pwc-archive/papers-with-abstracts huggingface dataset:
GraSSRep: Graph-Based Self-Supervised Learning for Repeat Detection in Metagenomic Assembly
Authors: Ali Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra
Date: 2024-02-14 00:00:00
Tasks: Node Classification, Self-Supervised Learning

Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene duplication, and gene loss/gain complicate accurate genome assembly from metagenomic communities. Detecting repeats is a crucial first step in overcoming these challenges. To address this issue, we propose GraSSRep, a novel approach that leverages the assembly graph's structure through graph neural networks (GNNs) within a self-supervised learning framework to classify DNA sequences into repetitive and non-repetitive categories. Specifically, we frame this problem as a node classification task within a metagenomic assembly graph. In a self-supervised fashion, we rely on a high-precision (but low-recall) heuristic to generate pseudo-labels for a small proportion of the nodes. We then use those pseudo-labels to train a GNN embedding and a random forest classifier to propagate the labels to the remaining nodes. In this way, GraSSRep combines sequencing features with pre-defined and learned graph features to achieve state-of-the-art performance in repeat detection. We evaluate our method using simulated and synthetic metagenomic datasets. The results on the simulated data highlight our GraSSRep's robustness to repeat attributes, demonstrating its effectiveness in handling the complexity of repeated sequences. Additionally, our experiments with synthetic metagenomic datasets reveal that incorporating the graph structure and the GNN enhances our detection performance. Finally, in comparative analyses, GraSSRep outperforms existing repeat detection tools with respect to precision and recall.
Loss Shaping Constraints for Long-Term Time Series Forecasting
Authors: Ignacio Hounie, Javier Porras-Valenzuela, Alejandro Ribeiro
Date: 2024-02-14 00:00:00
Tasks: Time Series, Time Series Forecasting

Several applications in time series forecasting require predicting multiple steps ahead. Despite the vast amount of literature in the topic, both classical and recent deep learning based approaches have mostly focused on minimising performance averaged over the predicted window. We observe that this can lead to disparate distributions of errors across forecasting steps, especially for recent transformer architectures trained on popular forecasting benchmarks. That is, optimising performance on average can lead to undesirably large errors at specific time-steps. In this work, we present a Constrained Learning approach for long-term time series forecasting that aims to find the best model in terms of average performance that respects a user-defined upper bound on the loss at each time-step. We call our approach loss shaping constraints because it imposes constraints on the loss at each time step, and leverage recent duality results to show that despite its non-convexity, the resulting problem has a bounded duality gap. We propose a practical Primal-Dual algorithm to tackle it, and demonstrate that the proposed approach exhibits competitive average performance in time series forecasting benchmarks, while shaping the distribution of errors across the predicted window.
3D-based RNA function prediction tools in rnaglib
Authors: Carlos Oliver, Vincent Mallet, Jérôme Waldispühl
Date: 2024-02-14 00:00:00
Tasks: Prediction

Understanding the connection between complex structural features of RNA and biological function is a fundamental challenge in evolutionary studies and in RNA design. However, building datasets of RNA 3D structures and making appropriate modeling choices remains time-consuming and lacks standardization. In this chapter, we describe the use of rnaglib, to train supervised and unsupervised machine learning-based function prediction models on datasets of RNA 3D structures.
Connecting Algorithmic Fairness to Quality Dimensions in Machine Learning in Official Statistics and Survey Production
Authors: Patrick Oliver Schenk, Christoph Kern
Date: 2024-02-14 00:00:00
Tasks: Fairness

