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We introduce a general framework for solving partial differential equations (PDEs) using generative diffusion models. In particular, we focus on the scenarios where we do not have the full knowledge of the scene necessary to apply classical solvers. Most existing forward or inverse PDE approaches perform poorly when the observations on the data or the underlying coefficients are incomplete, which is a common assumption for real-world measurements. In this work, we propose DiffusionPDE that can simultaneously fill in the missing information and solve a PDE by modeling the joint distribution of the solution and coefficient spaces. We show that the learned generative priors lead to a versatile framework for accurately solving a wide range of PDEs under partial observation, significantly outperforming the state-of-the-art methods for both forward and inverse directions., Comment: Project page: https://jhhuangchloe.github.io/Diffusion-PDE/

Graph machine learning (GML) is effective in many business applications. However, making GML easy to use and applicable to industry applications with massive datasets remain challenging. We developed GraphStorm, which provides an end-to-end solution for scalable graph construction, graph model training and inference. GraphStorm has the following desirable properties: (a) Easy to use: it can perform graph construction and model training and inference with just a single command; (b) Expert-friendly: GraphStorm contains many advanced GML modeling techniques to handle complex graph data and improve model performance; (c) Scalable: every component in GraphStorm can operate on graphs with billions of nodes and can scale model training and inference to different hardware without changing any code. GraphStorm has been used and deployed for over a dozen billion-scale industry applications after its release in May 2023. It is open-sourced in Github: https://github.com/awslabs/graphstorm.

We present a simple algorithm for differentiable rendering of surfaces represented by Signed Distance Fields (SDF), which makes it easy to integrate rendering into gradient-based optimization pipelines. To tackle visibility-related derivatives that make rendering non-differentiable, existing physically based differentiable rendering methods often rely on elaborate guiding data structures or reparameterization with a global impact on variance. In this article, we investigate an alternative that embraces nonzero bias in exchange for low variance and architectural simplicity. Our method expands the lower-dimensional boundary integral into a thin band that is easy to sample when the underlying surface is represented by an SDF. We demonstrate the performance and robustness of our formulation in end-to-end inverse rendering tasks, where it obtains results that are competitive with or superior to existing work.

The molecular-based ferrimagnetic insulator V(TCNE)x has gained recent interest for efficient spin-wave excitation due to its low Gilbert damping ratio a=4E-5, and narrow ferromagnetic resonance linewidth f=1Oe. Here we report a clean spin pumping signal detected on V(TCNE)x/metal bilayer structures, free from spin rectification or thermal artifacts. On-chip coupling of microwave power is achieved via a coplanar waveguide to measure the in-plane angle-dependence of the inverse spin-Hall effect under ferromagnetic resonance conditions with respect to a constant external magnetic field. A signature of pure spin current from V(TCNE)x is observed in both platinum and permalloy metal layers, demonstrating the utility of V(TCNE)x for magnon spintronics studies in molecule/solid-state heterostructures., Comment: Need to add more simulation results on EM coupling

Magnetic resonance methods offer a unique chance for in-depth study of conductive organic material systems, not only accounts for number of charge carriers, but also allows manipulations of spin dynamics of particles. Here we present a study of continuous-wave electrically detected magnetic resonance on a range of organic conjugate polymers under transistor architecture, with tunability in both carrier concentration and drifting electric field. We demonstrate the general existence of bipolaron between mobile and trapped charges at the magnetic resonance condition, then estimates the wavefunction expansion of charge carriers on their hopping sites along conductive pathways. This finding allows direct observation of energetically disordered trap sites under the charge hopping picture, linking-up the microscopic structural properties to the bulk electronic performances., Comment: No ready for publishing, need more about discussion about the wavefunctions

Few-shot object detection (FSOD) aims at extending a generic detector for novel object detection with only a few training examples. It attracts great concerns recently due to the practical meanings. Meta-learning has been demonstrated to be an effective paradigm for this task. In general, methods based on meta-learning employ an additional support branch to encode novel examples (a.k.a. support images) into class prototypes, which are then fused with query branch to facilitate the model prediction. However, the class-level prototypes are difficult to precisely generate, and they also lack detailed information, leading to instability in performance.New methods are required to capture the distinctive local context for more robust novel object detection. To this end, we propose to distill the most representative support features into fine-grained prototypes. These prototypes are then assigned into query feature maps based on the matching results, modeling the detailed feature relations between two branches. This process is realized by our Fine-Grained Feature Aggregation (FFA) module. Moreover, in terms of high-level feature fusion, we propose Balanced Class-Agnostic Sampling (B-CAS) strategy and Non-Linear Fusion (NLF) module from differenct perspectives. They are complementary to each other and depict the high-level feature relations more effectively. Extensive experiments on PASCAL VOC and MS COCO benchmarks show that our method sets a new state-of-the-art performance in most settings. Our code is available at https://github.com/wangchen1801/FPD., Comment: Accepted by AAAI2024

