pwc-archive/papers-with-abstracts huggingface dataset:
Contrastive Adapters for Foundation Model Group Robustness
Authors: Michael Zhang, Christopher Ré
Date: 2022-07-14 00:00:00
Tasks: Contrastive Learning, model, zero-shot-classification, Zero-Shot Learning

While large pretrained foundation models (FMs) have shown remarkable zero-shot classification robustness to dataset-level distribution shifts, their robustness to subpopulation or group shifts is relatively underexplored. We study this problem, and find that FMs such as CLIP may not be robust to various group shifts. Across 9 robustness benchmarks, zero-shot classification with their embeddings results in gaps of up to 80.7 percentage points (pp) between average and worst-group accuracy. Unfortunately, existing methods to improve robustness require retraining, which can be prohibitively expensive on large foundation models. We also find that efficient ways to improve model inference (e.g., via adapters, lightweight networks with FM embeddings as inputs) do not consistently improve and can sometimes hurt group robustness compared to zero-shot (e.g., increasing the accuracy gap by 50.1 pp on CelebA). We thus develop an adapter training strategy to effectively and efficiently improve FM group robustness. Our motivating observation is that while poor robustness results from groups in the same class being embedded far apart in the foundation model "embedding space," standard adapter training may not bring these points closer together. We thus propose contrastive adapting, which trains adapters with contrastive learning to bring sample embeddings close to both their ground-truth class embeddings and other sample embeddings in the same class. Across the 9 benchmarks, our approach consistently improves group robustness, raising worst-group accuracy by 8.5 to 56.0 pp over zero-shot. Our approach is also efficient, doing so without any FM finetuning and only a fixed set of frozen FM embeddings. On benchmarks such as Waterbirds and CelebA, this leads to worst-group accuracy comparable to state-of-the-art methods that retrain entire models, while only training $\leq$1% of the model parameters.
Attribute Graphs Underlying Molecular Generative Models: Path to Learning with Limited Data
Authors: Samuel C. Hoffman, Payel Das, Karthikeyan Shanmugam, Kahini Wadhawan, Prasanna Sattigeri
Date: 2022-07-14 00:00:00
Tasks: Attribute, Causal Discovery, feature selection, Self-Supervised Learning, Sparse Learning

Training generative models that capture rich semantics of the data and interpreting the latent representations encoded by such models are very important problems in un-/self-supervised learning. In this work, we provide a simple algorithm that relies on perturbation experiments on latent codes of a pre-trained generative autoencoder to uncover an attribute graph that is implied by the generative model. We perform perturbation experiments to check for influence of a given latent variable on a subset of attributes. Given this, we show that one can fit an effective graphical model that models a structural equation model between latent codes taken as exogenous variables and attributes taken as observed variables. One interesting aspect is that a single latent variable controls multiple overlapping subsets of attributes unlike conventional approaches that try to impose full independence. Using a pre-trained generative autoencoder trained on a large dataset of small molecules, we demonstrate that the graphical model between various molecular attributes and latent codes learned by our algorithm can be used to predict a specific property for molecules which are drawn from a different distribution. We compare prediction models trained on various feature subsets chosen by simple baselines, as well as existing causal discovery and sparse learning/feature selection methods, with the ones in the derived Markov blanket from our method. Results show empirically that the predictor that relies on our Markov blanket attributes is robust to distribution shifts when transferred or fine-tuned with a few samples from the new distribution, especially when training data is limited.
Audio-guided Album Cover Art Generation with Genetic Algorithms
Authors: James Marien, Sam Leroux, Bart Dhoedt, Cedric De Boom
Date: 2022-07-14 00:00:00

Over 60,000 songs are released on Spotify every day, and the competition for the listener's attention is immense. In that regard, the importance of captivating and inviting cover art cannot be underestimated, because it is deeply entangled with a song's character and the artist's identity, and remains one of the most important gateways to lead people to discover music. However, designing cover art is a highly creative, lengthy and sometimes expensive process that can be daunting, especially for non-professional artists. For this reason, we propose a novel deep-learning framework to generate cover art guided by audio features. Inspired by VQGAN-CLIP, our approach is highly flexible because individual components can easily be replaced without the need for any retraining. This paper outlines the architectural details of our models and discusses the optimization challenges that emerge from them. More specifically, we will exploit genetic algorithms to overcome bad local minima and adversarial examples. We find that our framework can generate suitable cover art for most genres, and that the visual features adapt themselves to audio feature changes. Given these results, we believe that our framework paves the road for extensions and more advanced applications in audio-guided visual generation tasks.
Case study on quantum convolutional neural network scalability
Authors: Marina O. Lisnichenko, Stanislav I. Protasov
Date: 2022-07-14 00:00:00

