pwc-archive/papers-with-abstracts huggingface dataset:
DEL-Dock: Molecular Docking-Enabled Modeling of DNA-Encoded Libraries
Authors: Kirill Shmilovich, Benson Chen, Theofanis Karaletsos, Mohammad M. Sultan
Date: 2022-11-30 00:00:00
Tasks: Denoising, Molecular Docking

DNA-Encoded Library (DEL) technology has enabled significant advances in hit identification by enabling efficient testing of combinatorially-generated molecular libraries. DEL screens measure protein binding affinity though sequencing reads of molecules tagged with unique DNA-barcodes that survive a series of selection experiments. Computational models have been deployed to learn the latent binding affinities that are correlated to the sequenced count data; however, this correlation is often obfuscated by various sources of noise introduced in its complicated data-generation process. In order to denoise DEL count data and screen for molecules with good binding affinity, computational models require the correct assumptions in their modeling structure to capture the correct signals underlying the data. Recent advances in DEL models have focused on probabilistic formulations of count data, but existing approaches have thus far been limited to only utilizing 2-D molecule-level representations. We introduce a new paradigm, DEL-Dock, that combines ligand-based descriptors with 3-D spatial information from docked protein-ligand complexes. 3-D spatial information allows our model to learn over the actual binding modality rather than using only structured-based information of the ligand. We show that our model is capable of effectively denoising DEL count data to predict molecule enrichment scores that are better correlated with experimental binding affinity measurements compared to prior works. Moreover, by learning over a collection of docked poses we demonstrate that our model, trained only on DEL data, implicitly learns to perform good docking pose selection without requiring external supervision from expensive-to-source protein crystal structures.
Answering Private Linear Queries Adaptively using the Common Mechanism
Authors: Yingtai Xiao, Guanhong Wang, Danfeng Zhang, Daniel Kifer
Date: 2022-11-30 00:00:00

When analyzing confidential data through a privacy filter, a data scientist often needs to decide which queries will best support their intended analysis. For example, an analyst may wish to study noisy two-way marginals in a dataset produced by a mechanism M1. But, if the data are relatively sparse, the analyst may choose to examine noisy one-way marginals, produced by a mechanism M2 instead. Since the choice of whether to use M1 or M2 is data-dependent, a typical differentially private workflow is to first split the privacy loss budget rho into two parts: rho1 and rho2, then use the first part rho1 to determine which mechanism to use, and the remainder rho2 to obtain noisy answers from the chosen mechanism. In a sense, the first step seems wasteful because it takes away part of the privacy loss budget that could have been used to make the query answers more accurate. In this paper, we consider the question of whether the choice between M1 and M2 can be performed without wasting any privacy loss budget. For linear queries, we propose a method for decomposing M1 and M2 into three parts: (1) a mechanism M* that captures their shared information, (2) a mechanism M1' that captures information that is specific to M1, (3) a mechanism M2' that captures information that is specific to M2. Running M* and M1' together is completely equivalent to running M1 (both in terms of query answer accuracy and total privacy cost rho). Similarly, running M* and M2' together is completely equivalent to running M2. Since M* will be used no matter what, the analyst can use its output to decide whether to subsequently run M1'(thus recreating the analysis supported by M1) or M2'(recreating the analysis supported by M2), without wasting privacy loss budget.
Universal Neural Optimal Transport
Authors: Jonathan Geuter, Gregor Kornhardt, Ingimar Tomasson, Vaios Laschos
Date: 2022-11-30 00:00:00

