OpenRaiser/Intern-Atlas huggingface dataset:
Investigating ADR mechanisms with knowledge graph mining and explainable AI
Venue: arXiv cs.LG 2020
Year: 2020

Adverse Drug Reactions (ADRs) are characterized within randomized clinical trials and postmarketing pharmacovigilance, but their molecular mechanism remains unknown in most cases. Aside from clinical trials, many elements of knowledge about drug ingredients are available in open-access knowledge graphs. In addition, drug classifications that label drugs as either causative or not for several ADRs, have been established. We propose to mine knowledge graphs for identifying biomolecular features that may enable reproducing automatically expert classifications that distinguish drug causative or not for a given type of ADR. In an explainable AI perspective, we explore simple classification techniques such as Decision Trees and Classification Rules because they provide human-readable models, which explain the classification itself, but may also provide elements of explanation for molecular mechanisms behind ADRs. In summary, we mine a knowledge graph for features; we train classifiers at distinguishing, drugs associated or not with ADRs; we isolate features that are both efficient in reproducing expert classifications and interpretable by experts (i.e., Gene Ontology terms, drug targets, or pathway names); and we manually evaluate how they may be explanatory. Extracted features reproduce with a good fidelity classifications of drugs causative or not for DILI and SCAR. Experts fully agreed that 73% and 38% of the most discriminative features are possibly explanatory for DILI and SCAR, respectively; and partially agreed (2/3) for 90% and 77% of them. Knowledge graphs provide diverse features to enable simple and explainable models to distinguish between drugs that are causative or not for ADRs. In addition to explaining classifications, most discriminative features appear to be good candidates for investigating ADR mechanisms further.
Multi-agent navigation based on deep reinforcement learning and traditional pathfinding algorithm
Venue: arXiv cs.MA 2020
Year: 2020

We develop a new framework for multi-agent collision avoidance problem. The framework combined traditional pathfinding algorithm and reinforcement learning. In our approach, the agents learn whether to be navigated or to take simple actions to avoid their partners via a deep neural network trained by reinforcement learning at each time step. This framework makes it possible for agents to arrive terminal points in abstract new scenarios. In our experiments, we use Unity3D and Tensorflow to build the model and environment for our scenarios. We analyze the results and modify the parameters to approach a well-behaved strategy for our agents. Our strategy could be attached in different environments under different cases, especially when the scale is large.
Learning-NUM: Network Utility Maximization with Unknown Utility Functions and Queueing Delay
Venue: arXiv cs.NI 2020
Year: 2020

Network Utility Maximization (NUM) studies the problems of allocating traffic rates to network users in order to maximize the users' total utility subject to network resource constraints. In this paper, we propose a new NUM framework, Learning-NUM, where the users' utility functions are unknown apriori and the utility function values of the traffic rates can be observed only after the corresponding traffic is delivered to the destination, which means that the utility feedback experiences \textit{queueing delay}. The goal is to design a policy that gradually learns the utility functions and makes rate allocation and network scheduling/routing decisions so as to maximize the total utility obtained over a finite time horizon $T$. In addition to unknown utility functions and stochastic constraints, a central challenge of our problem lies in the queueing delay of the observations, which may be unbounded and depends on the decisions of the policy. We first show that the expected total utility obtained by the best dynamic policy is upper bounded by the solution to a static optimization problem. Without the presence of feedback delay, we design an algorithm based on the ideas of gradient estimation and Max-Weight scheduling. To handle the feedback delay, we embed the algorithm in a parallel-instance paradigm to form a policy that achieves $\tilde{O}(T^{3/4})$-regret, i.e., the difference between the expected utility obtained by the best dynamic policy and our policy is in $\tilde{O}(T^{3/4})$. Finally, to demonstrate the practical applicability of the Learning-NUM framework, we apply it to three application scenarios including database query, job scheduling and video streaming. We further conduct simulations on the job scheduling application to evaluate the empirical performance of our policy.
Self-Supervised Sketch-to-Image Synthesis
Venue: arXiv cs.CV 2020
Year: 2020