One of the crucial tasks in computer science is the processing time reduction of various data types, i.e., images, which is important for different fields -- from medicine and logistics to virtual shopping. Compared to classical computers, quantum computers are capable of parallel data processing, which reduces the data processing time. This quality of quantum computers inspired intensive research of the potential of quantum technologies applicability to real-life tasks. Some progress has already revealed on a smaller volumes of the input data. In this research effort, I aimed to increase the amount of input data (I used images from 2 x 2 to 8 x 8), while reducing the processing time, by way of skipping intermediate measurement steps. The hypothesis was that, for increased input data, the omitting of intermediate measurement steps after each quantum convolution layer will improve output metric results and accelerate data processing. To test the hypothesis, I performed experiments to chose the best activation function and its derivative in each network. The hypothesis was partly confirmed in terms of output mean squared error (MSE) -- it dropped from 0.25 in the result of classical convolutional neural network (CNN) training to 0.23 in the result of quantum convolutional neural network (QCNN) training. In terms of the training time, however, which was 1.5 minutes for CNN and 4 hours 37 minutes in the least lengthy training iteration, the hypothesis was rejected.
Making Linear MDPs Practical via Contrastive Representation Learning
Authors: Tianjun Zhang, Tongzheng Ren, Mengjiao Yang, Joseph E. Gonzalez, Dale Schuurmans, Bo Dai
Date: 2022-07-14 00:00:00
Tasks: Representation Learning

It is common to address the curse of dimensionality in Markov decision processes (MDPs) by exploiting low-rank representations. This motivates much of the recent theoretical study on linear MDPs. However, most approaches require a given representation under unrealistic assumptions about the normalization of the decomposition or introduce unresolved computational challenges in practice. Instead, we consider an alternative definition of linear MDPs that automatically ensures normalization while allowing efficient representation learning via contrastive estimation. The framework also admits confidence-adjusted index algorithms, enabling an efficient and principled approach to incorporating optimism or pessimism in the face of uncertainty. To the best of our knowledge, this provides the first practical representation learning method for linear MDPs that achieves both strong theoretical guarantees and empirical performance. Theoretically, we prove that the proposed algorithm is sample efficient in both the online and offline settings. Empirically, we demonstrate superior performance over existing state-of-the-art model-based and model-free algorithms on several benchmarks.
Reasoning about Actions over Visual and Linguistic Modalities: A Survey
Authors: Shailaja Keyur Sampat, Maitreya Patel, Subhasish Das, Yezhou Yang, Chitta Baral
Date: 2022-07-15 00:00:00
Tasks: Common Sense Reasoning, Survey

'Actions' play a vital role in how humans interact with the world and enable them to achieve desired goals. As a result, most common sense (CS) knowledge for humans revolves around actions. While 'Reasoning about Actions & Change' (RAC) has been widely studied in the Knowledge Representation community, it has recently piqued the interest of NLP and computer vision researchers. This paper surveys existing tasks, benchmark datasets, various techniques and models, and their respective performance concerning advancements in RAC in the vision and language domain. Towards the end, we summarize our key takeaways, discuss the present challenges facing this research area, and outline potential directions for future research.
LIP: Lightweight Intelligent Preprocessor for meaningful text-to-speech
Authors: Harshvardhan Anand, Nansi Begam, Richa Verma, Sourav Ghosh, Harichandana B. S. S, Sumit Kumar
Date: 2022-07-11 00:00:00
Tasks: text-to-speech, Text to Speech

Existing Text-to-Speech (TTS) systems need to read messages from the email which may have Personal Identifiable Information (PII) to text messages that can have a streak of emojis and punctuation. 92% of the world's online population use emoji with more than 10 billion emojis sent everyday. Lack of preprocessor leads to messages being read as-is including punctuation and infographics like emoticons. This problem worsens if there is a continuous sequence of punctuation/emojis that are quite common in real-world communications like messaging, Social Networking Site (SNS) interactions, etc. In this work, we aim to introduce a lightweight intelligent preprocessor (LIP) that can enhance the readability of a message before being passed downstream to existing TTS systems. We propose multiple sub-modules including: expanding contraction, censoring swear words, and masking of PII, as part of our preprocessor to enhance the readability of text. With a memory footprint of only 3.55 MB and inference time of 4 ms for up to 50-character text, our solution is suitable for real-time deployment. This work being the first of its kind, we try to benchmark with an open independent survey, the result of which shows 76.5% preference towards LIP enabled TTS engine as compared to standard TTS.
CC-Fuzz: Genetic algorithm-based fuzzing for stress testing congestion control algorithms
Authors: Devdeep Ray, Srinivasan Seshan
Date: 2022-07-15 00:00:00