National Statistical Organizations (NSOs) increasingly draw on Machine Learning (ML) to improve the timeliness and cost-effectiveness of their products. When introducing ML solutions, NSOs must ensure that high standards with respect to robustness, reproducibility, and accuracy are upheld as codified, e.g., in the Quality Framework for Statistical Algorithms (QF4SA; Yung et al. 2022). At the same time, a growing body of research focuses on fairness as a pre-condition of a safe deployment of ML to prevent disparate social impacts in practice. However, fairness has not yet been explicitly discussed as a quality aspect in the context of the application of ML at NSOs. We employ Yung et al. (2022)'s QF4SA quality framework and present a mapping of its quality dimensions to algorithmic fairness. We thereby extend the QF4SA framework in several ways: we argue for fairness as its own quality dimension, we investigate the interaction of fairness with other dimensions, and we explicitly address data, both on its own and its interaction with applied methodology. In parallel with empirical illustrations, we show how our mapping can contribute to methodology in the domains of official statistics, algorithmic fairness, and trustworthy machine learning.
Information Complexity of Stochastic Convex Optimization: Applications to Generalization and Memorization
Authors: Idan Attias, Gintare Karolina Dziugaite, Mahdi Haghifam, Roi Livni, Daniel M. Roy
Date: 2024-02-14 00:00:00
Tasks: Generalization Bounds, Memorization

In this work, we investigate the interplay between memorization and learning in the context of \emph{stochastic convex optimization} (SCO). We define memorization via the information a learning algorithm reveals about its training data points. We then quantify this information using the framework of conditional mutual information (CMI) proposed by Steinke and Zakynthinou (2020). Our main result is a precise characterization of the tradeoff between the accuracy of a learning algorithm and its CMI, answering an open question posed by Livni (2023). We show that, in the $L^2$ Lipschitz--bounded setting and under strong convexity, every learner with an excess error $\varepsilon$ has CMI bounded below by $\Omega(1/\varepsilon^2)$ and $\Omega(1/\varepsilon)$, respectively. We further demonstrate the essential role of memorization in learning problems in SCO by designing an adversary capable of accurately identifying a significant fraction of the training samples in specific SCO problems. Finally, we enumerate several implications of our results, such as a limitation of generalization bounds based on CMI and the incompressibility of samples in SCO problems.
Stability and Multigroup Fairness in Ranking with Uncertain Predictions
Authors: Siddartha Devic, Aleksandra Korolova, David Kempe, Vatsal Sharan
Date: 2024-02-14 00:00:00
Tasks: Fairness

Rankings are ubiquitous across many applications, from search engines to hiring committees. In practice, many rankings are derived from the output of predictors. However, when predictors trained for classification tasks have intrinsic uncertainty, it is not obvious how this uncertainty should be represented in the derived rankings. Our work considers ranking functions: maps from individual predictions for a classification task to distributions over rankings. We focus on two aspects of ranking functions: stability to perturbations in predictions and fairness towards both individuals and subgroups. Not only is stability an important requirement for its own sake, but -- as we show -- it composes harmoniously with individual fairness in the sense of Dwork et al. (2012). While deterministic ranking functions cannot be stable aside from trivial scenarios, we show that the recently proposed uncertainty aware (UA) ranking functions of Singh et al. (2021) are stable. Our main result is that UA rankings also achieve multigroup fairness through successful composition with multiaccurate or multicalibrated predictors. Our work demonstrates that UA rankings naturally interpolate between group and individual level fairness guarantees, while simultaneously satisfying stability guarantees important whenever machine-learned predictions are used.
Trained Without My Consent: Detecting Code Inclusion In Language Models Trained on Code
Authors: Vahid Majdinasab, Amin Nikanjam, Foutse khomh
Date: 2024-02-14 00:00:00
Tasks: Clone Detection