Imagining a colored realistic image from an arbitrarily drawn sketch is one of the human capabilities that we eager machines to mimic. Unlike previous methods that either requires the sketch-image pairs or utilize low-quantity detected edges as sketches, we study the exemplar-based sketch-to-image (s2i) synthesis task in a self-supervised learning manner, eliminating the necessity of the paired sketch data. To this end, we first propose an unsupervised method to efficiently synthesize line-sketches for general RGB-only datasets. With the synthetic paired-data, we then present a self-supervised Auto-Encoder (AE) to decouple the content/style features from sketches and RGB-images, and synthesize images that are both content-faithful to the sketches and style-consistent to the RGB-images. While prior works employ either the cycle-consistence loss or dedicated attentional modules to enforce the content/style fidelity, we show AE's superior performance with pure self-supervisions. To further improve the synthesis quality in high resolution, we also leverage an adversarial network to refine the details of synthetic images. Extensive experiments on 1024*1024 resolution demonstrate a new state-of-art-art performance of the proposed model on CelebA-HQ and Wiki-Art datasets. Moreover, with the proposed sketch generator, the model shows a promising performance on style mixing and style transfer, which require synthesized images to be both style-consistent and semantically meaningful. Our code is available on https://github.com/odegeasslbc/Self-Supervised-Sketch-to-Image-Synthesis-PyTorch, and please visit https://create.playform.io/my-projects?mode=sketch for an online demo of our model.
Extending the Range of Drone-based Delivery Services by Exploration
Venue: arXiv cs.RO 2020
Year: 2020

Drones have a fairly short range due to their limited battery life. We propose an adaptive exploration techniques to extend the range of drones by taking advantage of physical structures such as tall buildings and trees in urban environments. Our goal is to extend the coverage of a drone delivery service by generating paths for a drone to reach its destination while learning about the energy consumption on each edge on its path in order to optimize its range for future missions. We evaluated the performance of our exploration strategy in finding the set of all reachable destinations in a city, and found that exploring locations near the boundary of the reachable sets according to the current energy model can speed up the learning process.
Assessing COVID-19 Impacts on College Students via Automated Processing of Free-form Text
Venue: arXiv cs.CL 2020
Year: 2020

In this paper, we report experimental results on assessing the impact of COVID-19 on college students by processing free-form texts generated by them. By free-form texts, we mean textual entries posted by college students (enrolled in a four year US college) via an app specifically designed to assess and improve their mental health. Using a dataset comprising of more than 9000 textual entries from 1451 students collected over four months (split between pre and post COVID-19), and established NLP techniques, a) we assess how topics of most interest to student change between pre and post COVID-19, and b) we assess the sentiments that students exhibit in each topic between pre and post COVID-19. Our analysis reveals that topics like Education became noticeably less important to students post COVID-19, while Health became much more trending. We also found that across all topics, negative sentiment among students post COVID-19 was much higher compared to pre-COVID-19. We expect our study to have an impact on policy-makers in higher education across several spectra, including college administrators, teachers, parents, and mental health counselors.
Event Camera Calibration of Per-pixel Biased Contrast Threshold
Venue: arXiv cs.CV 2020
Year: 2020

Event cameras output asynchronous events to represent intensity changes with a high temporal resolution, even under extreme lighting conditions. Currently, most of the existing works use a single contrast threshold to estimate the intensity change of all pixels. However, complex circuit bias and manufacturing imperfections cause biased pixels and mismatch contrast threshold among pixels, which may lead to undesirable outputs. In this paper, we propose a new event camera model and two calibration approaches which cover event-only cameras and hybrid image-event cameras. When intensity images are simultaneously provided along with events, we also propose an efficient online method to calibrate event cameras that adapts to time-varying event rates. We demonstrate the advantages of our proposed methods compared to the state-of-the-art on several different event camera datasets.
A Contrast Synthesized Thalamic Nuclei Segmentation Scheme using Convolutional Neural Networks
Venue: arXiv cs.LG 2020
Year: 2020

