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Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to millisecond scales remains challenging. To address these challenges, we introduce a novel deep learning architecture, Protein Transformer with Scattering, Attention, and Positional Embedding (ProtSCAPE), which leverages the geometric scattering transform alongside transformer-based attention mechanisms to capture protein dynamics from molecular dynamics (MD) simulations. ProtSCAPE utilizes the multi-scale nature of the geometric scattering transform to extract features from protein structures conceptualized as graphs and integrates these features with dual attention structures that focus on residues and amino acid signals, generating latent representations of protein trajectories. Furthermore, ProtSCAPE incorporates a regression head to enforce temporally coherent latent representations., Comment: Accepted as a short paper at the 5th Molecular Machine Learning Conference (MoML 2024)

Question-asking in collaborative dialogue has long been established as key to knowledge construction, both in internal and collaborative problem solving. In this work, we examine probing questions in collaborative dialogues: questions that explicitly elicit responses from the speaker's interlocutors. Specifically, we focus on modeling the causal relations that lead directly from utterances earlier in the dialogue to the emergence of the probing question. We model these relations using a novel graph-based framework of deliberation chains, and reframe the problem of constructing such chains as a coreference-style clustering problem. Our framework jointly models probing and causal utterances and the links between them, and we evaluate on two challenging collaborative task datasets: the Weights Task and DeliData. Our results demonstrate the effectiveness of our theoretically-grounded approach compared to both baselines and stronger coreference approaches, and establish a standard of performance in this novel task., Comment: Accepted at Findings of EMNLP 2024

In order to better understand manifold neural networks (MNNs), we introduce Manifold Filter-Combine Networks (MFCNs). The filter-combine framework parallels the popular aggregate-combine paradigm for graph neural networks (GNNs) and naturally suggests many interesting families of MNNs which can be interpreted as the manifold analog of various popular GNNs. We then propose a method for implementing MFCNs on high-dimensional point clouds that relies on approximating the manifold by a sparse graph. We prove that our method is consistent in the sense that it converges to a continuum limit as the number of data points tends to infinity., Comment: Accepted to NeurIPS Workshop on Symmetry and Geometry in Neural Representations (Extended Abstract Track)

Rapid growth of high-dimensional datasets in fields such as single-cell RNA sequencing and spatial genomics has led to unprecedented opportunities for scientific discovery, but it also presents unique computational and statistical challenges. Traditional methods struggle with geometry-aware data generation, interpolation along meaningful trajectories, and transporting populations via feasible paths. To address these issues, we introduce Geometry-Aware Generative Autoencoder (GAGA), a novel framework that combines extensible manifold learning with generative modeling. GAGA constructs a neural network embedding space that respects the intrinsic geometries discovered by manifold learning and learns a novel warped Riemannian metric on the data space. This warped metric is derived from both the points on the data manifold and negative samples off the manifold, allowing it to characterize a meaningful geometry across the entire latent space. Using this metric, GAGA can uniformly sample points on the manifold, generate points along geodesics, and interpolate between populations across the learned manifold using geodesic-guided flows. GAGA shows competitive performance in simulated and real-world datasets, including a 30% improvement over the state-of-the-art methods in single-cell population-level trajectory inference.

Reward modeling of human preferences is one of the cornerstones of building usable generative large language models (LLMs). While traditional RLHF-based alignment methods explicitly maximize the expected rewards from a separate reward model, more recent supervised alignment methods like Direct Preference Optimization (DPO) circumvent this phase to avoid problems including model drift and reward overfitting. Although popular due to its simplicity, DPO and similar direct alignment methods can still lead to degenerate policies, and rely heavily on the Bradley-Terry-based preference formulation to model reward differences between pairs of candidate outputs. This formulation is challenged by non-deterministic or noisy preference labels, for example human scoring of two candidate outputs is of low confidence. In this paper, we introduce DRDO (Direct Reward Distillation and policy-Optimization), a supervised knowledge distillation-based preference alignment method that simultaneously models rewards and preferences to avoid such degeneracy. DRDO directly mimics rewards assigned by an oracle while learning human preferences from a novel preference likelihood formulation. Our experimental results on the Ultrafeedback and TL;DR datasets demonstrate that policies trained using DRDO surpass previous methods such as DPO and e-DPO in terms of expected rewards and are more robust, on average, to noisy preference signals as well as out-of-distribution (OOD) settings.

