pwc-archive/papers-with-abstracts huggingface dataset:
State-Space Modeling in Long Sequence Processing: A Survey on Recurrence in the Transformer Era
Authors: Matteo Tiezzi, Michele Casoni, Alessandro Betti, Marco Gori, Stefano Melacci
Date: 2024-06-13 00:00:00
Tasks: State Space Models

Effectively learning from sequential data is a longstanding goal of Artificial Intelligence, especially in the case of long sequences. From the dawn of Machine Learning, several researchers engaged in the search of algorithms and architectures capable of processing sequences of patterns, retaining information about the past inputs while still leveraging the upcoming data, without losing precious long-term dependencies and correlations. While such an ultimate goal is inspired by the human hallmark of continuous real-time processing of sensory information, several solutions simplified the learning paradigm by artificially limiting the processed context or dealing with sequences of limited length, given in advance. These solutions were further emphasized by the large ubiquity of Transformers, that have initially shaded the role of Recurrent Neural Nets. However, recurrent networks are facing a strong recent revival due to the growing popularity of (deep) State-Space models and novel instances of large-context Transformers, which are both based on recurrent computations to go beyond several limits of currently ubiquitous technologies. In fact, the fast development of Large Language Models enhanced the interest in efficient solutions to process data over time. This survey provides an in-depth summary of the latest approaches that are based on recurrent models for sequential data processing. A complete taxonomy over the latest trends in architectural and algorithmic solutions is reported and discussed, guiding researchers in this appealing research field. The emerging picture suggests that there is room for thinking of novel routes, constituted by learning algorithms which depart from the standard Backpropagation Through Time, towards a more realistic scenario where patterns are effectively processed online, leveraging local-forward computations, opening to further research on this topic.
CGP++ : A Modern C++ Implementation of Cartesian Genetic Programming
Authors: Roman Kalkreuth, Thomas Baeck
Date: 2024-06-13 00:00:00

The reference implementation of Cartesian Genetic Programming (CGP) was written in the C programming language. C inherently follows a procedural programming paradigm, which entails challenges in providing a reusable and scalable implementation model for complex structures and methods. Moreover, due to the limiting factors of C, the reference implementation of CGP does not provide a generic framework and is therefore restricted to a set of predefined evaluation types. Besides the reference implementation, we also observe that other existing implementations are limited with respect to the features provided. In this work, we therefore propose the first version of a modern C++ implementation of CGP that pursues object-oriented design and generic programming paradigm to provide an efficient implementation model that can facilitate the discovery of new problem domains and the implementation of complex advanced methods that have been proposed for CGP over time. With the proposal of our new implementation, we aim to generally promote interpretability, accessibility and reproducibility in the field of CGP.
From Biased to Unbiased Dynamics: An Infinitesimal Generator Approach
Authors: Timothée Devergne, Vladimir Kostic, Michele Parrinello, Massimiliano Pontil
Date: 2024-06-13 00:00:00

We investigate learning the eigenfunctions of evolution operators for time-reversal invariant stochastic processes, a prime example being the Langevin equation used in molecular dynamics. Many physical or chemical processes described by this equation involve transitions between metastable states separated by high potential barriers that can hardly be crossed during a simulation. To overcome this bottleneck, data are collected via biased simulations that explore the state space more rapidly. We propose a framework for learning from biased simulations rooted in the infinitesimal generator of the process and the associated resolvent operator. We contrast our approach to more common ones based on the transfer operator, showing that it can provably learn the spectral properties of the unbiased system from biased data. In experiments, we highlight the advantages of our method over transfer operator approaches and recent developments based on generator learning, demonstrating its effectiveness in estimating eigenfunctions and eigenvalues. Importantly, we show that even with datasets containing only a few relevant transitions due to sub-optimal biasing, our approach recovers relevant information about the transition mechanism.
Schur's Positive-Definite Network: Deep Learning in the SPD cone with structure
Authors: Can Pouliquen, Mathurin Massias, Titouan Vayer
Date: 2024-06-13 00:00:00
Tasks: Graph Learning, Inductive Bias