Code auditing ensures that the developed code adheres to standards, regulations, and copyright protection by verifying that it does not contain code from protected sources. The recent advent of Large Language Models (LLMs) as coding assistants in the software development process poses new challenges for code auditing. The dataset for training these models is mainly collected from publicly available sources. This raises the issue of intellectual property infringement as developers' codes are already included in the dataset. Therefore, auditing code developed using LLMs is challenging, as it is difficult to reliably assert if an LLM used during development has been trained on specific copyrighted codes, given that we do not have access to the training datasets of these models. Given the non-disclosure of the training datasets, traditional approaches such as code clone detection are insufficient for asserting copyright infringement. To address this challenge, we propose a new approach, TraWiC; a model-agnostic and interpretable method based on membership inference for detecting code inclusion in an LLM's training dataset. We extract syntactic and semantic identifiers unique to each program to train a classifier for detecting code inclusion. In our experiments, we observe that TraWiC is capable of detecting 83.87% of codes that were used to train an LLM. In comparison, the prevalent clone detection tool NiCad is only capable of detecting 47.64%. In addition to its remarkable performance, TraWiC has low resource overhead in contrast to pair-wise clone detection that is conducted during the auditing process of tools like CodeWhisperer reference tracker, across thousands of code snippets.
EcoVal: An Efficient Data Valuation Framework for Machine Learning
Authors: Ayush K Tarun, Vikram S Chundawat, Murari Mandal, Hong Ming Tan, Bowei Chen, Mohan Kankanhalli
Date: 2024-02-14 00:00:00
Tasks: Data Valuation

Quantifying the value of data within a machine learning workflow can play a pivotal role in making more strategic decisions in machine learning initiatives. The existing Shapley value based frameworks for data valuation in machine learning are computationally expensive as they require considerable amount of repeated training of the model to obtain the Shapley value. In this paper, we introduce an efficient data valuation framework EcoVal, to estimate the value of data for machine learning models in a fast and practical manner. Instead of directly working with individual data sample, we determine the value of a cluster of similar data points. This value is further propagated amongst all the member cluster points. We show that the overall value of the data can be determined by estimating the intrinsic and extrinsic value of each data. This is enabled by formulating the performance of a model as a \textit{production function}, a concept which is popularly used to estimate the amount of output based on factors like labor and capital in a traditional free economic market. We provide a formal proof of our valuation technique and elucidate the principles and mechanisms that enable its accelerated performance. We demonstrate the real-world applicability of our method by showcasing its effectiveness for both in-distribution and out-of-sample data. This work addresses one of the core challenges of efficient data valuation at scale in machine learning models. The code is available at \underline{https://github.com/respai-lab/ecoval}.
Hybrid Machine Learning techniques in the management of harmful algal blooms impact
Authors: Andres Molares-Ulloa, Daniel Rivero, Jesus Gil Ruiz, Enrique Fernandez-Blanco, Luis de-la-Fuente-Valentín
Date: 2024-02-14 00:00:00
Tasks: Hybrid Machine Learning, Management

Harmful algal blooms (HABs) are episodes of high concentrations of algae that are potentially toxic for human consumption. Mollusc farming can be affected by HABs because, as filter feeders, they can accumulate high concentrations of marine biotoxins in their tissues. To avoid the risk to human consumption, harvesting is prohibited when toxicity is detected. At present, the closure of production areas is based on expert knowledge and the existence of a predictive model would help when conditions are complex and sampling is not possible. Although the concentration of toxin in meat is the method most commonly used by experts in the control of shellfish production areas, it is rarely used as a target by automatic prediction models. This is largely due to the irregularity of the data due to the established sampling programs. As an alternative, the activity status of production areas has been proposed as a target variable based on whether mollusc meat has a toxicity level below or above the legal limit. This new option is the most similar to the actual functioning of the control of shellfish production areas. For this purpose, we have made a comparison between hybrid machine learning models like Neural-Network-Adding Bootstrap (BAGNET) and Discriminative Nearest Neighbor Classification (SVM-KNN) when estimating the state of production areas. The study has been carried out in several estuaries with different levels of complexity in the episodes of algal blooms to demonstrate the generalization capacity of the models in bloom detection. As a result, we could observe that, with an average recall value of 93.41% and without dropping below 90% in any of the estuaries, BAGNET outperforms the other models both in terms of results and robustness.
Transformers, parallel computation, and logarithmic depth
Authors: Clayton Sanford, Daniel Hsu, Matus Telgarsky
Date: 2024-02-14 00:00:00