The proliferation of digital microscopy images, driven by advances in automated whole slide scanning, presents significant opportunities for biomedical research and clinical diagnostics. However, accurately annotating densely packed information in these images remains a major challenge. To address this, we introduce DiffKillR, a novel framework that reframes cell annotation as the combination of archetype matching and image registration tasks. DiffKillR employs two complementary neural networks: one that learns a diffeomorphism-invariant feature space for robust cell matching and another that computes the precise warping field between cells for annotation mapping. Using a small set of annotated archetypes, DiffKillR efficiently propagates annotations across large microscopy images, reducing the need for extensive manual labeling. More importantly, it is suitable for any type of pixel-level annotation. We will discuss the theoretical properties of DiffKillR and validate it on three microscopy tasks, demonstrating its advantages over existing supervised, semi-supervised, and unsupervised methods.

In this work, we explore the decoding of mental imagery from subjects using their fMRI measurements. In order to achieve this decoding, we first created a mapping between a subject's fMRI signals elicited by the videos the subjects watched. This mapping associates the high dimensional fMRI activation states with visual imagery. Next, we prompted the subjects textually, primarily with emotion labels which had no direct reference to visual objects. Then to decode visual imagery that may have been in a person's mind's eye, we align a latent representation of these fMRI measurements with a corresponding video-fMRI based on textual labels given to the videos themselves. This alignment has the effect of overlapping the video fMRI embedding with the text-prompted fMRI embedding, thus allowing us to use our fMRI-to-video mapping to decode. Additionally, we enhance an existing fMRI dataset, initially consisting of data from five subjects, by including recordings from three more subjects gathered by our team. We demonstrate the efficacy of our model on this augmented dataset both in accurately creating a mapping, as well as in plausibly decoding mental imagery.

Neuroscience employs diverse neuroimaging techniques, each offering distinct insights into brain activity, from electrophysiological recordings such as EEG, which have high temporal resolution, to hemodynamic modalities such as fMRI, which have increased spatial precision. However, integrating these heterogeneous data sources remains a challenge, which limits a comprehensive understanding of brain function. We present the Spatiotemporal Alignment of Multimodal Brain Activity (SAMBA) framework, which bridges the spatial and temporal resolution gaps across modalities by learning a unified latent space free of modality-specific biases. SAMBA introduces a novel attention-based wavelet decomposition for spectral filtering of electrophysiological recordings, graph attention networks to model functional connectivity between functional brain units, and recurrent layers to capture temporal autocorrelations in brain signal. We show that the training of SAMBA, aside from achieving translation, also learns a rich representation of brain information processing. We showcase this classify external stimuli driving brain activity from the representation learned in hidden layers of SAMBA, paving the way for broad downstream applications in neuroscience research and clinical contexts.

In cytometry, it is difficult to disentangle the contributions of population variance and instrument noise towards total measured variation. Fundamentally, this is due to the fact that one cannot measure the same particle multiple times. We propose a simple experiment that uses a cell sorter to distinguish instrument-specific variation. For a population of beads whose intensities are distributed around a single peak, the sorter is used to collect beads whose measured intensities lie below some threshold. This subset of particles is then remeasured. If the variation in the measured values is only due to the sample, the second set of measurements should also lie entirely below our threshold. Any 'spillover' is therefore due to instrument specific effects - we demonstrate how the distribution of the post-sort measurements is sufficient to extract an estimate of the cumulative variability induced by the instrument. A distinguishing feature of our work is that we do not make any assumptions about the sources of said noise. We then show how 'local affine transformations' let us transfer these estimates to cytometers not equipped with a sorter. We use our analysis to estimate noise for a set of three instruments and two bead types, across a range of sample flow rates. Lastly, we discuss the implications of instrument noise on optimal classification, as well as other applications., Comment: 24 pages, 10 figures

In many data-driven applications, higher-order relationships among multiple objects are essential in capturing complex interactions. Hypergraphs, which generalize graphs by allowing edges to connect any number of nodes, provide a flexible and powerful framework for modeling such higher-order relationships. In this work, we introduce hypergraph diffusion wavelets and describe their favorable spectral and spatial properties. We demonstrate their utility for biomedical discovery in spatially resolved transcriptomics by applying the method to represent disease-relevant cellular niches for Alzheimer's disease.