Vision-language foundation models, represented by Contrastive language-image pre-training (CLIP), have gained increasing attention for jointly understanding both vision and textual tasks. However, existing approaches primarily focus on training models to match global image representations with textual descriptions, thereby overlooking the critical alignment between local regions and corresponding text tokens. This paper extends CLIP with multi-granularity alignment. Notably, we deliberately construct a new dataset comprising pseudo annotations at various levels of granularities, encompassing image-level, region-level, and pixel-level captions/tags. Accordingly, we develop a unified multi-granularity learning framework, named UMG-CLIP, that simultaneously empowers the model with versatile perception abilities across different levels of detail. Equipped with parameter efficient tuning, UMG-CLIP surpasses current widely used CLIP models and achieves state-of-the-art performance on diverse image understanding benchmarks, including open-world recognition, retrieval, semantic segmentation, and panoptic segmentation tasks. We hope UMG-CLIP can serve as a valuable option for advancing vision-language foundation models., Comment: The paper is undergoing internal legal review and will be resubmitted once it passes the review

Neural fields have become widely used in various fields, from shape representation to neural rendering, and for solving partial differential equations (PDEs). With the advent of hybrid neural field representations like Instant NGP that leverage small MLPs and explicit representations, these models train quickly and can fit large scenes. Yet in many applications like rendering and simulation, hybrid neural fields can cause noticeable and unreasonable artifacts. This is because they do not yield accurate spatial derivatives needed for these downstream applications. In this work, we propose two ways to circumvent these challenges. Our first approach is a post hoc operator that uses local polynomial-fitting to obtain more accurate derivatives from pre-trained hybrid neural fields. Additionally, we also propose a self-supervised fine-tuning approach that refines the neural field to yield accurate derivatives directly while preserving the initial signal. We show the application of our method on rendering, collision simulation, and solving PDEs. We observe that using our approach yields more accurate derivatives, reducing artifacts and leading to more accurate simulations in downstream applications.

We study the federated pure exploration problem of multi-armed bandits and linear bandits, where $M$ agents cooperatively identify the best arm via communicating with the central server. To enhance the robustness against latency and unavailability of agents that are common in practice, we propose the first federated asynchronous multi-armed bandit and linear bandit algorithms for pure exploration with fixed confidence. Our theoretical analysis shows the proposed algorithms achieve near-optimal sample complexities and efficient communication costs in a fully asynchronous environment. Moreover, experimental results based on synthetic and real-world data empirically elucidate the effectiveness and communication cost-efficiency of the proposed algorithms.

Foundation models (FMs) are able to leverage large volumes of unlabeled data to demonstrate superior performance across a wide range of tasks. However, FMs developed for biomedical domains have largely remained unimodal, i.e., independently trained and used for tasks on protein sequences alone, small molecule structures alone, or clinical data alone. To overcome this limitation of biomedical FMs, we present BioBridge, a novel parameter-efficient learning framework, to bridge independently trained unimodal FMs to establish multimodal behavior. BioBridge achieves it by utilizing Knowledge Graphs (KG) to learn transformations between one unimodal FM and another without fine-tuning any underlying unimodal FMs. Our empirical results demonstrate that BioBridge can beat the best baseline KG embedding methods (on average by around 76.3%) in cross-modal retrieval tasks. We also identify BioBridge demonstrates out-of-domain generalization ability by extrapolating to unseen modalities or relations. Additionally, we also show that BioBridge presents itself as a general purpose retriever that can aid biomedical multimodal question answering as well as enhance the guided generation of novel drugs., Comment: ICLR 2024

In anti-cancer drug development, a major scientific challenge is disentangling the complex relationships between high-dimensional genomics data from patient tumor samples, the corresponding tumor's organ of origin, the drug targets associated with given treatments and the resulting treatment response. Furthermore, to realize the aspirations of precision medicine in identifying and adjusting treatments for patients depending on the therapeutic response, there is a need for building tumor dynamic models that can integrate both longitudinal tumor size as well as multimodal, high-content data. In this work, we take a step towards enhancing personalized tumor dynamic predictions by proposing a heterogeneous graph encoder that utilizes a bipartite Graph Convolutional Neural network (GCN) combined with Neural Ordinary Differential Equations (Neural-ODEs). We applied the methodology to a large collection of patient-derived xenograft (PDX) data, spanning a wide variety of treatments (as well as their combinations) on tumors that originated from a number of different organs. We first show that the methodology is able to discover a tumor dynamic model that significantly improves upon an empirical model which is in current use. Additionally, we show that the graph encoder is able to effectively utilize multimodal data to enhance tumor predictions. Our findings indicate that the methodology holds significant promise and offers potential applications in pre-clinical settings.

