pwc-archive/papers-with-abstracts huggingface dataset:
Improving the robustness and accuracy of biomedical language models through adversarial training
Authors: Milad Moradi, Matthias Samwald
Date: 2021-11-16 00:00:00
Tasks: Adversarial Attack

Deep transformer neural network models have improved the predictive accuracy of intelligent text processing systems in the biomedical domain. They have obtained state-of-the-art performance scores on a wide variety of biomedical and clinical Natural Language Processing (NLP) benchmarks. However, the robustness and reliability of these models has been less explored so far. Neural NLP models can be easily fooled by adversarial samples, i.e. minor changes to input that preserve the meaning and understandability of the text but force the NLP system to make erroneous decisions. This raises serious concerns about the security and trust-worthiness of biomedical NLP systems, especially when they are intended to be deployed in real-world use cases. We investigated the robustness of several transformer neural language models, i.e. BioBERT, SciBERT, BioMed-RoBERTa, and Bio-ClinicalBERT, on a wide range of biomedical and clinical text processing tasks. We implemented various adversarial attack methods to test the NLP systems in different attack scenarios. Experimental results showed that the biomedical NLP models are sensitive to adversarial samples; their performance dropped in average by 21 and 18.9 absolute percent on character-level and word-level adversarial noise, respectively. Conducting extensive adversarial training experiments, we fine-tuned the NLP models on a mixture of clean samples and adversarial inputs. Results showed that adversarial training is an effective defense mechanism against adversarial noise; the models robustness improved in average by 11.3 absolute percent. In addition, the models performance on clean data increased in average by 2.4 absolute present, demonstrating that adversarial training can boost generalization abilities of biomedical NLP systems.
CVSS-BERT: Explainable Natural Language Processing to Determine the Severity of a Computer Security Vulnerability from its Description
Authors: Mustafizur Shahid, Hervé Debar
Date: 2021-11-16 00:00:00
Tasks: Computer Security

When a new computer security vulnerability is publicly disclosed, only a textual description of it is available. Cybersecurity experts later provide an analysis of the severity of the vulnerability using the Common Vulnerability Scoring System (CVSS). Specifically, the different characteristics of the vulnerability are summarized into a vector (consisting of a set of metrics), from which a severity score is computed. However, because of the high number of vulnerabilities disclosed everyday this process requires lot of manpower, and several days may pass before a vulnerability is analyzed. We propose to leverage recent advances in the field of Natural Language Processing (NLP) to determine the CVSS vector and the associated severity score of a vulnerability from its textual description in an explainable manner. To this purpose, we trained multiple BERT classifiers, one for each metric composing the CVSS vector. Experimental results show that our trained classifiers are able to determine the value of the metrics of the CVSS vector with high accuracy. The severity score computed from the predicted CVSS vector is also very close to the real severity score attributed by a human expert. For explainability purpose, gradient-based input saliency method was used to determine the most relevant input words for a given prediction made by our classifiers. Often, the top relevant words include terms in agreement with the rationales of a human cybersecurity expert, making the explanation comprehensible for end-users.
Neural Class Expression Synthesis
Authors: N'Dah Jean Kouagou, Stefan Heindorf, Caglar Demir, Axel-Cyrille Ngonga Ngomo
Date: 2021-11-16 00:00:00
Tasks: Knowledge Graphs, Machine Translation, Node Classification, Translation

Many applications require explainable node classification in knowledge graphs. Towards this end, a popular ``white-box'' approach is class expression learning: Given sets of positive and negative nodes, class expressions in description logics are learned that separate positive from negative nodes. Most existing approaches are search-based approaches generating many candidate class expressions and selecting the best one. However, they often take a long time to find suitable class expressions. In this paper, we cast class expression learning as a translation problem and propose a new family of class expression learning approaches which we dub neural class expression synthesizers. Training examples are ``translated'' into class expressions in a fashion akin to machine translation. Consequently, our synthesizers are not subject to the runtime limitations of search-based approaches. We study three instances of this novel family of approaches based on LSTMs, GRUs, and set transformers, respectively. An evaluation of our approach on four benchmark datasets suggests that it can effectively synthesize high-quality class expressions with respect to the input examples in approximately one second on average. Moreover, a comparison to state-of-the-art approaches suggests that we achieve better F-measures on large datasets. For reproducibility purposes, we provide our implementation as well as pretrained models in our public GitHub repository at https://github.com/dice-group/NeuralClassExpressionSynthesis
Point detection through multi-instance deep heatmap regression for sutures in endoscopy
Authors: Lalith Sharan, Gabriele Romano, Julian Brand, Halvar Kelm, Matthias Karck, Raffaele De Simone, Sandy Engelhardt
Date: 2021-11-16 00:00:00
Tasks: Anatomical Landmark Detection, regression