Estimating matrices in the symmetric positive-definite (SPD) cone is of interest for many applications ranging from computer vision to graph learning. While there exist various convex optimization-based estimators, they remain limited in expressivity due to their model-based approach. The success of deep learning motivates the use of learning-based approaches to estimate SPD matrices with neural networks in a data-driven fashion. However, designing effective neural architectures for SPD learning is challenging, particularly when the task requires additional structural constraints, such as element-wise sparsity. Current approaches either do not ensure that the output meets all desired properties or lack expressivity. In this paper, we introduce SpodNet, a novel and generic learning module that guarantees SPD outputs and supports additional structural constraints. Notably, it solves the challenging task of learning jointly SPD and sparse matrices. Our experiments illustrate the versatility and relevance of SpodNet layers for such applications.
BTS: Building Timeseries Dataset: Empowering Large-Scale Building Analytics
Authors: Arian Prabowo, Xiachong Lin, Imran Razzak, Hao Xue, Emily W. Yap, Matthew Amos, Flora D. Salim
Date: 2024-06-13 00:00:00
Tasks: Benchmarking

Buildings play a crucial role in human well-being, influencing occupant comfort, health, and safety. Additionally, they contribute significantly to global energy consumption, accounting for one-third of total energy usage, and carbon emissions. Optimizing building performance presents a vital opportunity to combat climate change and promote human flourishing. However, research in building analytics has been hampered by the lack of accessible, available, and comprehensive real-world datasets on multiple building operations. In this paper, we introduce the Building TimeSeries (BTS) dataset. Our dataset covers three buildings over a three-year period, comprising more than ten thousand timeseries data points with hundreds of unique ontologies. Moreover, the metadata is standardized using the Brick schema. To demonstrate the utility of this dataset, we performed benchmarks on two tasks: timeseries ontology classification and zero-shot forecasting. These tasks represent an essential initial step in addressing challenges related to interoperability in building analytics. Access to the dataset and the code used for benchmarking are available here: https://github.com/cruiseresearchgroup/DIEF_BTS .
From Theory to Therapy: Reframing SBDD Model Evaluation via Practical Metrics
Authors: Bowen Gao, Haichuan Tan, Yanwen Huang, Minsi Ren, Xiao Huang, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan
Date: 2024-06-13 00:00:00
Tasks: Drug Design, Drug Discovery

Recent advancements in structure-based drug design (SBDD) have significantly enhanced the efficiency and precision of drug discovery by generating molecules tailored to bind specific protein pockets. Despite these technological strides, their practical application in real-world drug development remains challenging due to the complexities of synthesizing and testing these molecules. The reliability of the Vina docking score, the current standard for assessing binding abilities, is increasingly questioned due to its susceptibility to overfitting. To address these limitations, we propose a comprehensive evaluation framework that includes assessing the similarity of generated molecules to known active compounds, introducing a virtual screening-based metric for practical deployment capabilities, and re-evaluating binding affinity more rigorously. Our experiments reveal that while current SBDD models achieve high Vina scores, they fall short in practical usability metrics, highlighting a significant gap between theoretical predictions and real-world applicability. Our proposed metrics and dataset aim to bridge this gap, enhancing the practical applicability of future SBDD models and aligning them more closely with the needs of pharmaceutical research and development.
SIU: A Million-Scale Structural Small Molecule-Protein Interaction Dataset for Unbiased Bioactivity Prediction
Authors: Yanwen Huang, Bowen Gao, Yinjun Jia, Hongbo Ma, Wei-Ying Ma, Ya-Qin Zhang, Yanyan Lan
Date: 2024-06-13 00:00:00
Tasks: Prediction