Spatial disorientation is a leading cause of fatal aircraft accidents. This paper explores the potential of AI agents to aid pilots in maintaining balance and preventing unrecoverable losses of control by offering cues and corrective measures that ameliorate spatial disorientation. A multi-axis rotation system (MARS) was used to gather data from human subjects self-balancing in a spaceflight analog condition. We trained models over this data to create "digital twins" that exemplified performance characteristics of humans with different proficiency levels. We then trained various reinforcement learning and deep learning models to offer corrective cues if loss of control is predicted. Digital twins and assistant models then co-performed a virtual inverted pendulum (VIP) programmed with identical physics. From these simulations, we picked the 5 best-performing assistants based on task metrics such as crash frequency and mean distance from the direction of balance. These were used in a co-performance study with 20 new human subjects performing a version of the VIP task with degraded spatial information. We show that certain AI assistants were able to improve human performance and that reinforcement-learning based assistants were objectively more effective but rated as less trusted and preferable by humans., Comment: 10 pages, To be published in the International Conference on Human-Agent Interaction (HAI '24) proceedings

Two-photon polymerization (2PP) 3D printing is a well-known technique for fabricating passive micro/nanoscale structures, such as microlenses and inversely designed polarization splitters. The integration of light emitting nanoparticle (NP) dopants, such as quantum dots (QDs) and rare-earth doped nanoparticles (RENPs), into a polymer resist would enable 3D printing of active polymer micro-photonic devices, including sensors, lasers, and solid-state displays. Many NPs are stabilized with oleic acid ligands to prevent degradation, but oleate-capped NPs (oc-NPs) tend to agglomerate in nonpolar media despite the hydrophobicity of the ligand. This results in an uneven distribution of NPs in polymers and increased optical extinction properties. In this work, we propose a general approach for dispersing various oc-NPs in commercial 3D printable polymers. We achieve controlled growth of small carbon chains around the oc-NPs by functionalizing the NPs with methyl-methacrylate monomers. The proposed approach is validated on RENPs (~65 nm) and CdSe/ZnS quantum dots (~12 nm) using different commercial polymer resists (IP-Dip and IP-Visio). Dispersions of functionalized NPs (f-NPs) have improved NP density by an order of magnitude and are shown to be stable for several weeks with minimal impact on printing quality. Our approach is generalizable to a variety of oc-NPs and ultimately leads to higher quality polymer-based optical and electronic devices., Comment: 25 Pages, 12 Figures

Advances in medical imaging technologies have enabled the collection of longitudinal images, which involve repeated scanning of the same patients over time, to monitor disease progression. However, predictive modeling of such data remains challenging due to high dimensionality, irregular sampling, and data sparsity. To address these issues, we propose ImageFlowNet, a novel model designed to forecast disease trajectories from initial images while preserving spatial details. ImageFlowNet first learns multiscale joint representation spaces across patients and time points, then optimizes deterministic or stochastic flow fields within these spaces using a position-parameterized neural ODE/SDE framework. The model leverages a UNet architecture to create robust multiscale representations and mitigates data scarcity by combining knowledge from all patients. We provide theoretical insights that support our formulation of ODEs, and motivate our regularizations involving high-level visual features, latent space organization, and trajectory smoothness. We validate ImageFlowNet on three longitudinal medical image datasets depicting progression in geographic atrophy, multiple sclerosis, and glioblastoma, demonstrating its ability to effectively forecast disease progression and outperform existing methods. Our contributions include the development of ImageFlowNet, its theoretical underpinnings, and empirical validation on real-world datasets. The official implementation is available at https://github.com/KrishnaswamyLab/ImageFlowNet., Comment: Updated narration and moved ablation to main text

There is a dire need for medical imaging datasets with accompanying annotations to perform downstream patient analysis. However, it is difficult to manually generate these annotations, due to the time-consuming nature, and the variability in clinical conventions. Artificial intelligence has been adopted in the field as a potential method to annotate these large datasets, however, a lack of expert annotations or ground truth can inhibit the adoption of these annotations. We recently made a dataset publicly available including annotations and extracted features of up to 104 organs for the National Lung Screening Trial using the TotalSegmentator method. However, the released dataset does not include expert-derived annotations or an assessment of the accuracy of the segmentations, limiting its usefulness. We propose the development of heuristics to assess the quality of the segmentations, providing methods to measure the consistency of the annotations and a comparison of results to the literature. We make our code and related materials publicly available at https://github.com/ImagingDataCommons/CloudSegmentatorResults and interactive tools at https://huggingface.co/spaces/ImagingDataCommons/CloudSegmentatorResults.