Thalamic nuclei have been implicated in several neurological diseases. WMn-MPRAGE images have been shown to provide better intra-thalamic nuclear contrast compared to conventional MPRAGE images but the additional acquisition results in increased examination times. In this work, we investigated 3D Convolutional Neural Network (CNN) based techniques for thalamic nuclei parcellation from conventional MPRAGE images. Two 3D CNNs were developed and compared for thalamic nuclei parcellation using MPRAGE images: a) a native contrast segmentation (NCS) and b) a synthesized contrast segmentation (SCS) using WMn-MPRAGE images synthesized from MPRAGE images. We trained the two segmentation frameworks using MPRAGE images (n=35) and thalamic nuclei labels generated on WMn-MPRAGE images using a multi-atlas based parcellation technique. The segmentation accuracy and clinical utility were evaluated on a cohort comprising of healthy subjects and patients with alcohol use disorder (AUD) (n=45). The SCS network yielded higher Dice scores in the Medial geniculate nucleus (P=.003) and Centromedian nucleus (P=.01) with lower volume differences for Ventral anterior (P=.001) and Ventral posterior lateral (P=.01) nuclei when compared to the NCS network. A Bland-Altman analysis revealed tighter limits of agreement with lower coefficient of variation between true volumes and those predicted by the SCS network. The SCS network demonstrated a significant atrophy in Ventral lateral posterior nucleus in AUD patients compared to healthy age-matched controls (P=0.01), agreeing with previous studies on thalamic atrophy in alcoholism, whereas the NCS network showed spurious atrophy of the Ventral posterior lateral nucleus. CNN-based contrast synthesis prior to segmentation can provide fast and accurate thalamic nuclei segmentation from conventional MPRAGE images.
Characterizing the Evasion Attackability of Multi-label Classifiers
Venue: arXiv cs.LG 2020
Year: 2020

Evasion attack in multi-label learning systems is an interesting, widely witnessed, yet rarely explored research topic. Characterizing the crucial factors determining the attackability of the multi-label adversarial threat is the key to interpret the origin of the adversarial vulnerability and to understand how to mitigate it. Our study is inspired by the theory of adversarial risk bound. We associate the attackability of a targeted multi-label classifier with the regularity of the classifier and the training data distribution. Beyond the theoretical attackability analysis, we further propose an efficient empirical attackability estimator via greedy label space exploration. It provides provably computational efficiency and approximation accuracy. Substantial experimental results on real-world datasets validate the unveiled attackability factors and the effectiveness of the proposed empirical attackability indicator
Stabilizing Q Learning Via Soft Mellowmax Operator
Venue: arXiv cs.LG 2020
Year: 2020

Learning complicated value functions in high dimensional state space by function approximation is a challenging task, partially due to that the max-operator used in temporal difference updates can theoretically cause instability for most linear or non-linear approximation schemes. Mellowmax is a recently proposed differentiable and non-expansion softmax operator that allows a convergent behavior in learning and planning. Unfortunately, the performance bound for the fixed point it converges to remains unclear, and in practice, its parameter is sensitive to various domains and has to be tuned case by case. Finally, the Mellowmax operator may suffer from oversmoothing as it ignores the probability being taken for each action when aggregating them. In this paper, we address all the above issues with an enhanced Mellowmax operator, named SM2 (Soft Mellowmax). Particularly, the proposed operator is reliable, easy to implement, and has provable performance guarantee, while preserving all the advantages of Mellowmax. Furthermore, we show that our SM2 operator can be applied to the challenging multi-agent reinforcement learning scenarios, leading to stable value function approximation and state of the art performance.
The voice of COVID-19: Acoustic correlates of infection
Venue: arXiv cs.SD 2020
Year: 2020