Optimal Transport (OT) problems are a cornerstone of many applications, but solving them is computationally expensive. To address this problem, we propose UNOT (Universal Neural Optimal Transport), a novel framework capable of accurately predicting (entropic) OT distances and plans between discrete measures for a given cost function. UNOT builds on Fourier Neural Operators, a universal class of neural networks that map between function spaces and that are discretization-invariant, which enables our network to process measures of variable resolutions. The network is trained adversarially using a second, generating network and a self-supervised bootstrapping loss. We ground UNOT in an extensive theoretical framework. Through experiments on Euclidean and non-Euclidean domains, we show that our network not only accurately predicts OT distances and plans across a wide range of datasets, but also captures the geometry of the Wasserstein space correctly. Furthermore, we show that our network can be used as a state-of-the-art initialization for the Sinkhorn algorithm with speedups of up to $7.4\times$, significantly outperforming existing approaches.
Towards True Lossless Sparse Communication in Multi-Agent Systems
Authors: Seth Karten, Mycal Tucker, Siva Kailas, Katia Sycara
Date: 2022-11-30 00:00:00
Tasks: Representation Learning

Communication enables agents to cooperate to achieve their goals. Learning when to communicate, i.e., sparse (in time) communication, and whom to message is particularly important when bandwidth is limited. Recent work in learning sparse individualized communication, however, suffers from high variance during training, where decreasing communication comes at the cost of decreased reward, particularly in cooperative tasks. We use the information bottleneck to reframe sparsity as a representation learning problem, which we show naturally enables lossless sparse communication at lower budgets than prior art. In this paper, we propose a method for true lossless sparsity in communication via Information Maximizing Gated Sparse Multi-Agent Communication (IMGS-MAC). Our model uses two individualized regularization objectives, an information maximization autoencoder and sparse communication loss, to create informative and sparse communication. We evaluate the learned communication `language' through direct causal analysis of messages in non-sparse runs to determine the range of lossless sparse budgets, which allow zero-shot sparsity, and the range of sparse budgets that will inquire a reward loss, which is minimized by our learned gating function with few-shot sparsity. To demonstrate the efficacy of our results, we experiment in cooperative multi-agent tasks where communication is essential for success. We evaluate our model with both continuous and discrete messages. We focus our analysis on a variety of ablations to show the effect of message representations, including their properties, and lossless performance of our model.
Feature Selection with Distance Correlation
Authors: Ranit Das, Gregor Kasieczka, David Shih
Date: 2022-11-30 00:00:00
Tasks: Automated Feature Engineering, Feature Engineering, feature selection

Choosing which properties of the data to use as input to multivariate decision algorithms -- a.k.a. feature selection -- is an important step in solving any problem with machine learning. While there is a clear trend towards training sophisticated deep networks on large numbers of relatively unprocessed inputs (so-called automated feature engineering), for many tasks in physics, sets of theoretically well-motivated and well-understood features already exist. Working with such features can bring many benefits, including greater interpretability, reduced training and run time, and enhanced stability and robustness. We develop a new feature selection method based on Distance Correlation (DisCo), and demonstrate its effectiveness on the tasks of boosted top- and $W$-tagging. Using our method to select features from a set of over 7,000 energy flow polynomials, we show that we can match the performance of much deeper architectures, by using only ten features and two orders-of-magnitude fewer model parameters.
Quantum Neural Networks for a Supply Chain Logistics Application
Authors: Randall Correll, Sean J. Weinberg, Fabio Sanches, Takanori Ide, Takafumi Suzuki
Date: 2022-11-30 00:00:00

Problem instances of a size suitable for practical applications are not likely to be addressed during the noisy intermediate-scale quantum (NISQ) period with (almost) pure quantum algorithms. Hybrid classical-quantum algorithms have potential, however, to achieve good performance on much larger problem instances. We investigate one such hybrid algorithm on a problem of substantial importance: vehicle routing for supply chain logistics with multiple trucks and complex demand structure. We use reinforcement learning with neural networks with embedded quantum circuits. In such neural networks, projecting high-dimensional feature vectors down to smaller vectors is necessary to accommodate restrictions on the number of qubits of NISQ hardware. However, we use a multi-head attention mechanism where, even in classical machine learning, such projections are natural and desirable. We consider data from the truck routing logistics of a company in the automotive sector, and apply our methodology by decomposing into small teams of trucks, and we find results comparable to human truck assignment.
Data-driven Science and Machine Learning Methods in Laser-Plasma Physics
Authors: Andreas Döpp, Christoph Eberle, Sunny Howard, Faran Irshad, Jinpu Lin, Matthew Streeter
Date: 2022-11-30 00:00:00