Metacognition is the concept of reasoning about an agent's own internal processes and was originally introduced in the field of developmental psychology. In this position paper, we examine the concept of applying metacognition to artificial intelligence. We introduce a framework for understanding metacognitive artificial intelligence (AI) that we call TRAP: transparency, reasoning, adaptation, and perception. We discuss each of these aspects in-turn and explore how neurosymbolic AI (NSAI) can be leveraged to address challenges of metacognition.

A novel method to reconstruct the energy of hadronic showers in the CMS High Granularity Calorimeter (HGCAL) is presented. The HGCAL is a sampling calorimeter with very fine transverse and longitudinal granularity. The active media are silicon sensors and scintillator tiles readout by SiPMs and the absorbers are a combination of lead and Cu/CuW in the electromagnetic section, and steel in the hadronic section. The shower reconstruction method is based on graph neural networks and it makes use of a dynamic reduction network architecture. It is shown that the algorithm is able to capture and mitigate the main effects that normally hinder the reconstruction of hadronic showers using classical reconstruction methods, by compensating for fluctuations in the multiplicity, energy, and spatial distributions of the shower's constituents. The performance of the algorithm is evaluated using test beam data collected in 2018 prototype of the CMS HGCAL accompanied by a section of the CALICE AHCAL prototype. The capability of the method to mitigate the impact of energy leakage from the calorimeter is also demonstrated., Comment: Prepared for submission to JINST

We offer philosophical motivations for a method we call Virtual World Cognitive Science (VW CogSci), in which researchers use virtual embodied agents that are embedded in virtual worlds to explore questions in the field of Cognitive Science. We focus on questions about mental and linguistic representation and the ways that such computational modeling can add rigor to philosophical thought experiments, as well as the terminology used in the scientific study of such representations. We find that this method forces researchers to take a god's-eye view when describing dynamical relationships between entities in minds and entities in an environment in a way that eliminates the need for problematic talk of belief and concept types, such as the belief that cats are silly, and the concept CAT, while preserving belief and concept tokens in individual cognizers' minds. We conclude with some further key advantages of VW CogSci for the scientific study of mental and linguistic representation and for Cognitive Science more broadly., Comment: 6 pages, 4 figures, to appear at CogSci 2024

Quantum cloud computing is an emerging paradigm of computing that empowers quantum applications and their deployment on quantum computing resources without the need for a specialized environment to host and operate physical quantum computers. This paper reviews recent advances, identifies open problems, and proposes future directions in quantum cloud computing. It discusses the state-of-the-art quantum cloud advances, including the various cloud-based models, platforms, and recently developed technologies and software use cases. Furthermore, it discusses different aspects of the quantum cloud, including resource management, quantum serverless, security, and privacy problems. Finally, the paper examines open problems and proposes the future directions of quantum cloud computing, including potential opportunities and ongoing research in this emerging field.

With the wealth of medical image data, efficient curation is essential. Assigning the sequence type to magnetic resonance images is necessary for scientific studies and artificial intelligence-based analysis. However, incomplete or missing metadata prevents effective automation. We therefore propose a deep-learning method for classification of prostate cancer scanning sequences based on a combination of image data and DICOM metadata. We demonstrate superior results compared to metadata or image data alone, and make our code publicly available at https://github.com/deepakri201/DICOMScanClassification.