We show that a constant number of self-attention layers can efficiently simulate, and be simulated by, a constant number of communication rounds of Massively Parallel Computation. As a consequence, we show that logarithmic depth is sufficient for transformers to solve basic computational tasks that cannot be efficiently solved by several other neural sequence models and sub-quadratic transformer approximations. We thus establish parallelism as a key distinguishing property of transformers.
UR2M: Uncertainty and Resource-Aware Event Detection on Microcontrollers
Authors: Hong Jia, Young D. Kwon, Dong Ma, Nhat Pham, Lorena Qendro, Tam Vu, Cecilia Mascolo
Date: 2024-02-14 00:00:00
Tasks: Event Detection, Uncertainty Quantification

Traditional machine learning techniques are prone to generating inaccurate predictions when confronted with shifts in the distribution of data between the training and testing phases. This vulnerability can lead to severe consequences, especially in applications such as mobile healthcare. Uncertainty estimation has the potential to mitigate this issue by assessing the reliability of a model's output. However, existing uncertainty estimation techniques often require substantial computational resources and memory, making them impractical for implementation on microcontrollers (MCUs). This limitation hinders the feasibility of many important on-device wearable event detection (WED) applications, such as heart attack detection. In this paper, we present UR2M, a novel Uncertainty and Resource-aware event detection framework for MCUs. Specifically, we (i) develop an uncertainty-aware WED based on evidential theory for accurate event detection and reliable uncertainty estimation; (ii) introduce a cascade ML framework to achieve efficient model inference via early exits, by sharing shallower model layers among different event models; (iii) optimize the deployment of the model and MCU library for system efficiency. We conducted extensive experiments and compared UR2M to traditional uncertainty baselines using three wearable datasets. Our results demonstrate that UR2M achieves up to 864% faster inference speed, 857% energy-saving for uncertainty estimation, 55% memory saving on two popular MCUs, and a 22% improvement in uncertainty quantification performance. UR2M can be deployed on a wide range of MCUs, significantly expanding real-time and reliable WED applications.
Exploring the Relationship: Transformative Adaptive Activation Functions in Comparison to Other Activation Functions
Authors: Vladimír Kunc
Date: 2024-02-14 00:00:00
Tasks: Translation

Neural networks are the state-of-the-art approach for many tasks and the activation function is one of the main building blocks that allow such performance. Recently, a novel transformative adaptive activation function (TAAF) allowing for any vertical and horizontal translation and scaling was proposed. This work sets the TAAF into the context of other activation functions. It shows that the TAAFs generalize over 50 existing activation functions and utilize similar concepts as over 70 other activation functions, underscoring the versatility of TAAFs. This comprehensive exploration positions TAAFs as a promising and adaptable addition to neural networks.
Momentum Approximation in Asynchronous Private Federated Learning
Authors: Tao Yu, Congzheng Song, Jianyu Wang, Mona Chitnis
Date: 2024-02-14 00:00:00
Tasks: Federated Learning

Asynchronous protocols have been shown to improve the scalability of federated learning (FL) with a massive number of clients. Meanwhile, momentum-based methods can achieve the best model quality in synchronous FL. However, naively applying momentum in asynchronous FL algorithms leads to slower convergence and degraded model performance. It is still unclear how to effective combinie these two techniques together to achieve a win-win. In this paper, we find that asynchrony introduces implicit bias to momentum updates. In order to address this problem, we propose momentum approximation that minimizes the bias by finding an optimal weighted average of all historical model updates. Momentum approximation is compatible with secure aggregation as well as differential privacy, and can be easily integrated in production FL systems with a minor communication and storage cost. We empirically demonstrate that on benchmark FL datasets, momentum approximation can achieve $1.15 \textrm{--}4\times$ speed up in convergence compared to naively combining asynchronous FL with momentum.
Overview of the L3DAS23 Challenge on Audio-Visual Extended Reality
Authors: Christian Marinoni, Riccardo Fosco Gramaccioni, Changan Chen, Aurelio Uncini, Danilo Comminiello
Date: 2024-02-14 00:00:00
Tasks: Audio Signal Processing, Sound Event Localization and Detection, Speech Enhancement

