pwc-archive/papers-with-abstracts huggingface dataset:
Spatial Pathomics Toolkit for Quantitative Analysis of Podocyte Nuclei with Histology and Spatial Transcriptomics Data in Renal Pathology
Authors: Jiayuan Chen, Yu Wang, Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Yilin Liu, Jianyong Zhong, Agnes B. Fogo, Haichun Yang, Shilin Zhao, Yuankai Huo
Date: 2023-08-10 00:00:00
Tasks: Semantic Segmentation, whole slide images

Podocytes, specialized epithelial cells that envelop the glomerular capillaries, play a pivotal role in maintaining renal health. The current description and quantification of features on pathology slides are limited, prompting the need for innovative solutions to comprehensively assess diverse phenotypic attributes within Whole Slide Images (WSIs). In particular, understanding the morphological characteristics of podocytes, terminally differentiated glomerular epithelial cells, is crucial for studying glomerular injury. This paper introduces the Spatial Pathomics Toolkit (SPT) and applies it to podocyte pathomics. The SPT consists of three main components: (1) instance object segmentation, enabling precise identification of podocyte nuclei; (2) pathomics feature generation, extracting a comprehensive array of quantitative features from the identified nuclei; and (3) robust statistical analyses, facilitating a comprehensive exploration of spatial relationships between morphological and spatial transcriptomics features.The SPT successfully extracted and analyzed morphological and textural features from podocyte nuclei, revealing a multitude of podocyte morphomic features through statistical analysis. Additionally, we demonstrated the SPT's ability to unravel spatial information inherent to podocyte distribution, shedding light on spatial patterns associated with glomerular injury. By disseminating the SPT, our goal is to provide the research community with a powerful and user-friendly resource that advances cellular spatial pathomics in renal pathology. The implementation and its complete source code of the toolkit are made openly accessible at https://github.com/hrlblab/spatial_pathomics.
DiffSED: Sound Event Detection with Denoising Diffusion
Authors: Swapnil Bhosale, Sauradip Nag, Diptesh Kanojia, Jiankang Deng, Xiatian Zhu
Date: 2023-08-14 00:00:00
Tasks: Decoder, Denoising, Event Detection, Sound Event Detection

Sound Event Detection (SED) aims to predict the temporal boundaries of all the events of interest and their class labels, given an unconstrained audio sample. Taking either the splitand-classify (i.e., frame-level) strategy or the more principled event-level modeling approach, all existing methods consider the SED problem from the discriminative learning perspective. In this work, we reformulate the SED problem by taking a generative learning perspective. Specifically, we aim to generate sound temporal boundaries from noisy proposals in a denoising diffusion process, conditioned on a target audio sample. During training, our model learns to reverse the noising process by converting noisy latent queries to the groundtruth versions in the elegant Transformer decoder framework. Doing so enables the model generate accurate event boundaries from even noisy queries during inference. Extensive experiments on the Urban-SED and EPIC-Sounds datasets demonstrate that our model significantly outperforms existing alternatives, with 40+% faster convergence in training.
The Devil is in the Errors: Leveraging Large Language Models for Fine-grained Machine Translation Evaluation
Authors: Patrick Fernandes, Daniel Deutsch, Mara Finkelstein, Parker Riley, André F. T. Martins, Graham Neubig, Ankush Garg, Jonathan H. Clark, Markus Freitag, Orhan Firat
Date: 2023-08-14 00:00:00
Tasks: In-Context Learning, Informativeness, Machine Translation