Event coreference resolution (ECR) is the task of determining whether distinct mentions of events within a multi-document corpus are actually linked to the same underlying occurrence. Images of the events can help facilitate resolution when language is ambiguous. Here, we propose a multimodal cross-document event coreference resolution method that integrates visual and textual cues with a simple linear map between vision and language models. As existing ECR benchmark datasets rarely provide images for all event mentions, we augment the popular ECB+ dataset with event-centric images scraped from the internet and generated using image diffusion models. We establish three methods that incorporate images and text for coreference: 1) a standard fused model with finetuning, 2) a novel linear mapping method without finetuning and 3) an ensembling approach based on splitting mention pairs by semantic and discourse-level difficulty. We evaluate on 2 datasets: the augmented ECB+, and AIDA Phase 1. Our ensemble systems using cross-modal linear mapping establish an upper limit (91.9 CoNLL F1) on ECB+ ECR performance given the preprocessing assumptions used, and establish a novel baseline on AIDA Phase 1. Our results demonstrate the utility of multimodal information in ECR for certain challenging coreference problems, and highlight a need for more multimodal resources in the coreference resolution space., Comment: To appear at LREC-COLING 2024

In NLP, Event Coreference Resolution (ECR) is the task of connecting event clusters that refer to the same underlying real-life event, usually via neural systems. In this work, we investigate using abductive free-text rationales (FTRs) generated by modern autoregressive LLMs as distant supervision of smaller student models for cross-document coreference (CDCR) of events. We implement novel rationale-oriented event clustering and knowledge distillation methods for event coreference scoring that leverage enriched information from the FTRs for improved CDCR without additional annotation or expensive document clustering. Our model using coreference specific knowledge distillation achieves SOTA B3 F1 on the ECB+ and GVC corpora and we establish a new baseline on the AIDA Phase 1 corpus. Our code can be found at https://github.com/csu-signal/llama_cdcr, Comment: To be published in NAACL 2024 Main

In the era of generative artificial intelligence and the Internet of Things, while there is explosive growth in the volume of data and the associated need for processing, analysis, and storage, several new challenges are faced in identifying spurious and fake information and protecting the privacy of sensitive data. This has led to an increasing demand for more robust and resilient schemes for authentication, integrity protection, encryption, non-repudiation, and privacy-preservation of data. The chapters in this book present some of the state-of-the-art research works in the field of cryptography and security in computing and communications., Comment: Published by IntechOpen, London Uk in Nov 2023, the book contains 8 chapters spanning over 131 pages. arXiv admin note: text overlap with arXiv:2307.02055, arXiv:2304.00258

Multilingual Language Models (MLLMs) exhibit robust cross-lingual transfer capabilities, or the ability to leverage information acquired in a source language and apply it to a target language. These capabilities find practical applications in well-established Natural Language Processing (NLP) tasks such as Named Entity Recognition (NER). This study aims to investigate the effectiveness of a source language when applied to a target language, particularly in the context of perturbing the input test set. We evaluate on 13 pairs of languages, each including one high-resource language (HRL) and one low-resource language (LRL) with a geographic, genetic, or borrowing relationship. We evaluate two well-known MLLMs--MBERT and XLM-R--on these pairs, in native LRL and cross-lingual transfer settings, in two tasks, under a set of different perturbations. Our findings indicate that NER cross-lingual transfer depends largely on the overlap of entity chunks. If a source and target language have more entities in common, the transfer ability is stronger. Models using cross-lingual transfer also appear to be somewhat more robust to certain perturbations of the input, perhaps indicating an ability to leverage stronger representations derived from the HRL. Our research provides valuable insights into cross-lingual transfer and its implications for NLP applications, and underscores the need to consider linguistic nuances and potential limitations when employing MLLMs across distinct languages., Comment: accepted in LREC-COLING 2024

Within Dialogue Modeling research in AI and NLP, considerable attention has been spent on ``dialogue state tracking'' (DST), which is the ability to update the representations of the speaker's needs at each turn in the dialogue by taking into account the past dialogue moves and history. Less studied but just as important to dialogue modeling, however, is ``common ground tracking'' (CGT), which identifies the shared belief space held by all of the participants in a task-oriented dialogue: the task-relevant propositions all participants accept as true. In this paper we present a method for automatically identifying the current set of shared beliefs and ``questions under discussion'' (QUDs) of a group with a shared goal. We annotate a dataset of multimodal interactions in a shared physical space with speech transcriptions, prosodic features, gestures, actions, and facets of collaboration, and operationalize these features for use in a deep neural model to predict moves toward construction of common ground. Model outputs cascade into a set of formal closure rules derived from situated evidence and belief axioms and update operations. We empirically assess the contribution of each feature type toward successful construction of common ground relative to ground truth, establishing a benchmark in this novel, challenging task.