COVID-19 is a global health crisis that has been affecting many aspects of our daily lives throughout the past year. The symptomatology of COVID-19 is heterogeneous with a severity continuum. A considerable proportion of symptoms are related to pathological changes in the vocal system, leading to the assumption that COVID-19 may also affect voice production. For the very first time, the present study aims to investigate voice acoustic correlates of an infection with COVID-19 on the basis of a comprehensive acoustic parameter set. We compare 88 acoustic features extracted from recordings of the vowels /i:/, /e:/, /o:/, /u:/, and /a:/ produced by 11 symptomatic COVID-19 positive and 11 COVID-19 negative German-speaking participants. We employ the Mann-Whitney U test and calculate effect sizes to identify features with the most prominent group differences. The mean voiced segment length and the number of voiced segments per second yield the most important differences across all vowels indicating discontinuities in the pulmonic airstream during phonation in COVID-19 positive participants. Group differences in the front vowels /i:/ and /e:/ are additionally reflected in the variation of the fundamental frequency and the harmonics-to-noise ratio, group differences in back vowels /o:/ and /u:/ in statistics of the Mel-frequency cepstral coefficients and the spectral slope. Findings of this study can be considered an important proof-of-concept contribution for a potential future voice-based identification of individuals infected with COVID-19.
CT Film Recovery via Disentangling Geometric Deformation and Illumination Variation: Simulated Datasets and Deep Models
Venue: arXiv cs.CV 2020
Year: 2020

While medical images such as computed tomography (CT) are stored in DICOM format in hospital PACS, it is still quite routine in many countries to print a film as a transferable medium for the purposes of self-storage and secondary consultation. Also, with the ubiquitousness of mobile phone cameras, it is quite common to take pictures of the CT films, which unfortunately suffer from geometric deformation and illumination variation. In this work, we study the problem of recovering a CT film, which marks the first attempt in the literature, to the best of our knowledge. We start with building a large-scale head CT film database CTFilm20K, consisting of approximately 20,000 pictures, using the widely used computer graphics software Blender. We also record all accompanying information related to the geometric deformation (such as 3D coordinate, depth, normal, and UV maps) and illumination variation (such as albedo map). Then we propose a deep framework to disentangle geometric deformation and illumination variation using the multiple maps extracted from the CT films to collaboratively guide the recovery process. Extensive experiments on simulated and real images demonstrate the superiority of our approach over the previous approaches. We plan to open source the simulated images and deep models for promoting the research on CT film recovery (https://anonymous.4open.science/r/e6b1f6e3-9b36-423f-a225-55b7d0b55523/).
Towards Grad-CAM Based Explainability in a Legal Text Processing Pipeline
Venue: arXiv cs.HC 2020
Year: 2020

Explainable AI(XAI)is a domain focused on providing interpretability and explainability of a decision-making process. In the domain of law, in addition to system and data transparency, it also requires the (legal-) decision-model transparency and the ability to understand the models inner working when arriving at the decision. This paper provides the first approaches to using a popular image processing technique, Grad-CAM, to showcase the explainability concept for legal texts. With the help of adapted Grad-CAM metrics, we show the interplay between the choice of embeddings, its consideration of contextual information, and their effect on downstream processing.
Predictive K-means with local models
Venue: arXiv cs.LG 2020
Year: 2020

Supervised classification can be effective for prediction but sometimes weak on interpretability or explainability (XAI). Clustering, on the other hand, tends to isolate categories or profiles that can be meaningful but there is no guarantee that they are useful for labels prediction. Predictive clustering seeks to obtain the best of the two worlds. Starting from labeled data, it looks for clusters that are as pure as possible with regards to the class labels. One technique consists in tweaking a clustering algorithm so that data points sharing the same label tend to aggregate together. With distance-based algorithms, such as k-means, a solution is to modify the distance used by the algorithm so that it incorporates information about the labels of the data points. In this paper, we propose another method which relies on a change of representation guided by class densities and then carries out clustering in this new representation space. We present two new algorithms using this technique and show on a variety of data sets that they are competitive for prediction performance with pure supervised classifiers while offering interpretability of the clusters discovered.
On the Importance of Diversity in Re-Sampling for Imbalanced Data and Rare Events in Mortality Risk Models
Venue: arXiv cs.LG 2020
Year: 2020