Automatic evaluation of machine translation (MT) is a critical tool driving the rapid iterative development of MT systems. While considerable progress has been made on estimating a single scalar quality score, current metrics lack the informativeness of more detailed schemes that annotate individual errors, such as Multidimensional Quality Metrics (MQM). In this paper, we help fill this gap by proposing AutoMQM, a prompting technique which leverages the reasoning and in-context learning capabilities of large language models (LLMs) and asks them to identify and categorize errors in translations. We start by evaluating recent LLMs, such as PaLM and PaLM-2, through simple score prediction prompting, and we study the impact of labeled data through in-context learning and finetuning. We then evaluate AutoMQM with PaLM-2 models, and we find that it improves performance compared to just prompting for scores (with particularly large gains for larger models) while providing interpretability through error spans that align with human annotations.
Dialogue for Prompting: a Policy-Gradient-Based Discrete Prompt Generation for Few-shot Learning
Authors: Chengzhengxu Li, Xiaoming Liu, Yichen Wang, Duyi Li, Yu Lan, Chao Shen
Date: 2023-08-14 00:00:00
Tasks: Few-Shot Learning, Reinforcement Learning (RL)

Prompt-based pre-trained language models (PLMs) paradigm have succeeded substantially in few-shot natural language processing (NLP) tasks. However, prior discrete prompt optimization methods require expert knowledge to design the base prompt set and identify high-quality prompts, which is costly, inefficient, and subjective. Meanwhile, existing continuous prompt optimization methods improve the performance by learning the ideal prompts through the gradient information of PLMs, whose high computational cost, and low readability and generalizability are often concerning. To address the research gap, we propose a Dialogue-comprised Policy-gradient-based Discrete Prompt Optimization ($DP_2O$) method. We first design a multi-round dialogue alignment strategy for readability prompt set generation based on GPT-4. Furthermore, we propose an efficient prompt screening metric to identify high-quality prompts with linear complexity. Finally, we construct a reinforcement learning (RL) framework based on policy gradients to match the prompts to inputs optimally. By training a policy network with only 0.67% of the PLM parameter size on the tasks in the few-shot setting, $DP_2O$ outperforms the state-of-the-art (SOTA) method by 1.52% in accuracy on average on four open-source datasets. Moreover, subsequent experiments also demonstrate that $DP_2O$ has good universality, robustness, and generalization ability.
LCE: An Augmented Combination of Bagging and Boosting in Python
Authors: Kevin Fauvel, Élisa Fromont, Véronique Masson, Philippe Faverdin, Alexandre Termier
Date: 2023-08-14 00:00:00
Tasks: Model Selection, regression

lcensemble is a high-performing, scalable and user-friendly Python package for the general tasks of classification and regression. The package implements Local Cascade Ensemble (LCE), a machine learning method that further enhances the prediction performance of the current state-of-the-art methods Random Forest and XGBoost. LCE combines their strengths and adopts a complementary diversification approach to obtain a better generalizing predictor. The package is compatible with scikit-learn, therefore it can interact with scikit-learn pipelines and model selection tools. It is distributed under the Apache 2.0 license, and its source code is available at https://github.com/LocalCascadeEnsemble/LCE.
A Unifying Generator Loss Function for Generative Adversarial Networks
Authors: Justin Veiner, Fady Alajaji, Bahman Gharesifard
Date: 2023-08-14 00:00:00
Tasks: Generative Adversarial Network

A unifying $\alpha$-parametrized generator loss function is introduced for a dual-objective generative adversarial network (GAN), which uses a canonical (or classical) discriminator loss function such as the one in the original GAN (VanillaGAN) system. The generator loss function is based on a symmetric class probability estimation type function, $\mathcal{L}_\alpha$, and the resulting GAN system is termed $\mathcal{L}_\alpha$-GAN. Under an optimal discriminator, it is shown that the generator's optimization problem consists of minimizing a Jensen-$f_\alpha$-divergence, a natural generalization of the Jensen-Shannon divergence, where $f_\alpha$ is a convex function expressed in terms of the loss function $\mathcal{L}_\alpha$. It is also demonstrated that this $\mathcal{L}_\alpha$-GAN problem recovers as special cases a number of GAN problems in the literature, including VanillaGAN, Least Squares GAN (LSGAN), Least $k$th order GAN (L$k$GAN) and the recently introduced $(\alpha_D,\alpha_G)$-GAN with $\alpha_D=1$. Finally, experimental results are conducted on three datasets, MNIST, CIFAR-10, and Stacked MNIST to illustrate the performance of various examples of the $\mathcal{L}_\alpha$-GAN system.
gSASRec: Reducing Overconfidence in Sequential Recommendation Trained with Negative Sampling
Authors: Aleksandr Petrov, Craig Macdonald
Date: 2023-08-14 00:00:00
Tasks: Sequential Recommendation