Small molecules play a pivotal role in modern medicine, and scrutinizing their interactions with protein targets is essential for the discovery and development of novel, life-saving therapeutics. The term "bioactivity" encompasses various biological effects resulting from these interactions, including both binding and functional responses. The magnitude of bioactivity dictates the therapeutic or toxic pharmacological outcomes of small molecules, rendering accurate bioactivity prediction crucial for the development of safe and effective drugs. However, existing structural datasets of small molecule-protein interactions are often limited in scale and lack systematically organized bioactivity labels, thereby impeding our understanding of these interactions and precise bioactivity prediction. In this study, we introduce a comprehensive dataset of small molecule-protein interactions, consisting of over a million binding structures, each annotated with real biological activity labels. This dataset is designed to facilitate unbiased bioactivity prediction. We evaluated several classical models on this dataset, and the results demonstrate that the task of unbiased bioactivity prediction is challenging yet essential.
An Unsupervised Approach to Achieve Supervised-Level Explainability in Healthcare Records
Authors: Joakim Edin, Maria Maistro, Lars Maaløe, Lasse Borgholt, Jakob D. Havtorn, Tuukka Ruotsalo
Date: 2024-06-13 00:00:00
Tasks: Adversarial Robustness, Explainable Artificial Intelligence (XAI), Feature Importance, Medical Code Prediction

Electronic healthcare records are vital for patient safety as they document conditions, plans, and procedures in both free text and medical codes. Language models have significantly enhanced the processing of such records, streamlining workflows and reducing manual data entry, thereby saving healthcare providers significant resources. However, the black-box nature of these models often leaves healthcare professionals hesitant to trust them. State-of-the-art explainability methods increase model transparency but rely on human-annotated evidence spans, which are costly. In this study, we propose an approach to produce plausible and faithful explanations without needing such annotations. We demonstrate on the automated medical coding task that adversarial robustness training improves explanation plausibility and introduce AttInGrad, a new explanation method superior to previous ones. By combining both contributions in a fully unsupervised setup, we produce explanations of comparable quality, or better, to that of a supervised approach. We release our code and model weights.
Mirror and Preconditioned Gradient Descent in Wasserstein Space
Authors: Clément Bonet, Théo Uscidda, Adam David, Pierre-Cyril Aubin-Frankowski, Anna Korba
Date: 2024-06-13 00:00:00

As the problem of minimizing functionals on the Wasserstein space encompasses many applications in machine learning, different optimization algorithms on $\mathbb{R}^d$ have received their counterpart analog on the Wasserstein space. We focus here on lifting two explicit algorithms: mirror descent and preconditioned gradient descent. These algorithms have been introduced to better capture the geometry of the function to minimize and are provably convergent under appropriate (namely relative) smoothness and convexity conditions. Adapting these notions to the Wasserstein space, we prove guarantees of convergence of some Wasserstein-gradient-based discrete-time schemes for new pairings of objective functionals and regularizers. The difficulty here is to carefully select along which curves the functionals should be smooth and convex. We illustrate the advantages of adapting the geometry induced by the regularizer on ill-conditioned optimization tasks, and showcase the improvement of choosing different discrepancies and geometries in a computational biology task of aligning single-cells.
LaCoOT: Layer Collapse through Optimal Transport
Authors: Victor Quétu, Nour Hezbri, Enzo Tartaglione
Date: 2024-06-13 00:00:00
Tasks: image-classification, Image Classification

Although deep neural networks are well-known for their remarkable performance in tackling complex tasks, their hunger for computational resources remains a significant hurdle, posing energy-consumption issues and restricting their deployment on resource-constrained devices, which stalls their widespread adoption. In this paper, we present an optimal transport method to reduce the depth of over-parametrized deep neural networks, alleviating their computational burden. More specifically, we propose a new regularization strategy based on the Max-Sliced Wasserstein distance to minimize the distance between the intermediate feature distributions in the neural network. We show that minimizing this distance enables the complete removal of intermediate layers in the network, with almost no performance loss and without requiring any finetuning. We assess the effectiveness of our method on traditional image classification setups. We commit to releasing the source code upon acceptance of the article.
Predicting Fault-Ride-Through Probability of Inverter-Dominated Power Grids using Machine Learning
Authors: Christian Nauck, Anna Büttner, Sebastian Liemann, Frank Hellmann, Michael Lindner
Date: 2024-06-13 00:00:00