Deep learning has shown great promise in the ability to automatically annotate organs in magnetic resonance imaging (MRI) scans, for example, of the brain. However, despite advancements in the field, the ability to accurately segment abdominal organs remains difficult across MR. In part, this may be explained by the much greater variability in image appearance and severely limited availability of training labels. The inherent nature of computed tomography (CT) scans makes it easier to annotate, resulting in a larger availability of expert annotations for the latter. We leverage a modality-agnostic domain randomization approach, utilizing CT label maps to generate synthetic images on-the-fly during training, further used to train a U-Net segmentation network for abdominal organs segmentation. Our approach shows comparable results compared to fully-supervised segmentation methods trained on MR data. Our method results in Dice scores of 0.90 (0.08) and 0.91 (0.08) for the right and left kidney respectively, compared to a pretrained nnU-Net model yielding 0.87 (0.20) and 0.91 (0.03). We will make our code publicly available., Comment: 13 pages

We utilize click-counting theory for the reconstruction of photon statistics. Our approach employs an analytic pseudo-inversion method to estimate photon counts from measured click counts. A reconfigurable time-bin multiplexing, click-counting detector is set up that renders it possible to alter the photon-number resolution as needed. A detector tomography is carried out, yielding vital measurement features, such as quantum efficiencies, cross-talk rates, etc. We gauge the success of the pseudo-inversion by applying the Mandel and binomial parameters, resulting in an additional interpretation of these parameters for the discrimination of distinct quantum statistics. In addition, we apply a loss deconvolution technique to account for detection losses., Comment: 10 pages, 8 figures

In this paper, we present an exploration of LLMs' abilities to problem solve with physical reasoning in situated environments. We construct a simple simulated environment and demonstrate examples of where, in a zero-shot setting, both text and multimodal LLMs display atomic world knowledge about various objects but fail to compose this knowledge in correct solutions for an object manipulation and placement task. We also use BLIP, a vision-language model trained with more sophisticated cross-modal attention, to identify cases relevant to object physical properties that that model fails to ground. Finally, we present a procedure for discovering the relevant properties of objects in the environment and propose a method to distill this knowledge back into the LLM., Comment: 10 pages, 10 figures, Proceedings of AAAI Spring Symposium: Empowering Machine Learning and Large Language Models with Domain and Commonsense Knowledge (MAKE). AAAI (2024)

Full-duplex (FD) wireless can significantly enhance spectrum efficiency but requires effective self-interference (SI) cancellers. RF SI cancellation (SIC) via frequency-domain equalization (FDE), where bandpass filters channelize the SI, is suited for integrated circuits (ICs). In this paper, we explore the limits and higher layer challenges associated with using such cancellers. We evaluate the performance of a custom FDE-based canceller using two testbeds; one with mobile FD radios and the other with upgraded, static FD radios in the PAWR COSMOS testbed. The latter is a lasting artifact for the research community, alongside a dataset containing baseband waveforms captured on the COSMOS FD radios, facilitating FD-related experimentation at the higher networking layers. We evaluate the performance of the FDE-based FD radios in both testbeds, with experiments showing 95 dB overall achieved SIC (52 dB from RF SIC) across 20 MHz bandwidth, and an average link-level FD rate gain of 1.87x. We also conduct experiments in (i) uplink-downlink networks with inter-user interference, and (ii) heterogeneous networks with half-duplex and FD users. The experimental FD gains in the two types of networks depend on the users' SNR values and the number of FD users, and are 1.14x-1.25x and 1.25x-1.73x, respectively, confirming previous analytical results., Comment: 13 pages, 22 figures. arXiv admin note: substantial text overlap with arXiv:1812.01126

In this paper, we consider differentially private classification when some features are sensitive, while the rest of the features and the label are not. We adapt the definition of differential privacy naturally to this setting. Our main contribution is a novel adaptation of AdaBoost that is not only provably differentially private, but also significantly outperforms a natural benchmark that assumes the entire data of the individual is sensitive in the experiments. As a surprising observation, we show that boosting randomly generated classifiers suffices to achieve high accuracy. Our approach easily adapts to the classical setting where all the features are sensitive, providing an alternate algorithm for differentially private linear classification with a much simpler privacy proof and comparable or higher accuracy than differentially private logistic regression on real-world datasets.