A large catalogue size is one of the central challenges in training recommendation models: a large number of items makes them memory and computationally inefficient to compute scores for all items during training, forcing these models to deploy negative sampling. However, negative sampling increases the proportion of positive interactions in the training data, and therefore models trained with negative sampling tend to overestimate the probabilities of positive interactions a phenomenon we call overconfidence. While the absolute values of the predicted scores or probabilities are not important for the ranking of retrieved recommendations, overconfident models may fail to estimate nuanced differences in the top-ranked items, resulting in degraded performance. In this paper, we show that overconfidence explains why the popular SASRec model underperforms when compared to BERT4Rec. This is contrary to the BERT4Rec authors explanation that the difference in performance is due to the bi-directional attention mechanism. To mitigate overconfidence, we propose a novel Generalised Binary Cross-Entropy Loss function (gBCE) and theoretically prove that it can mitigate overconfidence. We further propose the gSASRec model, an improvement over SASRec that deploys an increased number of negatives and the gBCE loss. We show through detailed experiments on three datasets that gSASRec does not exhibit the overconfidence problem. As a result, gSASRec can outperform BERT4Rec (e.g. +9.47% NDCG on the MovieLens-1M dataset), while requiring less training time (e.g. -73% training time on MovieLens-1M). Moreover, in contrast to BERT4Rec, gSASRec is suitable for large datasets that contain more than 1 million items.
Efficient Learning of Quantum States Prepared With Few Non-Clifford Gates II: Single-Copy Measurements
Authors: Sabee Grewal, Vishnu Iyer, William Kretschmer, Daniel Liang
Date: 2023-08-14 00:00:00

Recent work has shown that $n$-qubit quantum states output by circuits with at most $t$ single-qubit non-Clifford gates can be learned to trace distance $\epsilon$ using $\mathsf{poly}(n,2^t,1/\epsilon)$ time and samples. All prior algorithms achieving this runtime use entangled measurements across two copies of the input state. In this work, we give a similarly efficient algorithm that learns the same class of states using only single-copy measurements.
Human Voice Pitch Estimation: A Convolutional Network with Auto-Labeled and Synthetic Data
Authors: Jeremy Cochoy
Date: 2023-08-14 00:00:00

In the domain of music and sound processing, pitch extraction plays a pivotal role. Our research presents a specialized convolutional neural network designed for pitch extraction, particularly from the human singing voice in acapella performances. Notably, our approach combines synthetic data with auto-labeled acapella sung audio, creating a robust training environment. Evaluation across datasets comprising synthetic sounds, opera recordings, and time-stretched vowels demonstrates its efficacy. This work paves the way for enhanced pitch extraction in both music and voice settings.
Pairing interacting protein sequences using masked language modeling
Authors: Umberto Lupo, Damiano Sgarbossa, Anne-Florence Bitbol
Date: 2023-08-14 00:00:00
Tasks: Language Modeling, Language Modelling, Masked Language Modeling, Protein Language Model

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids. We show that it captures inter-chain coevolution, while it was trained on single-chain data, which means that it can be used out-of-distribution. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer, without significantly deteriorating any of those we tested. It also achieves competitive performance with using orthology-based pairing.
Active Bird2Vec: Towards End-to-End Bird Sound Monitoring with Transformers
Authors: Lukas Rauch, Raphael Schwinger, Moritz Wirth, Bernhard Sick, Sven Tomforde, Christoph Scholz
Date: 2023-08-14 00:00:00
Tasks: Active Learning, Decision Making

