As the COVID-19 pandemic puts pressure on healthcare systems worldwide, the computed tomography image based AI diagnostic system has become a sustainable solution for early diagnosis. However, the model-wise vulnerability under adversarial perturbation hinders its deployment in practical situation. The existing adversarial training strategies are difficult to generalized into medical imaging field challenged by complex medical texture features. To overcome this challenge, we propose a Contour Attention Preserving (CAP) method based on lung cavity edge extraction. The contour prior features are injected to attention layer via a parameter regularization and we optimize the robust empirical risk with hybrid distance metric. We then introduce a new cross-nation CT scan dataset to evaluate the generalization capability of the adversarial robustness under distribution shift. Experimental results indicate that the proposed method achieves state-of-the-art performance in multiple adversarial defense and generalization tasks. The code and dataset are available at https://github.com/Quinn777/CAP.

We introduce the initial release of our software Robustar, which aims to improve the robustness of vision classification machine learning models through a data-driven perspective. Building upon the recent understanding that the lack of machine learning model's robustness is the tendency of the model's learning of spurious features, we aim to solve this problem from its root at the data perspective by removing the spurious features from the data before training. In particular, we introduce a software that helps the users to better prepare the data for training image classification models by allowing the users to annotate the spurious features at the pixel level of images. To facilitate this process, our software also leverages recent advances to help identify potential images and pixels worthy of attention and to continue the training with newly annotated data. Our software is hosted at the GitHub Repository https://github.com/HaohanWang/Robustar.

Neural machine translation has achieved remarkable empirical performance over standard benchmark datasets, yet recent evidence suggests that the models can still fail easily dealing with substandard inputs such as misspelled words, To overcome this issue, we introduce a new encoding heuristic of the input symbols for character-level NLP models: it encodes the shape of each character through the images depicting the letters when printed. We name this new strategy visual embedding and it is expected to improve the robustness of NLP models because humans also process the corpus visually through printed letters, instead of machinery one-hot vectors. Empirically, our method improves models' robustness against substandard inputs, even in the test scenario where the models are tested with the noises that are beyond what is available during the training phase.

Nature language inference (NLI) task is a predictive task of determining the inference relationship of a pair of natural language sentences. With the increasing popularity of NLI, many state-of-the-art predictive models have been proposed with impressive performances. However, several works have noticed the statistical irregularities in the collected NLI data set that may result in an over-estimated performance of these models and proposed remedies. In this paper, we further investigate the statistical irregularities, what we refer as confounding factors, of the NLI data sets. With the belief that some NLI labels should preserve under swapping operations, we propose a simple yet effective way (swapping the two text fragments) of evaluating the NLI predictive models that naturally mitigate the observed problems. Further, we continue to train the predictive models with our swapping manner and propose to use the deviation of the model's evaluation performances under different percentages of training text fragments to be swapped to describe the robustness of a predictive model. Our evaluation metrics leads to some interesting understandings of recent published NLI methods. Finally, we also apply the swapping operation on NLI models to see the effectiveness of this straightforward method in mitigating the confounding factor problems in training generic sentence embeddings for other NLP transfer tasks.

The rapid development of deep learning methods has permitted the fast and accurate medical decision making from complex structured data, like CT images or MRI. However, some problems still exist in such applications that may lead to imperfect predictions. Previous observations have shown that, confounding factors, if handled inappropriately, will lead to biased prediction results towards some major properties of the data distribution. In other words, naively applying deep learning methods in these applications will lead to unfair prediction results for the minority group defined by the characteristics including age, gender, or even the hospital that collects the data, etc. In this paper, extending previous successes in correcting confounders, we propose a more stable method, namely Confounder Filtering, that can effectively reduce the influence of confounding factors, leading to better generalizability of trained discriminative deep neural networks, therefore, fairer prediction results. Our experimental results indicate that the Confounder Filtering method is able to improve the performance for different neural networks including CNN, LSTM, and other arbitrary architecture, different data types including CT-scan, MRI, and EEG brain wave data, as well as different confounding factors including age, gender, and physical factors of medical devices etc

While linear mixed model (LMM) has shown a competitive performance in correcting spurious associations raised by population stratification, family structures, and cryptic relatedness, more challenges are still to be addressed regarding the complex structure of genotypic and phenotypic data. For example, geneticists have discovered that some clusters of phenotypes are more co-expressed than others. Hence, a joint analysis that can utilize such relatedness information in a heterogeneous data set is crucial for genetic modeling. We proposed the sparse graph-structured linear mixed model (sGLMM) that can incorporate the relatedness information from traits in a dataset with confounding correction. Our method is capable of uncovering the genetic associations of a large number of phenotypes together while considering the relatedness of these phenotypes. Through extensive simulation experiments, we show that the proposed model outperforms other existing approaches and can model correlation from both population structure and shared signals. Further, we validate the effectiveness of sGLMM in the real-world genomic dataset on two different species from plants and humans. In Arabidopsis thaliana data, sGLMM behaves better than all other baseline models for 63.4% traits. We also discuss the potential causal genetic variation of Human Alzheimer's disease discovered by our model and justify some of the most important genetic loci.

Protein-protein interaction (PPI) prediction is an important problem in machine learning and computational biology. However, there is no data set for training or evaluation purposes, where all the instances are accurately labeled. Instead, what is available are instances of positive class (with possibly noisy labels) and no instances of negative class. The non-availability of negative class data is typically handled with the observation that randomly chosen protein-pairs have a nearly 100% chance of being negative class, as only 1 in 1,500 protein pairs expected is expected to be an interacting pair. In this paper, we focused on the problem that non-availability of accurately labeled testing data sets in the domain of protein-protein interaction (PPI) prediction may lead to biased evaluation results. We first showed that not acknowledging the inherent skew in the interactome (i.e. rare occurrence of positive instances) leads to an over-estimated accuracy of the predictor. Then we show that, with the belief that positive interactions are a rare category, sampling random pairs of proteins excluding known interacting proteins set as the negative testing data set could lead to an under-estimated evaluation result. We formalized those two problems to validate the above claim, and based on the formalization, we proposed a balancing method to cancel out the over-estimation with under-estimation. Finally, our experiments validated the theoretical aspects and showed that this balancing evaluation could evaluate the exact performance without availability of golden standard data sets.

A major problem in road network analysis is discovery of important crossroads, which can provide useful information for transport planning. However, none of existing approaches addresses the problem of identifying network-wide important crossroads in real road network. In this paper, we propose a novel data-driven based approach named CRRank to rank important crossroads. Our key innovation is that we model the trip network reflecting real travel demands with a tripartite graph, instead of solely analysis on the topology of road network. To compute the importance scores of crossroads accurately, we propose a HITS-like ranking algorithm, in which a procedure of score propagation on our tripartite graph is performed. We conduct experiments on CRRank using a real-world dataset of taxi trajectories. Experiments verify the utility of CRRank.