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Digital pathological analysis is run as the main examination used for cancer diagnosis. Recently, deep learning-driven feature extraction from pathology images is able to detect genetic variations and tumor environment, but few studies focus on differential gene expression in tumor cells. In this paper, we propose a self-supervised contrastive learning framework, HistCode, to infer differential gene expressions from whole slide images (WSIs). We leveraged contrastive learning on large-scale unannotated WSIs to derive slide-level histopathological feature in latent space, and then transfer it to tumor diagnosis and prediction of differentially expressed cancer driver genes. Our extensive experiments showed that our method outperformed other state-of-the-art models in tumor diagnosis tasks, and also effectively predicted differential gene expressions. Interestingly, we found the higher fold-changed genes can be more precisely predicted. To intuitively illustrate the ability to extract informative features from pathological images, we spatially visualized the WSIs colored by the attentive scores of image tiles. We found that the tumor and necrosis areas were highly consistent with the annotations of experienced pathologists. Moreover, the spatial heatmap generated by lymphocyte-specific gene expression patterns was also consistent with the manually labeled WSI.

Neural ranking models (NRMs) have shown remarkable success in recent years, especially with pre-trained language models. However, deep neural models are notorious for their vulnerability to adversarial examples. Adversarial attacks may become a new type of web spamming technique given our increased reliance on neural information retrieval models. Therefore, it is important to study potential adversarial attacks to identify vulnerabilities of NRMs before they are deployed. In this paper, we introduce the Word Substitution Ranking Attack (WSRA) task against NRMs, which aims to promote a target document in rankings by adding adversarial perturbations to its text. We focus on the decision-based black-box attack setting, where the attackers cannot directly get access to the model information, but can only query the target model to obtain the rank positions of the partial retrieved list. This attack setting is realistic in real-world search engines. We propose a novel Pseudo Relevance-based ADversarial ranking Attack method (PRADA) that learns a surrogate model based on Pseudo Relevance Feedback (PRF) to generate gradients for finding the adversarial perturbations. Experiments on two web search benchmark datasets show that PRADA can outperform existing attack strategies and successfully fool the NRM with small indiscernible perturbations of text.

Even though electrowetting-on-dielectric (EWOD) is a useful strategy in a wide array of biological and engineering processes with numerous droplet-manipulation applications, there is still a lack of complete theoretical interpretation on the dynamics of electrowetting. In this paper, we present an effective theoretical model and use Onsager variational principle to successfully derive the governing equations of non-equilibrium electrowetting dynamics for a droplet in both overdamped and underdamped regimes. It is found that the spreading and retraction dynamics of a droplet on EWOD substrates can be fairly well captured in the overdamped regime. By varying liquid viscosity, droplet size, and applied voltage, we confirm that the transient dynamics of EW can be characterized by a timescale independent of liquid viscosity, droplet size and applied voltage. Our model provides a complete fundamental explanation of EW-driven spreading dynamics, which is important for a wide range of applications, from self-cleaning to novel optical and digital microfluidic devices.

The spontaneous muonium to antimuonium conversion is one of the interesting charged lepton flavor violation processes. It serves as a clear indication of new physics and plays an important role in constraining the parameter space beyond Standard Model. MACE is a proposed experiment to probe such a phenomenon and expected to enhance the sensitivity to the conversion probability by more than two orders of magnitude from the current best upper constraint obtained by the PSI experiment two decades ago. Recent developments in the theoretical and experimental aspects to search for such a rare process are summarized., Comment: 13 pages, 10 figures, 3 tables, contribution to Snowmass 2021

Mining aligned natural language (NL) and programming language (PL) pairs is a critical task to NL-PL understanding. Existing methods applied specialized hand-crafted features or separately-trained models for each PL. However, they usually suffered from low transferability across multiple PLs, especially for niche PLs with less annotated data. Fortunately, a Stack Overflow answer post is essentially a sequence of text and code blocks and its global textual context can provide PL-agnostic supplementary information. In this paper, we propose a Sequence Labeling based Question Answering (SLQA) method to mine NL-PL pairs in a PL-agnostic manner. In particular, we propose to apply the BIO tagging scheme instead of the conventional binary scheme to mine the code solutions which are often composed of multiple blocks of a post. Experiments on current single-PL single-block benchmarks and a manually-labeled cross-PL multi-block benchmark prove the effectiveness and transferability of SLQA. We further present a parallel NL-PL corpus named Lang2Code automatically mined with SLQA, which contains about 1.4M pairs on 6 PLs. Under statistical analysis and downstream evaluation, we demonstrate that Lang2Code is a large-scale high-quality data resource for further NL-PL research.