We propose a shift towards end-to-end learning in bird sound monitoring by combining self-supervised (SSL) and deep active learning (DAL). Leveraging transformer models, we aim to bypass traditional spectrogram conversions, enabling direct raw audio processing. ActiveBird2Vec is set to generate high-quality bird sound representations through SSL, potentially accelerating the assessment of environmental changes and decision-making processes for wind farms. Additionally, we seek to utilize the wide variety of bird vocalizations through DAL, reducing the reliance on extensively labeled datasets by human experts. We plan to curate a comprehensive set of tasks through Huggingface Datasets, enhancing future comparability and reproducibility of bioacoustic research. A comparative analysis between various transformer models will be conducted to evaluate their proficiency in bird sound recognition tasks. We aim to accelerate the progression of avian bioacoustic research and contribute to more effective conservation strategies.
Neural radiance fields in the industrial and robotics domain: applications, research opportunities and use cases
Authors: Eugen Šlapak, Enric Pardo, Matúš Dopiriak, Taras Maksymyuk, Juraj Gazda
Date: 2023-08-14 00:00:00
Tasks: Collision Avoidance, Motion Estimation, NeRF, SSIM, Video Compression

The proliferation of technologies, such as extended reality (XR), has increased the demand for high-quality three-dimensional (3D) graphical representations. Industrial 3D applications encompass computer-aided design (CAD), finite element analysis (FEA), scanning, and robotics. However, current methods employed for industrial 3D representations suffer from high implementation costs and reliance on manual human input for accurate 3D modeling. To address these challenges, neural radiance fields (NeRFs) have emerged as a promising approach for learning 3D scene representations based on provided training 2D images. Despite a growing interest in NeRFs, their potential applications in various industrial subdomains are still unexplored. In this paper, we deliver a comprehensive examination of NeRF industrial applications while also providing direction for future research endeavors. We also present a series of proof-of-concept experiments that demonstrate the potential of NeRFs in the industrial domain. These experiments include NeRF-based video compression techniques and using NeRFs for 3D motion estimation in the context of collision avoidance. In the video compression experiment, our results show compression savings up to 48\% and 74\% for resolutions of 1920x1080 and 300x168, respectively. The motion estimation experiment used a 3D animation of a robotic arm to train Dynamic-NeRF (D-NeRF) and achieved an average peak signal-to-noise ratio (PSNR) of disparity map with the value of 23 dB and an structural similarity index measure (SSIM) 0.97.
iSTFTNet2: Faster and More Lightweight iSTFT-Based Neural Vocoder Using 1D-2D CNN
Authors: Takuhiro Kaneko, Hirokazu Kameoka, Kou Tanaka, Shogo Seki
Date: 2023-08-14 00:00:00
Tasks: Speech Synthesis

The inverse short-time Fourier transform network (iSTFTNet) has garnered attention owing to its fast, lightweight, and high-fidelity speech synthesis. It obtains these characteristics using a fast and lightweight 1D CNN as the backbone and replacing some neural processes with iSTFT. Owing to the difficulty of a 1D CNN to model high-dimensional spectrograms, the frequency dimension is reduced via temporal upsampling. However, this strategy compromises the potential to enhance the speed. Therefore, we propose iSTFTNet2, an improved variant of iSTFTNet with a 1D-2D CNN that employs 1D and 2D CNNs to model temporal and spectrogram structures, respectively. We designed a 2D CNN that performs frequency upsampling after conversion in a few-frequency space. This design facilitates the modeling of high-dimensional spectrograms without compromising the speed. The results demonstrated that iSTFTNet2 made iSTFTNet faster and more lightweight with comparable speech quality. Audio samples are available at https://www.kecl.ntt.co.jp/people/kaneko.takuhiro/projects/istftnet2/.
Fourier neural operator for learning solutions to macroscopic traffic flow models: Application to the forward and inverse problems
Authors: Bilal Thonnam Thodi, Sai Venkata Ramana Ambadipudi, Saif Eddin Jabari
Date: 2023-08-14 00:00:00