Surgical risk increases significantly when patients present with comorbid conditions. This has resulted in the creation of numerous risk stratification tools with the objective of formulating associated surgical risk to assist both surgeons and patients in decision-making. The Surgical Outcome Risk Tool (SORT) is one of the tools developed to predict mortality risk throughout the entire perioperative period for major elective in-patient surgeries in the UK. In this study, we enhance the original SORT prediction model (UK SORT) by addressing the class imbalance within the dataset. Our proposed method investigates the application of diversity-based selection on top of common re-sampling techniques to enhance the classifier's capability in detecting minority (mortality) events. Diversity amongst training datasets is an essential factor in ensuring re-sampled data keeps an accurate depiction of the minority/majority class region, thereby solving the generalization problem of mainstream sampling approaches. We incorporate the use of the Solow-Polasky measure as a drop-in functionality to evaluate diversity, with the addition of greedy algorithms to identify and discard subsets that share the most similarity. Additionally, through empirical experiments, we prove that the performance of the classifier trained over diversity-based dataset outperforms the original classifier over ten external datasets. Our diversity-based re-sampling method elevates the performance of the UK SORT algorithm by 1.4$.
A White Box Analysis of ColBERT
Venue: arXiv cs.IR 2020
Year: 2020

Transformer-based models are nowadays state-of-the-art in ad-hoc Information Retrieval, but their behavior is far from being understood. Recent work has claimed that BERT does not satisfy the classical IR axioms. However, we propose to dissect the matching process of ColBERT, through the analysis of term importance and exact/soft matching patterns. Even if the traditional axioms are not formally verified, our analysis reveals that ColBERT: (i) is able to capture a notion of term importance; (ii) relies on exact matches for important terms.
Firearm Detection via Convolutional Neural Networks: Comparing a Semantic Segmentation Model Against End-to-End Solutions
Venue: arXiv cs.CV 2020
Year: 2020

Threat detection of weapons and aggressive behavior from live video can be used for rapid detection and prevention of potentially deadly incidents such as terrorism, general criminal offences, or even domestic violence. One way for achieving this is through the use of artificial intelligence and, in particular, machine learning for image analysis. In this paper we conduct a comparison between a traditional monolithic end-to-end deep learning model and a previously proposed model based on an ensemble of simpler neural networks detecting fire-weapons via semantic segmentation. We evaluated both models from different points of view, including accuracy, computational and data complexity, flexibility and reliability. Our results show that a semantic segmentation model provides considerable amount of flexibility and resilience in the low data environment compared to classical deep model models, although its configuration and tuning presents a challenge in achieving the same levels of accuracy as an end-to-end model.
Trajectory Planning Under Stochastic and Bounded Sensing Uncertainties Using Reachability Analysis
Venue: arXiv cs.RO 2020
Year: 2020

Trajectory planning under uncertainty is an active research topic. Previous works predict state and state estimation uncertainties along trajectories to check for collision safety. They assume either stochastic or bounded sensing uncertainties. However, GNSS pseudoranges are typically modeled to contain stochastic uncertainties with additional biases in urban environments. Thus, given bounds for the bias, the planner needs to account for both stochastic and bounded sensing uncertainties. In our prior work we presented a reachability analysis to predict state and state estimation uncertainties under stochastic and bounded uncertainties. However, we ignored the correlation between these uncertainties, leading to an imperfect approximation of the state uncertainty. In this paper we improve our reachability analysis by predicting state uncertainty as a function of independent quantities. We design a metric for the predicted uncertainty to compare candidate trajectories during planning. Finally, we validate the planner for GNSS-based urban navigation of fixed-wing UAS.