Due to the increasing share of renewables, the analysis of the dynamical behavior of power grids gains importance. Effective risk assessments necessitate the analysis of large number of fault scenarios. The computational costs inherent in dynamic simulations impose constraints on the number of configurations that can be analyzed. Machine Learning (ML) has proven to efficiently predict complex power grid properties. Hence, we analyze the potential of ML for predicting dynamic stability of future power grids with large shares of inverters. For this purpose, we generate a new dataset consisting of synthetic power grid models and perform dynamical simulations. As targets for the ML training, we calculate the fault-ride-through probability, which we define as the probability of staying within a ride-through curve after a fault at a bus has been cleared. Importantly, we demonstrate that ML models accurately predict the fault-ride-through probability of synthetic power grids. Finally, we also show that the ML models generalize to an IEEE-96 Test System, which emphasizes the potential of deploying ML methods to study probabilistic stability of power grids.
Transcription-Free Fine-Tuning of Speech Separation Models for Noisy and Reverberant Multi-Speaker Automatic Speech Recognition
Authors: William Ravenscroft, George Close, Stefan Goetze, Thomas Hain, Mohammad Soleymanpour, Anurag Chowdhury, Mark C. Fuhs
Date: 2024-06-13 00:00:00
Tasks: Automatic Speech Recognition, Automatic Speech Recognition (ASR), speech-recognition, Speech Recognition, Speech Separation

One solution to automatic speech recognition (ASR) of overlapping speakers is to separate speech and then perform ASR on the separated signals. Commonly, the separator produces artefacts which often degrade ASR performance. Addressing this issue typically requires reference transcriptions to jointly train the separation and ASR networks. This is often not viable for training on real-world in-domain audio where reference transcript information is not always available. This paper proposes a transcription-free method for joint training using only audio signals. The proposed method uses embedding differences of pre-trained ASR encoders as a loss with a proposed modification to permutation invariant training (PIT) called guided PIT (GPIT). The method achieves a 6.4% improvement in word error rate (WER) measures over a signal-level loss and also shows enhancement improvements in perceptual measures such as short-time objective intelligibility (STOI).
AdaPTwin: Low-Cost Adaptive Compression of Product Twins in Transformers
Authors: Emil Biju, Anirudh Sriram, Mert Pilanci
Date: 2024-06-13 00:00:00
Tasks: speech-recognition, Speech Recognition

While large transformer-based models have exhibited remarkable performance in speaker-independent speech recognition, their large size and computational requirements make them expensive or impractical to use in resource-constrained settings. In this work, we propose a low-rank adaptive compression technique called AdaPTwin that jointly compresses product-dependent pairs of weight matrices in the transformer attention layer. Our approach can prioritize the compressed model's performance on a specific speaker while maintaining generalizability to new speakers and acoustic conditions. Notably, our technique requires only 8 hours of speech data for fine-tuning, which can be accomplished in under 20 minutes, making it highly cost-effective compared to other compression methods. We demonstrate the efficacy of our approach by compressing the Whisper and Distil-Whisper models by up to 45% while incurring less than a 2% increase in word error rate.
Motif-driven Subgraph Structure Learning for Graph Classification
Authors: Zhiyao Zhou, Sheng Zhou, Bochao Mao, Jiawei Chen, Qingyun Sun, Yan Feng, Chun Chen, Can Wang
Date: 2024-06-13 00:00:00
Tasks: Classification, Graph Classification, Graph structure learning