Deep learning methods are emerging as popular computational tools for solving forward and inverse problems in traffic flow. In this paper, we study a neural operator framework for learning solutions to nonlinear hyperbolic partial differential equations with applications in macroscopic traffic flow models. In this framework, an operator is trained to map heterogeneous and sparse traffic input data to the complete macroscopic traffic state in a supervised learning setting. We chose a physics-informed Fourier neural operator ($\pi$-FNO) as the operator, where an additional physics loss based on a discrete conservation law regularizes the problem during training to improve the shock predictions. We also propose to use training data generated from random piecewise constant input data to systematically capture the shock and rarefied solutions. From experiments using the LWR traffic flow model, we found superior accuracy in predicting the density dynamics of a ring-road network and urban signalized road. We also found that the operator can be trained using simple traffic density dynamics, e.g., consisting of $2-3$ vehicle queues and $1-2$ traffic signal cycles, and it can predict density dynamics for heterogeneous vehicle queue distributions and multiple traffic signal cycles $(\geq 2)$ with an acceptable error. The extrapolation error grew sub-linearly with input complexity for a proper choice of the model architecture and training data. Adding a physics regularizer aided in learning long-term traffic density dynamics, especially for problems with periodic boundary data.
UIPC-MF: User-Item Prototype Connection Matrix Factorization for Explainable Collaborative Filtering
Authors: Lei Pan, Von-Wun Soo
Date: 2023-08-14 00:00:00
Tasks: Collaborative Filtering

Recommending items to potentially interested users has been an important commercial task that faces two main challenges: accuracy and explainability. While most collaborative filtering models rely on statistical computations on a large scale of interaction data between users and items and can achieve high performance, they often lack clear explanatory power. We propose UIPC-MF, a prototype-based matrix factorization method for explainable collaborative filtering recommendations. In UIPC-MF, both users and items are associated with sets of prototypes, capturing general collaborative attributes. To enhance explainability, UIPC-MF learns connection weights that reflect the associative relations between user and item prototypes for recommendations. UIPC-MF outperforms other prototype-based baseline methods in terms of Hit Ratio and Normalized Discounted Cumulative Gain on three datasets, while also providing better transparency.
No Regularization is Needed: An Efficient and Effective Model for Incomplete Label Distribution Learning
Authors: Xiang Li, Songcan Chen
Date: 2023-08-14 00:00:00
Tasks: Model Selection

Label Distribution Learning (LDL) assigns soft labels, a.k.a. degrees, to a sample. In reality, it is always laborious to obtain complete degrees, giving birth to the Incomplete LDL (InLDL). However, InLDL often suffers from performance degeneration. To remedy it, existing methods need one or more explicit regularizations, leading to burdensome parameter tuning and extra computation. We argue that label distribution itself may provide useful prior, when used appropriately, the InLDL problem can be solved without any explicit regularization. In this paper, we offer a rational alternative to use such a prior. Our intuition is that large degrees are likely to get more concern, the small ones are easily overlooked, whereas the missing degrees are completely neglected in InLDL. To learn an accurate label distribution, it is crucial not to ignore the small observed degrees but to give them properly large weights, while gradually increasing the weights of the missing degrees. To this end, we first define a weighted empirical risk and derive upper bounds between the expected risk and the weighted empirical risk, which reveals in principle that weighting plays an implicit regularization role. Then, by using the prior of degrees, we design a weighted scheme and verify its effectiveness. To sum up, our model has four advantages, it is 1) model selection free, as no explicit regularization is imposed; 2) with closed form solution (sub-problem) and easy-to-implement (a few lines of codes); 3) with linear computational complexity in the number of samples, thus scalable to large datasets; 4) competitive with state-of-the-arts even without any explicit regularization.