Weakly-Supervised Semantic Segmentation (WSSS) methods with image-level labels generally train a classification network to generate the Class Activation Maps (CAMs) as the initial coarse segmentation labels. However, current WSSS methods still perform far from satisfactorily because their adopted CAMs 1) typically focus on partial discriminative object regions and 2) usually contain useless background regions. These two problems are attributed to the sole image-level supervision and aggregation of global information when training the classification networks. In this work, we propose the visual words learning module and hybrid pooling approach, and incorporate them in the classification network to mitigate the above problems. In the visual words learning module, we counter the first problem by enforcing the classification network to learn fine-grained visual word labels so that more object extents could be discovered. Specifically, the visual words are learned with a codebook, which could be updated via two proposed strategies, i.e. learning-based strategy and memory-bank strategy. The second drawback of CAMs is alleviated with the proposed hybrid pooling, which incorporates the global average and local discriminative information to simultaneously ensure object completeness and reduce background regions. We evaluated our methods on PASCAL VOC 2012 and MS COCO 2014 datasets. Without any extra saliency prior, our method achieved 70.6% and 70.7% mIoU on the $val$ and $test$ set of PASCAL VOC dataset, respectively, and 36.2% mIoU on the $val$ set of MS COCO dataset, which significantly surpassed the performance of state-of-the-art WSSS methods., Comment: Accepted to IJCV

The recent measurement of the mass of neutron stars (PSR J1614 - 2230, PSR J0348 + 0432, MSP J0740 + 6620) restricts the lower limit $\sim 2M_{\odot}$ of the maximum mass of such compact stars, making it possible for dense matter to exist in massive stars. The relativistic mean field theory with parameter sets FSUGold including Kaon condensation is used to describe the properties of neutron stars in $\beta$ equilibrium. Through careful choice of the parameter of the $\sigma$-cut $c_{\sigma}$, we are able to produce a maximum mass neutron star with Kaon condensation heavier than $2M_{\odot}$, and we find that the parameter $\Lambda_{\nu}$ of the $\rho-\omega$ interaction term in this model has a significant effect on $K^{-}$ condensation. In the case of using $\sigma$-cut scheme, $K^{-}$ condensation occurs only when the $\rho-\omega$ interaction $\Lambda_{\nu}$ is switched off., Comment: 9 pages, 9 figures

Semantic code search is the task of retrieving relevant code snippet given a natural language query. Different from typical information retrieval tasks, code search requires to bridge the semantic gap between the programming language and natural language, for better describing intrinsic concepts and semantics. Recently, deep neural network for code search has been a hot research topic. Typical methods for neural code search first represent the code snippet and query text as separate embeddings, and then use vector distance (e.g. dot-product or cosine) to calculate the semantic similarity between them. There exist many different ways for aggregating the variable length of code or query tokens into a learnable embedding, including bi-encoder, cross-encoder, and poly-encoder. The goal of the query encoder and code encoder is to produce embeddings that are close with each other for a related pair of query and the corresponding desired code snippet, in which the choice and design of encoder is very significant. In this paper, we propose a novel deep semantic model which makes use of the utilities of not only the multi-modal sources, but also feature extractors such as self-attention, the aggregated vectors, combination of the intermediate representations. We apply the proposed model to tackle the CodeSearchNet challenge about semantic code search. We align cross-lingual embedding for multi-modality learning with large batches and hard example mining, and combine different learned representations for better enhancing the representation learning. Our model is trained on CodeSearchNet corpus and evaluated on the held-out data, the final model achieves 0.384 NDCG and won the first place in this benchmark. Models and code are available at https://github.com/overwindows/SemanticCodeSearch.git.