Entropy and mutual information in neural networks provide rich information on the learning process, but they have proven difficult to compute reliably in high dimensions. Indeed, in noisy and high-dimensional data, traditional estimates in ambient dimensions approach a fixed entropy and are prohibitively hard to compute. To address these issues, we leverage data geometry to access the underlying manifold and reliably compute these information-theoretic measures. Specifically, we define diffusion spectral entropy (DSE) in neural representations of a dataset as well as diffusion spectral mutual information (DSMI) between different variables representing data. First, we show that they form noise-resistant measures of intrinsic dimensionality and relationship strength in high-dimensional simulated data that outperform classic Shannon entropy, nonparametric estimation, and mutual information neural estimation (MINE). We then study the evolution of representations in classification networks with supervised learning, self-supervision, or overfitting. We observe that (1) DSE of neural representations increases during training; (2) DSMI with the class label increases during generalizable learning but stays stagnant during overfitting; (3) DSMI with the input signal shows differing trends: on MNIST it increases, while on CIFAR-10 and STL-10 it decreases. Finally, we show that DSE can be used to guide better network initialization and that DSMI can be used to predict downstream classification accuracy across 962 models on ImageNet. The official implementation is available at https://github.com/ChenLiu-1996/DiffusionSpectralEntropy.

Here we consider the problem of denoising features associated to complex data, modeled as signals on a graph, via a smoothness prior. This is motivated in part by settings such as single-cell RNA where the data is very high-dimensional, but its structure can be captured via an affinity graph. This allows us to utilize ideas from graph signal processing. In particular, we present algorithms for the cases where the signal is perturbed by Gaussian noise, dropout, and uniformly distributed noise. The signals are assumed to follow a prior distribution defined in the frequency domain which favors signals which are smooth across the edges of the graph. By pairing this prior distribution with our three models of noise generation, we propose Maximum A Posteriori (M.A.P.) estimates of the true signal in the presence of noisy data and provide algorithms for computing the M.A.P. Finally, we demonstrate the algorithms' ability to effectively restore signals from white noise on image data and from severe dropout in single-cell RNA sequence data.

Machine learning (ML) is emerging as a transformative tool for the design of architected materials, offering properties that far surpass those achievable through lab-based trial-and-error methods. However, a major challenge in current inverse design strategies is their reliance on extensive computational and/or experimental datasets, which becomes particularly problematic for designing micro-scale stochastic architected materials that exhibit nonlinear mechanical behaviors. Here, we introduce a new end-to-end scientific ML framework, leveraging deep neural operators (DeepONet), to directly learn the relationship between the complete microstructure and mechanical response of architected metamaterials from sparse but high-quality in situ experimental data. The approach facilitates the inverse design of structures tailored to specific nonlinear mechanical behaviors. Results obtained from spinodal microstructures, printed using two-photon lithography, reveal that the prediction error for mechanical responses is within a range of 5 - 10%. Our work underscores that by employing neural operators with advanced micro-mechanics experimental techniques, the design of complex micro-architected materials with desired properties becomes feasible, even in scenarios constrained by data scarcity. Our work marks a significant advancement in the field of materials-by-design, potentially heralding a new era in the discovery and development of next-generation metamaterials with unparalleled mechanical characteristics derived directly from experimental insights., Comment: 29 pages, 5 figures

Production systems use heuristics because they are faster or scale better than their optimal counterparts. Yet, practitioners are often unaware of the performance gap between a heuristic and the optimum or between two heuristics in realistic scenarios. We present MetaOpt, a system that helps analyze heuristics. Users specify the heuristic and the optimal (or another heuristic) as input, and MetaOpt automatically encodes these efficiently for a solver to find performance gaps and their corresponding adversarial inputs. Its suite of built-in optimizations helps it scale its analysis to practical problem sizes. To show it is versatile, we used MetaOpt to analyze heuristics from three domains (traffic engineering, vector bin packing, and packet scheduling). We found a production traffic engineering heuristic can require 30% more capacity than the optimal to satisfy realistic demands. Based on the patterns in the adversarial inputs MetaOpt produced, we modified the heuristic to reduce its performance gap by 12.5$\times$. We examined adversarial inputs to a vector bin packing heuristic and proved a new lower bound on its performance.