Laser-plasma physics has developed rapidly over the past few decades as high-power lasers have become both increasingly powerful and more widely available. Early experimental and numerical research in this field was restricted to single-shot experiments with limited parameter exploration. However, recent technological improvements make it possible to gather an increasing amount of data, both in experiments and simulations. This has sparked interest in using advanced techniques from mathematics, statistics and computer science to deal with, and benefit from, big data. At the same time, sophisticated modeling techniques also provide new ways for researchers to effectively deal with situations in which still only sparse amounts of data are available. This paper aims to present an overview of relevant machine learning methods with focus on applicability to laser-plasma physics, including its important sub-fields of laser-plasma acceleration and inertial confinement fusion.
Random Copolymer inverse design system orienting on Accurate discovering of Antimicrobial peptide-mimetic copolymers
Authors: Tianyu Wu, Yang Tang
Date: 2022-11-30 00:00:00
Tasks: Activity Prediction, Knowledge Distillation, reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL), Representation Learning

Antimicrobial resistance is one of the biggest health problem, especially in the current period of COVID-19 pandemic. Due to the unique membrane-destruction bactericidal mechanism, antimicrobial peptide-mimetic copolymers are paid more attention and it is urgent to find more potential candidates with broad-spectrum antibacterial efficacy and low toxicity. Artificial intelligence has shown significant performance on small molecule or biotech drugs, however, the higher-dimension of polymer space and the limited experimental data restrict the application of existing methods on copolymer design. Herein, we develop a universal random copolymer inverse design system via multi-model copolymer representation learning, knowledge distillation and reinforcement learning. Our system realize a high-precision antimicrobial activity prediction with few-shot data by extracting various chemical information from multi-modal copolymer representations. By pre-training a scaffold-decorator generative model via knowledge distillation, copolymer space are greatly contracted to the near space of existing data for exploration. Thus, our reinforcement learning algorithm can be adaptive for customized generation on specific scaffolds and requirements on property or structures. We apply our system on collected antimicrobial peptide-mimetic copolymers data, and we discover candidate copolymers with desired properties.
Optical multi-task learning using multi-wavelength diffractive deep neural networks
Authors: Zhengyang Duan, Hang Chen, Xing Lin
Date: 2022-11-30 00:00:00
Tasks: Multi-Task Learning

Photonic neural networks are brain-inspired information processing technology using photons instead of electrons to perform artificial intelligence (AI) tasks. However, existing architectures are designed for a single task but fail to multiplex different tasks in parallel within a single monolithic system due to the task competition that deteriorates the model performance. This paper proposes a novel optical multi-task learning system by designing multi-wavelength diffractive deep neural networks (D2NNs) with the joint optimization method. By encoding multi-task inputs into multi-wavelength channels, the system can increase the computing throughput and significantly alle-viate the competition to perform multiple tasks in parallel with high accuracy. We design the two-task and four-task D2NNs with two and four spectral channels, respectively, for classifying different inputs from MNIST, FMNIST, KMNIST, and EMNIST databases. The numerical evaluations demonstrate that, under the same network size, mul-ti-wavelength D2NNs achieve significantly higher classification accuracies for multi-task learning than single-wavelength D2NNs. Furthermore, by increasing the network size, the multi-wavelength D2NNs for simultaneously performing multiple tasks achieve comparable classification accuracies with respect to the individual training of multiple single-wavelength D2NNs to perform tasks separately. Our work paves the way for developing the wave-length-division multiplexing technology to achieve high-throughput neuromorphic photonic computing and more general AI systems to perform multiple tasks in parallel.
Location analysis of players in UEFA EURO 2020 and 2022 using generalized valuation of defense by estimating probabilities
Authors: Rikuhei Umemoto, Kazushi Tsutsui, Keisuke Fujii
Date: 2022-11-30 00:00:00
Tasks: All