Accurate and fine-grained information about the extent of damage to buildings is essential for humanitarian relief and disaster response. However, as the most commonly used architecture in remote sensing interpretation tasks, Convolutional Neural Networks (CNNs) have limited ability to model the non-local relationship between pixels. Recently, Transformer architecture first proposed for modeling long-range dependency in natural language processing has shown promising results in computer vision tasks. Considering the frontier advances of Transformer architecture in the computer vision field, in this paper, we present the first attempt at designing a Transformer-based damage assessment architecture (DamFormer). In DamFormer, a siamese Transformer encoder is first constructed to extract non-local and representative deep features from input multitemporal image-pairs. Then, a multitemporal fusion module is designed to fuse information for downstream tasks. Finally, a lightweight dual-tasks decoder aggregates multi-level features for final prediction. To the best of our knowledge, it is the first time that such a deep Transformer-based network is proposed for multitemporal remote sensing interpretation tasks. The experimental results on the large-scale damage assessment dataset xBD demonstrate the potential of the Transformer-based architecture., Comment: IGARSS 2022

Federated Learning (FL) is designed to protect the data privacy of each client during the training process by transmitting only models instead of the original data. However, the trained model may memorize certain information about the training data. With the recent legislation on right to be forgotten, it is crucially essential for the FL model to possess the ability to forget what it has learned from each client. We propose a novel federated unlearning method to eliminate a client's contribution by subtracting the accumulated historical updates from the model and leveraging the knowledge distillation method to restore the model's performance without using any data from the clients. This method does not have any restrictions on the type of neural networks and does not rely on clients' participation, so it is practical and efficient in the FL system. We further introduce backdoor attacks in the training process to help evaluate the unlearning effect. Experiments on three canonical datasets demonstrate the effectiveness and efficiency of our method.

Deep learning for change detection is one of the current hot topics in the field of remote sensing. However, most end-to-end networks are proposed for supervised change detection, and unsupervised change detection models depend on traditional pre-detection methods. Therefore, we proposed a fully convolutional change detection framework with generative adversarial network, to conclude unsupervised, weakly supervised, regional supervised, and fully supervised change detection tasks into one framework. A basic Unet segmentor is used to obtain change detection map, an image-to-image generator is implemented to model the spectral and spatial variation between multi-temporal images, and a discriminator for changed and unchanged is proposed for modeling the semantic changes in weakly and regional supervised change detection task. The iterative optimization of segmentor and generator can build an end-to-end network for unsupervised change detection, the adversarial process between segmentor and discriminator can provide the solutions for weakly and regional supervised change detection, the segmentor itself can be trained for fully supervised task. The experiments indicate the effectiveness of the propsed framework in unsupervised, weakly supervised and regional supervised change detection. This paper provides theorical definitions for unsupervised, weakly supervised and regional supervised change detection tasks, and shows great potentials in exploring end-to-end network for remote sensing change detection., Comment: 13 pages, 19 figures

Structured knowledge grounding (SKG) leverages structured knowledge to complete user requests, such as semantic parsing over databases and question answering over knowledge bases. Since the inputs and outputs of SKG tasks are heterogeneous, they have been studied separately by different communities, which limits systematic and compatible research on SKG. In this paper, we overcome this limitation by proposing the UnifiedSKG framework, which unifies 21 SKG tasks into a text-to-text format, aiming to promote systematic SKG research, instead of being exclusive to a single task, domain, or dataset. We use UnifiedSKG to benchmark T5 with different sizes and show that T5, with simple modifications when necessary, achieves state-of-the-art performance on almost all of the 21 tasks. We further demonstrate that multi-task prefix-tuning improves the performance on most tasks, largely improving the overall performance. UnifiedSKG also facilitates the investigation of zero-shot and few-shot learning, and we show that T0, GPT-3, and Codex struggle in zero-shot and few-shot learning for SKG. We also use UnifiedSKG to conduct a series of controlled experiments on structured knowledge encoding variants across SKG tasks. UnifiedSKG is easily extensible to more tasks, and it is open-sourced at https://github.com/hkunlp/unifiedskg., Comment: EMNLP 2022