Congestion control research has experienced a significant increase in interest in the past few years, with many purpose-built algorithms being designed with the needs of specific applications in mind. These algorithms undergo limited testing before being deployed on the Internet, where they interact with other congestion control algorithms and run across a variety of network conditions. This often results in unforeseen performance issues in the wild due to algorithmic inadequacies or implementation bugs, and these issues are often hard to identify since packet traces are not available. In this paper, we present CC-Fuzz, an automated congestion control testing framework that uses a genetic search algorithm in order to stress test congestion control algorithms by generating adversarial network traces and traffic patterns. Initial results using this approach are promising - CC-Fuzz automatically found a bug in BBR that causes it to stall permanently, and is able to automatically discover the well-known low-rate TCP attack, among other things.
Deep Hedging: Continuous Reinforcement Learning for Hedging of General Portfolios across Multiple Risk Aversions
Authors: Phillip Murray, Ben Wood, Hans Buehler, Magnus Wiese, Mikko S. Pakkanen
Date: 2022-07-15 00:00:00
Tasks: Reinforcement Learning (RL)

We present a method for finding optimal hedging policies for arbitrary initial portfolios and market states. We develop a novel actor-critic algorithm for solving general risk-averse stochastic control problems and use it to learn hedging strategies across multiple risk aversion levels simultaneously. We demonstrate the effectiveness of the approach with a numerical example in a stochastic volatility environment.
On the Selection of Tuning Parameters for Patch-Stitching Embedding Methods
Authors: Ery Arias-Castro, Phong Alain Chau
Date: 2022-07-14 00:00:00
Tasks: Dimensionality Reduction

While classical scaling, just like principal component analysis, is parameter-free, other methods for embedding multivariate data require the selection of one or several tuning parameters. This tuning can be difficult due to the unsupervised nature of the situation. We propose a simple, almost obvious, approach to supervise the choice of tuning parameter(s): minimize a notion of stress. We apply this approach to the selection of the patch size in a prototypical patch-stitching embedding method, both in the multidimensional scaling (aka network localization) setting and in the dimensionality reduction (aka manifold learning) setting. In our study, we uncover a new bias--variance tradeoff phenomenon.
A Comparison of Source Distribution and Result Overlap in Web Search Engines
Authors: Nurce Yagci, Sebastian Sünkler, Helena Häußler, Dirk Lewandowski
Date: 2022-07-15 00:00:00

When it comes to search engines, users generally prefer Google. Our study aims to find the differences between the results found in Google compared to other search engines. We compared the top 10 results from Google, Bing, DuckDuckGo, and Metager, using 3,537 queries generated from Google Trends from Germany and the US. Google displays more unique domains in the top results than its competitors. Wikipedia and news websites are the most popular sources overall. With some top sources dominating search results, the distribution of domains is also consistent across all search engines. The overlap between Google and Bing is always under 32%, while Metager has a higher overlap with Bing than DuckDuckGo, going up to 78%. This study shows that the use of another search engine, especially in addition to Google, provides a wider variety in sources and might lead the user to find new perspectives.
Bug Fix Time Optimization Using Matrix Factorization and Iterative Gale-Shaply Algorithms
Authors: Madonna Mayez, Khaled Nagaty, Abeer Hamdy
Date: 2022-07-14 00:00:00
Tasks: Bug fixing, Information Retrieval, Retrieval

Bug triage is an essential task in software maintenance phase. It assigns developers (fixers) to bug reports to fix them. This process is performed manually by a triager, who analyzes developers profiles and submitted bug reports to make suitable assignments. Bug triaging process is time consuming thus automating this process is essential to improve the quality of software. Previous work addressed triaging problem either as an information retrieval or classification problem. This paper tackles this problem as a resource allocation problem, that aims at the best assignments of developers to bug reports, that reduces the total fixing time of the newly submitted bug reports, in addition to the even distribution of bug reports over developers. In this paper, a combination of matrix factorization and Gale Shapely algorithm, supported by the differential evolution is firstly introduced to optimize the total fix time and normalize developers work load. Matrix factorization is used to establish a recommendation system for Gale-Shapley to make assignment decisions. Differential evolution provides the best set of weights to build developers score profiles. The proposed approach is assessed over three repositories, Linux, Apache and Eclipse. Experimental results show that the proposed approach reduces the bug fixing time, in comparison to the manual triage, by 80.67%, 23.61% and 60.22% over Linux, Eclipse and Apache respectively. Moreover, the workload for the developers is uniform.
Adaptive sequencing using nanopores and deep learning of mitochondrial DNA
Authors: Artem Danilevsky, Avital Luba Polsky, Noam Shomron
Date: 2022-07-09 00:00:00
Proceeding: Briefings in Bioinformatics 2022 7
Tasks: Deep Learning