Analyzing defenses in team sports is generally challenging because of the limited event data. Researchers have previously proposed methods to evaluate football team defense by predicting the events of ball gain and being attacked using locations of all players and the ball. However, they did not consider the importance of the events, assumed the perfect observation of all 22 players, and did not fully investigated the influence of the diversity (e.g., nationality and sex). Here, we propose a generalized valuation method of defensive teams by score-scaling the predicted probabilities of the events. Using the open-source location data of all players in broadcast video frames in football games of men's Euro 2020 and women's Euro 2022, we investigated the effect of the number of players on the prediction and validated our approach by analyzing the games. Results show that for the predictions of being attacked, scoring, and conceding, all players' information was not necessary, while that of ball gain required information on three to four offensive and defensive players. With game analyses we explained the excellence in defense of finalist teams in Euro 2020. Our approach might be applicable to location data from broadcast video frames in football games.
Scalable Pathogen Detection from Next Generation DNA Sequencing with Deep Learning
Authors: Sai Narayanan, Sathyanarayanan N. Aakur, Priyadharsini Ramamurthy, Arunkumar Bagavathi, Vishalini Ramnath, Akhilesh Ramachandran
Date: 2022-11-30 00:00:00
Tasks: Diagnostic, Representation Learning

Next-generation sequencing technologies have enhanced the scope of Internet-of-Things (IoT) to include genomics for personalized medicine through the increased availability of an abundance of genome data collected from heterogeneous sources at a reduced cost. Given the sheer magnitude of the collected data and the significant challenges offered by the presence of highly similar genomic structure across species, there is a need for robust, scalable analysis platforms to extract actionable knowledge such as the presence of potentially zoonotic pathogens. The emergence of zoonotic diseases from novel pathogens, such as the influenza virus in 1918 and SARS-CoV-2 in 2019 that can jump species barriers and lead to pandemic underscores the need for scalable metagenome analysis. In this work, we propose MG2Vec, a deep learning-based solution that uses the transformer network as its backbone, to learn robust features from raw metagenome sequences for downstream biomedical tasks such as targeted and generalized pathogen detection. Extensive experiments on four increasingly challenging, yet realistic diagnostic settings, show that the proposed approach can help detect pathogens from uncurated, real-world clinical samples with minimal human supervision in the form of labels. Further, we demonstrate that the learned representations can generalize to completely unrelated pathogens across diseases and species for large-scale metagenome analysis. We provide a comprehensive evaluation of a novel representation learning framework for metagenome-based disease diagnostics with deep learning and provide a way forward for extracting and using robust vector representations from low-cost next generation sequencing to develop generalizable diagnostic tools.
Transformer-based Hand Gesture Recognition via High-Density EMG Signals: From Instantaneous Recognition to Fusion of Motor Unit Spike Trains
Authors: Mansooreh Montazerin, Elahe Rahimian, Farnoosh Naderkhani, S. Farokh Atashzar, Svetlana Yanushkevich, Arash Mohammadi
Date: 2022-11-29 00:00:00
Tasks: blind source separation, Gesture Recognition, Hand Gesture Recognition, Hand-Gesture Recognition, Transfer Learning

Designing efficient and labor-saving prosthetic hands requires powerful hand gesture recognition algorithms that can achieve high accuracy with limited complexity and latency. In this context, the paper proposes a compact deep learning framework referred to as the CT-HGR, which employs a vision transformer network to conduct hand gesture recognition using highdensity sEMG (HD-sEMG) signals. The attention mechanism in the proposed model identifies similarities among different data segments with a greater capacity for parallel computations and addresses the memory limitation problems while dealing with inputs of large sequence lengths. CT-HGR can be trained from scratch without any need for transfer learning and can simultaneously extract both temporal and spatial features of HD-sEMG data. Additionally, the CT-HGR framework can perform instantaneous recognition using sEMG image spatially composed from HD-sEMG signals. A variant of the CT-HGR is also designed to incorporate microscopic neural drive information in the form of Motor Unit Spike Trains (MUSTs) extracted from HD-sEMG signals using Blind Source Separation (BSS). This variant is combined with its baseline version via a hybrid architecture to evaluate potentials of fusing macroscopic and microscopic neural drive information. The utilized HD-sEMG dataset involves 128 electrodes that collect the signals related to 65 isometric hand gestures of 20 subjects. The proposed CT-HGR framework is applied to 31.25, 62.5, 125, 250 ms window sizes of the above-mentioned dataset utilizing 32, 64, 128 electrode channels. The average accuracy over all the participants using 32 electrodes and a window size of 31.25 ms is 86.23%, which gradually increases till reaching 91.98% for 128 electrodes and a window size of 250 ms. The CT-HGR achieves accuracy of 89.13% for instantaneous recognition based on a single frame of HD-sEMG image.
Attentional Ptycho-Tomography (APT) for three-dimensional nanoscale X-ray imaging with minimal data acquisition and computation time
Authors: Iksung Kang, Ziling Wu, Yi Jiang, YuDong Yao, Junjing Deng, Jeffrey Klug, Stefan Vogt, George Barbastathis
Date: 2022-11-29 00:00:00