Graph neural networks (GNNs) have emerged as a powerful tool for tasks such as node classification and graph classification. However, much less work has been done on signal classification, where the data consists of many functions (referred to as signals) defined on the vertices of a single graph. These tasks require networks designed differently from those designed for traditional GNN tasks. Indeed, traditional GNNs rely on localized low-pass filters, and signals of interest may have intricate multi-frequency behavior and exhibit long range interactions. This motivates us to introduce the BLIS-Net (Bi-Lipschitz Scattering Net), a novel GNN that builds on the previously introduced geometric scattering transform. Our network is able to capture both local and global signal structure and is able to capture both low-frequency and high-frequency information. We make several crucial changes to the original geometric scattering architecture which we prove increase the ability of our network to capture information about the input signal and show that BLIS-Net achieves superior performance on both synthetic and real-world data sets based on traffic flow and fMRI data.

We consider the max-min fair resource allocation problem. The best-known solutions use either a sequence of optimizations or waterfilling, which only applies to a narrow set of cases. These solutions have become a practical bottleneck in WAN traffic engineering and cluster scheduling, especially at larger problem sizes. We improve both approaches: (1) we show how to convert the optimization sequence into a single fast optimization, and (2) we generalize waterfilling to the multi-path case. We empirically show our new algorithms Pareto-dominate prior techniques: they produce faster, fairer, and more efficient allocations. Some of our allocators also have theoretical guarantees: they trade off a bounded amount of unfairness for faster allocation. We have deployed our allocators in Azure's WAN traffic engineering pipeline, where we preserve solution quality and achieve a roughly $3\times$ speedup., Comment: Accepted to USENIX NSDI 2024

In this paper we introduce DYMAG: a message passing paradigm for GNNs built on the expressive power of continuous, multiscale graph-dynamics. Standard discrete-time message passing algorithms implicitly make use of simplistic graph dynamics and aggregation schemes which limit their ability to capture fundamental graph topological properties. By contrast, DYMAG makes use of complex graph dynamics based on the heat and wave equation as well as a more complex equation which admits chaotic solutions. The continuous nature of the dynamics are leveraged to generate multiscale (dynamic-time snapshot) representations which we prove are linked to various graph topological and spectral properties. We demonstrate experimentally that DYMAG achieves superior performance in recovering the generating parameters of Erd\"os-Renyi and stochastic block model random graphs and the persistent homology of synthetic graphs and citation network. Since the behavior of proteins and biomolecules is sensitive to graph topology and exhibits important structure at multiple scales, we find that DYMAG outperforms other methods at predicting salient features of various biomolecules.

Directed graphs are a natural model for many phenomena, in particular scientific knowledge graphs such as molecular interaction or chemical reaction networks that define cellular signaling relationships. In these situations, source nodes typically have distinct biophysical properties from sinks. Due to their ordered and unidirectional relationships, many such networks also have hierarchical and multiscale structure. However, the majority of methods performing node- and edge-level tasks in machine learning do not take these properties into account, and thus have not been leveraged effectively for scientific tasks such as cellular signaling network inference. We propose a new framework called Directed Scattering Autoencoder (DSAE) which uses a directed version of a geometric scattering transform, combined with the non-linear dimensionality reduction properties of an autoencoder and the geometric properties of the hyperbolic space to learn latent hierarchies. We show this method outperforms numerous others on tasks such as embedding directed graphs and learning cellular signaling networks., Comment: 5 pages, 3 figures

In this paper, we obtain the functional derivatives of a finite horizon error norm between a full-order and a reduced-order continuous-time linear time-varying (LTV) system. Based on the functional derivatives, first-order necessary conditions for optimality of the error norm are derived, and a projection-based iterative scheme for model reduction is proposed. The iterative scheme upon convergence produces reduced-order models satisfying the optimality conditions. Finally, through a numerical example, we demonstrate the better performance of the proposed model reduction scheme in comparison to the finite horizon balanced truncation algorithm for continuous-time LTV systems.