To mitigate the suboptimal nature of graph structure, Graph Structure Learning (GSL) has emerged as a promising approach to improve graph structure and boost performance in downstream tasks. Despite the proposal of numerous GSL methods, the progresses in this field mostly concentrated on node-level tasks, while graph-level tasks (e.g., graph classification) remain largely unexplored. Notably, applying node-level GSL to graph classification is non-trivial due to the lack of find-grained guidance for intricate structure learning. Inspired by the vital role of subgraph in graph classification, in this paper we explore the potential of subgraph structure learning for graph classification by tackling the challenges of key subgraph selection and structure optimization. We propose a novel Motif-driven Subgraph Structure Learning method for Graph Classification (MOSGSL). Specifically, MOSGSL incorporates a subgraph structure learning module which can adaptively select important subgraphs. A motif-driven structure guidance module is further introduced to capture key subgraph-level structural patterns (motifs) and facilitate personalized structure learning. Extensive experiments demonstrate a significant and consistent improvement over baselines, as well as its flexibility and generalizability for various backbones and learning procedures.
CIMRL: Combining IMitation and Reinforcement Learning for Safe Autonomous Driving
Authors: Jonathan Booher, Khashayar Rohanimanesh, Junhong Xu, Vladislav Isenbaev, Ashwin Balakrishna, Ishan Gupta, Wei Liu, Aleksandr Petiushko
Date: 2024-06-13 00:00:00
Tasks: Autonomous Driving, Autonomous Vehicles, Imitation Learning, reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL), Safe Reinforcement Learning

Modern approaches to autonomous driving rely heavily on learned components trained with large amounts of human driving data via imitation learning. However, these methods require large amounts of expensive data collection and even then face challenges with safely handling long-tail scenarios and compounding errors over time. At the same time, pure Reinforcement Learning (RL) methods can fail to learn performant policies in sparse, constrained, and challenging-to-define reward settings such as autonomous driving. Both of these challenges make deploying purely cloned or pure RL policies in safety critical applications such as autonomous vehicles challenging. In this paper we propose Combining IMitation and Reinforcement Learning (CIMRL) approach - a safe reinforcement learning framework that enables training driving policies in simulation through leveraging imitative motion priors and safety constraints. CIMRL does not require extensive reward specification and improves on the closed loop behavior of pure cloning methods. By combining RL and imitation, we demonstrate that our method achieves state-of-the-art results in closed loop simulation and real world driving benchmarks.
Cognitively Inspired Energy-Based World Models
Authors: Alexi Gladstone, Ganesh Nanduru, Md Mofijul Islam, Aman Chadha, Jundong Li, Tariq Iqbal
Date: 2024-06-13 00:00:00
Tasks: GPU

One of the predominant methods for training world models is autoregressive prediction in the output space of the next element of a sequence. In Natural Language Processing (NLP), this takes the form of Large Language Models (LLMs) predicting the next token; in Computer Vision (CV), this takes the form of autoregressive models predicting the next frame/token/pixel. However, this approach differs from human cognition in several respects. First, human predictions about the future actively influence internal cognitive processes. Second, humans naturally evaluate the plausibility of predictions regarding future states. Based on this capability, and third, by assessing when predictions are sufficient, humans allocate a dynamic amount of time to make a prediction. This adaptive process is analogous to System 2 thinking in psychology. All these capabilities are fundamental to the success of humans at high-level reasoning and planning. Therefore, to address the limitations of traditional autoregressive models lacking these human-like capabilities, we introduce Energy-Based World Models (EBWM). EBWM involves training an Energy-Based Model (EBM) to predict the compatibility of a given context and a predicted future state. In doing so, EBWM enables models to achieve all three facets of human cognition described. Moreover, we developed a variant of the traditional autoregressive transformer tailored for Energy-Based models, termed the Energy-Based Transformer (EBT). Our results demonstrate that EBWM scales better with data and GPU Hours than traditional autoregressive transformers in CV, and that EBWM offers promising early scaling in NLP. Consequently, this approach offers an exciting path toward training future models capable of System 2 thinking and intelligently searching across state spaces.