Nanopore sequencing is an emerging technology that reads DNA by utilizing a unique method of detecting nucleic acid sequences and identifies the various chemical modifications they carry. Deep learning has increased in popularity as a useful technique to solve many complex computational tasks. ‘Adaptive sequencing’ is an implementation of selective sequencing, intended for use on the nanopore sequencing platform. In this study, we demonstrated an alternative method of software-based selective sequencing that is performed in real time by combining nanopore sequencing and deep learning. Our results showed the feasibility of using deep learning for classifying signals from only the first 200 nucleotides in a raw nanopore sequencing signal format. This was further demonstrated by comparing the accuracy of our deep learning classification model across data from several human cell lines and other eukaryotic organisms. We used custom deep learning models and a script that utilizes a ‘Read Until’ framework to target mitochondrial molecules in real time from a human cell line sample. This achieved a significant separation and enrichment ability of 2.3-fold. In a series of very short sequencing experiments (10, 30 and 120 min), we identified genomic and mitochondrial reads with accuracy above 90%, although mitochondrial DNA comprised only 0.1% of the total input material. The uniqueness of our method is the ability to distinguish two groups of DNA even without a labeled reference. This contrasts with studies that required a well-defined reference, whether of a DNA sequence or of another type of representation. Additionally, our method showed higher correlation to the theoretically possible enrichment factor, compared with other published methods. We believe that our results will lay the foundation for rapid and selective sequencing using nanopore technology and will pave the approach for clinical applications that use nanopore sequencing data.
Motion Aware Double Attention Network for Dynamic Scene Deblurring
Authors: Dan Yang, Mehmet Yamac
Date: 2020-06-19 00:00:00
Proceeding: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) Workshops 2020 6
Tasks: Deblurring, Image Deblurring

Motion deblurring in dynamic scenes is a challenging
task when the blurring is caused by one or a combination of
various reasons such as moving objects, camera movement,
etc. Since event cameras can detect changes in intensity
with a low latency, necessary motion information is inherently captured in event data, which could be quite useful
for deblurring standard camera images. The degradation
intensity does not show homogeneity across an image due
to factors like object depth, speed, etc. We propose a twobranch network structure, Motion Aware Double Attention
Network (MADANet), that pays special attention to areas
with high blur. As part of the network, event data is first
used by the high blur region segmentation module that creates a probability-like score for areas exhibiting high relative motion to the camera. Then, the event data is also
injected to feature maps in the main body, where there is
a second attention mechanism available for each branch.
The effective usage of event data and two-level attention
mechanisms makes the network very compact. During the
experiment, it was shown that the proposed network could
achieve state-of-the-art performance not only on the benchmark dataset from GoPro, but also on two newly collected
datasets, one of which contains real event data
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics
Authors: Tiago Almeida, Rui Antunes, João F. Silva, João R. Almeida, Sérgio Matos
Date: 2022-07-01 00:00:00
Proceeding: Database: The Journal of Biological Databases and Curation 2022 7
Tasks: Articles, Chemical Indexing, Entity Linking, named-entity-recognition, Named Entity Recognition, Named Entity Recognition (NER)

The identification of chemicals in articles has attracted a large interest in the biomedical scientific community, given its importance in drug development research. Most of previous research have focused on PubMed abstracts, and further investigation using full-text documents is required because these contain additional valuable information that must be explored. The manual expert task of indexing Medical Subject Headings (MeSH) terms to these articles later helps researchers find the most relevant publications for their ongoing work. The BioCreative VII NLM-Chem track fostered the development of systems for chemical identification and indexing in PubMed full-text articles. Chemical identification consisted in identifying the chemical mentions and linking these to unique MeSH identifiers. This manuscript describes our participation system and the post-challenge improvements we made. We propose a three-stage pipeline that individually performs chemical mention detection, entity normalization and indexing. Regarding chemical identification, we adopted a deep-learning solution that utilizes the PubMedBERT contextualized embeddings followed by a multilayer perceptron and a conditional random field tagging layer. For the normalization approach, we use a sieve-based dictionary filtering followed by a deep-learning similarity search strategy. Finally, for the indexing we developed rules for identifying the more relevant MeSH codes for each article. During the challenge, our system obtained the best official results in the normalization and indexing tasks despite the lower performance in the chemical mention recognition task. In a post-contest phase we boosted our results by improving our named entity recognition model with additional techniques. The final system achieved 0.8731, 0.8275 and 0.4849 in the chemical identification, normalization and indexing tasks, respectively. The code to reproduce our experiments and run the pipeline is publicly available.

Database URL: https://github.com/bioinformatics-ua/biocreativeVII_track2