Purpose: Mitral valve repair is a complex minimally invasive surgery of the heart valve. In this context, suture detection from endoscopic images is a highly relevant task that provides quantitative information to analyse suturing patterns, assess prosthetic configurations and produce augmented reality visualisations. Facial or anatomical landmark detection tasks typically contain a fixed number of landmarks, and use regression or fixed heatmap-based approaches to localize the landmarks. However in endoscopy, there are a varying number of sutures in every image, and the sutures may occur at any location in the annulus, as they are not semantically unique. Method: In this work, we formulate the suture detection task as a multi-instance deep heatmap regression problem, to identify entry and exit points of sutures. We extend our previous work, and introduce the novel use of a 2D Gaussian layer followed by a differentiable 2D spatial Soft-Argmax layer to function as a local non-maximum suppression. Results: We present extensive experiments with multiple heatmap distribution functions and two variants of the proposed model. In the intra-operative domain, Variant 1 showed a mean F1 of +0.0422 over the baseline. Similarly, in the simulator domain, Variant 1 showed a mean F1 of +0.0865 over the baseline. Conclusion: The proposed model shows an improvement over the baseline in the intra-operative and the simulator domains. The data is made publicly available within the scope of the MICCAI AdaptOR2021 Challenge https://adaptor2021.github.io/, and the code at https://github.com/Cardio-AI/suture-detection-pytorch/. DOI:10.1007/s11548-021-02523-w. The link to the open access article can be found here: https://link.springer.com/article/10.1007%2Fs11548-021-02523-w
Interpretable and Fair Boolean Rule Sets via Column Generation
Authors: Connor Lawless, Sanjeeb Dash, Oktay Gunluk, Dennis Wei
Date: 2021-11-16 00:00:00
Tasks: Classification, Fairness

This paper considers the learning of Boolean rules in disjunctive normal form (DNF, OR-of-ANDs, equivalent to decision rule sets) as an interpretable model for classification. An integer program is formulated to optimally trade classification accuracy for rule simplicity. We also consider the fairness setting and extend the formulation to include explicit constraints on two different measures of classification parity: equality of opportunity and equalized odds. Column generation (CG) is used to efficiently search over an exponential number of candidate rules without the need for heuristic rule mining. To handle large data sets, we propose an approximate CG algorithm using randomization. Compared to three recently proposed alternatives, the CG algorithm dominates the accuracy-simplicity trade-off in 8 out of 16 data sets. When maximized for accuracy, CG is competitive with rule learners designed for this purpose, sometimes finding significantly simpler solutions that are no less accurate. Compared to other fair and interpretable classifiers, our method is able to find rule sets that meet stricter notions of fairness with a modest trade-off in accuracy.
Causal policy ranking
Authors: Daniel McNamee, Hana Chockler
Date: 2021-11-16 00:00:00
Tasks: counterfactual, Counterfactual Reasoning, Reinforcement Learning (RL)

Policies trained via reinforcement learning (RL) are often very complex even for simple tasks. In an episode with $n$ time steps, a policy will make $n$ decisions on actions to take, many of which may appear non-intuitive to the observer. Moreover, it is not clear which of these decisions directly contribute towards achieving the reward and how significant is their contribution. Given a trained policy, we propose a black-box method based on counterfactual reasoning that estimates the causal effect that these decisions have on reward attainment and ranks the decisions according to this estimate. In this preliminary work, we compare our measure against an alternative, non-causal, ranking procedure, highlight the benefits of causality-based policy ranking, and discuss potential future work integrating causal algorithms into the interpretation of RL agent policies.
STAMP 4 NLP -- An Agile Framework for Rapid Quality-Driven NLP Applications Development
Authors: Philipp Kohl, Oliver Schmidts, Lars Klöser, Henri Werth, Bodo Kraft, Albert Zündorf
Date: 2021-11-16 00:00:00

The progress in natural language processing (NLP) research over the last years, offers novel business opportunities for companies, as automated user interaction or improved data analysis. Building sophisticated NLP applications requires dealing with modern machine learning (ML) technologies, which impedes enterprises from establishing successful NLP projects. Our experience in applied NLP research projects shows that the continuous integration of research prototypes in production-like environments with quality assurance builds trust in the software and shows convenience and usefulness regarding the business goal. We introduce STAMP 4 NLP as an iterative and incremental process model for developing NLP applications. With STAMP 4 NLP, we merge software engineering principles with best practices from data science. Instantiating our process model allows efficiently creating prototypes by utilizing templates, conventions, and implementations, enabling developers and data scientists to focus on the business goals. Due to our iterative-incremental approach, businesses can deploy an enhanced version of the prototype to their software environment after every iteration, maximizing potential business value and trust early and avoiding the cost of successful yet never deployed experiments.
Towards Generating Real-World Time Series Data
Authors: Hengzhi Pei, Kan Ren, Yuqing Yang, Chang Liu, Tao Qin, Dongsheng Li
Date: 2021-11-16 00:00:00
Tasks: Decoder, Generative Adversarial Network, Missing Values, Time Series, Time Series Analysis

