based on the top-performing models using 1,658 whole-slide images of colon tissue. With around 700 million detected nuclei per model, associated features were used for dysplasia grading and survival analysis, where we demonstrated that the challenge's improvement over the previous state-of-the-art led to significant boosts in downstream performance. Our findings also suggest that eosinophils and neutrophils play an important role in the tumour microevironment. We release challenge models and WSI-level results to foster the development of further methods for biomarker discovery.

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Capturing the motion of every joint: 3D human pose and shape estimation with independent tokens

Mar 01, 2023
Sen Yang, Wen Heng, Gang Liu, Guozhong Luo, Wankou Yang, Gang Yu

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In this paper we present a novel method to estimate 3D human pose and shape from monocular videos. This task requires directly recovering pixel-alignment 3D human pose and body shape from monocular images or videos, which is challenging due to its inherent ambiguity. To improve precision, existing methods highly rely on the initialized mean pose and shape as prior estimates and parameter regression with an iterative error feedback manner. In addition, video-based approaches model the overall change over the image-level features to temporally enhance the single-frame feature, but fail to capture the rotational motion at the joint level, and cannot guarantee local temporal consistency. To address these issues, we propose a novel Transformer-based model with a design of independent tokens. First, we introduce three types of tokens independent of the image feature: \textit{joint rotation tokens, shape token, and camera token}. By progressively interacting with image features through Transformer layers, these tokens learn to encode the prior knowledge of human 3D joint rotations, body shape, and position information from large-scale data, and are updated to estimate SMPL parameters conditioned on a given image. Second, benefiting from the proposed token-based representation, we further use a temporal model to focus on capturing the rotational temporal information of each joint, which is empirically conducive to preventing large jitters in local parts. Despite being conceptually simple, the proposed method attains superior performances on the 3DPW and Human3.6M datasets. Using ResNet-50 and Transformer architectures, it obtains 42.0 mm error on the PA-MPJPE metric of the challenging 3DPW, outperforming state-of-the-art counterparts by a large margin. Code will be publicly available at https://github.com/yangsenius/INT_HMR_Model

* 17 pages, 12 figures. ICLR 2023 (spotlight) 
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