Noninvasive X-ray imaging of nanoscale three-dimensional objects, e.g. integrated circuits (ICs), generally requires two types of scanning: ptychographic, which is translational and returns estimates of complex electromagnetic field through ICs; and tomographic scanning, which collects complex field projections from multiple angles. Here, we present Attentional Ptycho-Tomography (APT), an approach trained to provide accurate reconstructions of ICs despite incomplete measurements, using a dramatically reduced amount of angular scanning. Training process includes regularizing priors based on typical IC patterns and the physics of X-ray propagation. We demonstrate that APT with 12-time reduced angles achieves fidelity comparable to the gold standard with the original set of angles. With the same set of reduced angles, APT also outperforms baseline reconstruction methods. In our experiments, APT achieves 108-time aggregate reduction in data acquisition and computation without compromising quality. We expect our physics-assisted machine learning framework could also be applied to other branches of nanoscale imaging.
Penalized Overdamped and Underdamped Langevin Monte Carlo Algorithms for Constrained Sampling
Authors: Mert Gürbüzbalaban, Yuanhan Hu, Lingjiong Zhu
Date: 2022-11-29 00:00:00

We consider the constrained sampling problem where the goal is to sample from a target distribution $\pi(x)\propto e^{-f(x)}$ when $x$ is constrained to lie on a convex body $\mathcal{C}$. Motivated by penalty methods from continuous optimization, we propose penalized Langevin Dynamics (PLD) and penalized underdamped Langevin Monte Carlo (PULMC) methods that convert the constrained sampling problem into an unconstrained sampling problem by introducing a penalty function for constraint violations. When $f$ is smooth and gradients are available, we get $\tilde{\mathcal{O}}(d/\varepsilon^{10})$ iteration complexity for PLD to sample the target up to an $\varepsilon$-error where the error is measured in the TV distance and $\tilde{\mathcal{O}}(\cdot)$ hides logarithmic factors. For PULMC, we improve the result to $\tilde{\mathcal{O}}(\sqrt{d}/\varepsilon^{7})$ when the Hessian of $f$ is Lipschitz and the boundary of $\mathcal{C}$ is sufficiently smooth. To our knowledge, these are the first convergence results for underdamped Langevin Monte Carlo methods in the constrained sampling that handle non-convex $f$ and provide guarantees with the best dimension dependency among existing methods with deterministic gradient. If unbiased stochastic estimates of the gradient of $f$ are available, we propose PSGLD and PSGULMC methods that can handle stochastic gradients and are scaleable to large datasets without requiring Metropolis-Hasting correction steps. For PSGLD and PSGULMC, when $f$ is strongly convex and smooth, we obtain $\tilde{\mathcal{O}}(d/\varepsilon^{18})$ and $\tilde{\mathcal{O}}(d\sqrt{d}/\varepsilon^{39})$ iteration complexity in W2 distance. When $f$ is smooth and can be non-convex, we provide finite-time performance bounds and iteration complexity results. Finally, we illustrate the performance on Bayesian LASSO regression and Bayesian constrained deep learning problems.