Time series data generation has drawn increasing attention in recent years. Several generative adversarial network (GAN) based methods have been proposed to tackle the problem usually with the assumption that the targeted time series data are well-formatted and complete. However, real-world time series (RTS) data are far away from this utopia, e.g., long sequences with variable lengths and informative missing data raise intractable challenges for designing powerful generation algorithms. In this paper, we propose a novel generative framework for RTS data - RTSGAN to tackle the aforementioned challenges. RTSGAN first learns an encoder-decoder module which provides a mapping between a time series instance and a fixed-dimension latent vector and then learns a generation module to generate vectors in the same latent space. By combining the generator and the decoder, RTSGAN is able to generate RTS which respect the original feature distributions and the temporal dynamics. To generate time series with missing values, we further equip RTSGAN with an observation embedding layer and a decide-and-generate decoder to better utilize the informative missing patterns. Experiments on the four RTS datasets show that the proposed framework outperforms the previous generation methods in terms of synthetic data utility for downstream classification and prediction tasks.
Literature-Augmented Clinical Outcome Prediction
Authors: Aakanksha Naik, Sravanthi Parasa, Sergey Feldman, Lucy Lu Wang, Tom Hope
Date: 2021-11-16 00:00:00
Proceeding: Findings (NAACL) 2022 7
Tasks: Decision Making, Prediction

We present BEEP (Biomedical Evidence-Enhanced Predictions), a novel approach for clinical outcome prediction that retrieves patient-specific medical literature and incorporates it into predictive models. Based on each individual patient's clinical notes, we train language models (LMs) to find relevant papers and fuse them with information from notes to predict outcomes such as in-hospital mortality. We develop methods to retrieve literature based on noisy, information-dense patient notes, and to augment existing outcome prediction models with retrieved papers in a manner that maximizes predictive accuracy. Our approach boosts predictive performance on three important clinical tasks in comparison to strong recent LM baselines, increasing F1 by up to 5 points and precision@Top-K by a large margin of over 25%.
From Convolutions towards Spikes: The Environmental Metric that the Community currently Misses
Authors: Aviral Chharia, Shivu Chauhan, Rahul Upadhyay, Vinay Kumar
Date: 2021-11-16 00:00:00
Proceeding: NeurIPS Workshop AI4Scien 2021 12

Today, the AI community is obsessed with 'state-of-the-art' scores (80% papers in NeurIPS) as the major performance metrics, due to which an important parameter, i.e., the environmental metric, remains unreported. Computational capabilities were a limiting factor a decade ago; however, in foreseeable future circumstances, the challenge will be to develop environment-friendly and power-efficient algorithms. The human brain, which has been optimizing itself for almost a million years, consumes the same amount of power as a typical laptop. Therefore, developing nature-inspired algorithms is one solution to it. In this study, we show that currently used ANNs are not what we find in nature, and why, although having lower performance, spiking neural networks, which mirror the mammalian visual cortex, have attracted much interest. We further highlight the hardware gaps restricting the researchers from using spike-based computation for developing neuromorphic energy-efficient microchips on a large scale. Using neuromorphic processors instead of traditional GPUs might be more environment friendly and efficient. These processors will turn SNNs into an ideal solution for the problem. This paper presents in-depth attention highlighting the current gaps, the lack of comparative research, while proposing new research directions at the intersection of two fields -- neuroscience and deep learning. Further, we define a new evaluation metric 'NATURE' for reporting the carbon footprint of AI models.
A first approach to closeness distributions
Authors: JesUs Cerquides
Date: 2021-11-16 00:00:00

Probabilistic graphical models allow us to encode a large probability distribution as a composition of smaller ones. It is oftentimes the case that we are interested in incorporating in the model the idea that some of these smaller distributions are likely to be similar to one another. In this paper we provide an information geometric approach on how to incorporate this information, and see that it allows us to reinterpret some already existing models.
An Empirical Study of Finding Similar Exercises
Authors: Tongwen Huang, Xihua Li
Date: 2021-11-16 00:00:00
Tasks: Diversity, Language Modeling, Language Modelling, Paper generation