The primary goal of the L3DAS23 Signal Processing Grand Challenge at ICASSP 2023 is to promote and support collaborative research on machine learning for 3D audio signal processing, with a specific emphasis on 3D speech enhancement and 3D Sound Event Localization and Detection in Extended Reality applications. As part of our latest competition, we provide a brand-new dataset, which maintains the same general characteristics of the L3DAS21 and L3DAS22 datasets, but with first-order Ambisonics recordings from multiple reverberant simulated environments. Moreover, we start exploring an audio-visual scenario by providing images of these environments, as perceived by the different microphone positions and orientations. We also propose updated baseline models for both tasks that can now support audio-image couples as input and a supporting API to replicate our results. Finally, we present the results of the participants. Further details about the challenge are available at https://www.l3das.com/icassp2023.
Robust Training of Temporal GNNs using Nearest Neighbours based Hard Negatives
Authors: Shubham Gupta, Srikanta Bedathur
Date: 2024-02-14 00:00:00
Tasks: Link Prediction

Temporal graph neural networks Tgnn have exhibited state-of-art performance in future-link prediction tasks. Training of these TGNNs is enumerated by uniform random sampling based unsupervised loss. During training, in the context of a positive example, the loss is computed over uninformative negatives, which introduces redundancy and sub-optimal performance. In this paper, we propose modified unsupervised learning of Tgnn, by replacing the uniform negative sampling with importance-based negative sampling. We theoretically motivate and define the dynamically computed distribution for a sampling of negative examples. Finally, using empirical evaluations over three real-world datasets, we show that Tgnn trained using loss based on proposed negative sampling provides consistent superior performance.
Multi-Hierarchical Surrogate Learning for Structural Dynamical Crash Simulations Using Graph Convolutional Neural Networks
Authors: Jonas Kneifl, Jörg Fehr, Steven L. Brunton, J. Nathan Kutz
Date: 2024-02-14 00:00:00
Tasks: Transfer Learning

Crash simulations play an essential role in improving vehicle safety, design optimization, and injury risk estimation. Unfortunately, numerical solutions of such problems using state-of-the-art high-fidelity models require significant computational effort. Conventional data-driven surrogate modeling approaches create low-dimensional embeddings for evolving the dynamics in order to circumvent this computational effort. Most approaches directly operate on high-resolution data obtained from numerical discretization, which is both costly and complicated for mapping the flow of information over large spatial distances. Furthermore, working with a fixed resolution prevents the adaptation of surrogate models to environments with variable computing capacities, different visualization resolutions, and different accuracy requirements. We thus propose a multi-hierarchical framework for structurally creating a series of surrogate models for a kart frame, which is a good proxy for industrial-relevant crash simulations, at different levels of resolution. For multiscale phenomena, macroscale features are captured on a coarse surrogate, whereas microscale effects are resolved by finer ones. The learned behavior of the individual surrogates is passed from coarse to finer levels through transfer learning. In detail, we perform a mesh simplification on the kart model to obtain multi-resolution representations of it. We then train a graph-convolutional neural network-based surrogate that learns parameter-dependent low-dimensional latent dynamics on the coarsest representation. Subsequently, another, similarly structured surrogate is trained on the residual of the first surrogate using a finer resolution. This step can be repeated multiple times. By doing so, we construct multiple surrogates for the same system with varying hardware requirements and increasing accuracy.