Education artificial intelligence aims to profit tasks in the education domain such as intelligent test paper generation and consolidation exercises where the main technique behind is how to match the exercises, known as the finding similar exercises(FSE) problem. Most of these approaches emphasized their model abilities to represent the exercise, unfortunately there are still many challenges such as the scarcity of data, insufficient understanding of exercises and high label noises. We release a Chinese education pre-trained language model BERT$_{Edu}$ for the label-scarce dataset and introduce the exercise normalization to overcome the diversity of mathematical formulas and terms in exercise. We discover new auxiliary tasks in an innovative way depends on problem-solving ideas and propose a very effective MoE enhanced multi-task model for FSE task to attain better understanding of exercises. In addition, confidence learning was utilized to prune train-set and overcome high noises in labeling data. Experiments show that these methods proposed in this paper are very effective.
Accounting for Gaussian Process Imprecision in Bayesian Optimization
Authors: Julian Rodemann, Thomas Augustin
Date: 2021-11-16 00:00:00
Tasks: Bayesian Optimization, Gaussian Processes

Bayesian optimization (BO) with Gaussian processes (GP) as surrogate models is widely used to optimize analytically unknown and expensive-to-evaluate functions. In this paper, we propose Prior-mean-RObust Bayesian Optimization (PROBO) that outperforms classical BO on specific problems. First, we study the effect of the Gaussian processes' prior specifications on classical BO's convergence. We find the prior's mean parameters to have the highest influence on convergence among all prior components. In response to this result, we introduce PROBO as a generalization of BO that aims at rendering the method more robust towards prior mean parameter misspecification. This is achieved by explicitly accounting for GP imprecision via a prior near-ignorance model. At the heart of this is a novel acquisition function, the generalized lower confidence bound (GLCB). We test our approach against classical BO on a real-world problem from material science and observe PROBO to converge faster. Further experiments on multimodal and wiggly target functions confirm the superiority of our method.
Switching Recurrent Kalman Networks
Authors: Giao Nguyen-Quynh, Philipp Becker, Chen Qiu, Maja Rudolph, Gerhard Neumann
Date: 2021-11-16 00:00:00
Tasks: Autonomous Driving, Time Series, Time Series Analysis

Forecasting driving behavior or other sensor measurements is an essential component of autonomous driving systems. Often real-world multivariate time series data is hard to model because the underlying dynamics are nonlinear and the observations are noisy. In addition, driving data can often be multimodal in distribution, meaning that there are distinct predictions that are likely, but averaging can hurt model performance. To address this, we propose the Switching Recurrent Kalman Network (SRKN) for efficient inference and prediction on nonlinear and multi-modal time-series data. The model switches among several Kalman filters that model different aspects of the dynamics in a factorized latent state. We empirically test the resulting scalable and interpretable deep state-space model on toy data sets and real driving data from taxis in Porto. In all cases, the model can capture the multimodal nature of the dynamics in the data.
HADFL: Heterogeneity-aware Decentralized Federated Learning Framework
Authors: Jing Cao, Zirui Lian, Weihong Liu, Zongwei Zhu, Cheng Ji
Date: 2021-11-16 00:00:00
Tasks: Federated Learning

Federated learning (FL) supports training models on geographically distributed devices. However, traditional FL systems adopt a centralized synchronous strategy, putting high communication pressure and model generalization challenge. Existing optimizations on FL either fail to speedup training on heterogeneous devices or suffer from poor communication efficiency. In this paper, we propose HADFL, a framework that supports decentralized asynchronous training on heterogeneous devices. The devices train model locally with heterogeneity-aware local steps using local data. In each aggregation cycle, they are selected based on probability to perform model synchronization and aggregation. Compared with the traditional FL system, HADFL can relieve the central server's communication pressure, efficiently utilize heterogeneous computing power, and can achieve a maximum speedup of 3.15x than decentralized-FedAvg and 4.68x than Pytorch distributed training scheme, respectively, with almost no loss of convergence accuracy.
Solving Probability and Statistics Problems by Program Synthesis
Authors: Leonard Tang, Elizabeth Ke, Nikhil Singh, Nakul Verma, Iddo Drori
Date: 2021-11-16 00:00:00
Tasks: Form, Program Synthesis, Prompt Engineering

We solve university level probability and statistics questions by program synthesis using OpenAI's Codex, a Transformer trained on text and fine-tuned on code. We transform course problems from MIT's 18.05 Introduction to Probability and Statistics and Harvard's STAT110 Probability into programming tasks. We then execute the generated code to get a solution. Since these course questions are grounded in probability, we often aim to have Codex generate probabilistic programs that simulate a large number of probabilistic dependencies to compute its solution. Our approach requires prompt engineering to transform the question from its original form to an explicit, tractable form that results in a correct program and solution. To estimate the amount of work needed to translate an original question into its tractable form, we measure the similarity between original and transformed questions. Our work is the first to introduce a new dataset of university-level probability and statistics problems and solve these problems in a scalable fashion using the program synthesis capabilities of large language models.