Large language models (LLMs) have shown remarkable generalization capability with exceptional performance in various language modeling tasks. However, they still exhibit inherent limitations in precisely capturing and returning grounded knowledge. While existing work has explored utilizing knowledge graphs (KGs) to enhance language modeling via joint training and customized model architectures, applying this to LLMs is problematic owing to their large number of parameters and high computational cost. Therefore, how to enhance pre-trained LLMs using grounded knowledge, e.g., retrieval-augmented generation, remains an open question. In this work, we propose Graph Neural Prompting (GNP), a novel plug-and-play method to assist pre-trained LLMs in learning beneficial knowledge from KGs. GNP encompasses various designs, including a standard graph neural network encoder, a cross-modality pooling module, a domain projector, and a self-supervised link prediction objective. Extensive experiments on multiple datasets demonstrate the superiority of GNP on both commonsense and biomedical reasoning tasks across different LLM sizes and settings. Code is available at https://github.com/meettyj/GNP., Comment: Accepted by AAAI 2024

Understanding the framing of political issues is of paramount importance as it significantly shapes how individuals perceive, interpret, and engage with these matters. While prior research has independently explored framing within news media and by social media users, there remains a notable gap in our comprehension of the disparities in framing political issues between these two distinct groups. To address this gap, we conduct a comprehensive investigation, focusing on the nuanced distinctions both qualitatively and quantitatively in the framing of social media and traditional media outlets concerning a series of American Supreme Court rulings on affirmative action, student loans, and abortion rights. Our findings reveal that, while some overlap in framing exists between social media and traditional media outlets, substantial differences emerge both across various topics and within specific framing categories. Compared to traditional news media, social media platforms tend to present more polarized stances across all framing categories. Further, we observe significant polarization in the news media's treatment (i.e., Left vs. Right leaning media) of affirmative action and abortion rights, whereas the topic of student loans tends to exhibit a greater degree of consensus. The disparities in framing between traditional and social media platforms carry significant implications for the formation of public opinion, policy decision-making, and the broader political landscape.

The increasing reliance on Large Language Models (LLMs) across academia and industry necessitates a comprehensive understanding of their robustness to prompts. In response to this vital need, we introduce PromptRobust, a robustness benchmark designed to measure LLMs' resilience to adversarial prompts. This study uses a plethora of adversarial textual attacks targeting prompts across multiple levels: character, word, sentence, and semantic. The adversarial prompts, crafted to mimic plausible user errors like typos or synonyms, aim to evaluate how slight deviations can affect LLM outcomes while maintaining semantic integrity. These prompts are then employed in diverse tasks including sentiment analysis, natural language inference, reading comprehension, machine translation, and math problem-solving. Our study generates 4,788 adversarial prompts, meticulously evaluated over 8 tasks and 13 datasets. Our findings demonstrate that contemporary LLMs are not robust to adversarial prompts. Furthermore, we present a comprehensive analysis to understand the mystery behind prompt robustness and its transferability. We then offer insightful robustness analysis and pragmatic recommendations for prompt composition, beneficial to both researchers and everyday users., Comment: Technical report; code is at: https://github.com/microsoft/promptbench

This paper revisits the 2-approximation algorithm for $k$-MST presented by Garg in light of a recent paper of Paul et al.. In the $k$-MST problem, the goal is to return a tree spanning $k$ vertices of minimum total edge cost. Paul et al. extend Garg's primal-dual subroutine to improve the approximation ratios for the budgeted prize-collecting traveling salesman and minimum spanning tree problems. We follow their algorithm and analysis to provide a cleaner version of Garg's result. Additionally, we introduce the novel concept of a kernel which allows an easier visualization of the stages of the algorithm and a clearer understanding of the pruning phase. Other notable updates include presenting a linear programming formulation of the $k$-MST problem, including pseudocode, replacing the coloring scheme used by Garg with the simpler concept of neutral sets, and providing an explicit potential function., Comment: Proceedings of SIAM Symposium on Simplicity in Algorithms (SOSA) 2023

We propose the first study of adversarial attacks on online learning to rank. The goal of the adversary is to misguide the online learning to rank algorithm to place the target item on top of the ranking list linear times to time horizon $T$ with a sublinear attack cost. We propose generalized list poisoning attacks that perturb the ranking list presented to the user. This strategy can efficiently attack any no-regret ranker in general stochastic click models. Furthermore, we propose a click poisoning-based strategy named attack-then-quit that can efficiently attack two representative OLTR algorithms for stochastic click models. We theoretically analyze the success and cost upper bound of the two proposed methods. Experimental results based on synthetic and real-world data further validate the effectiveness and cost-efficiency of the proposed attack strategies.

There is a broad consensus that news media outlets incorporate ideological biases in their news articles. However, prior studies on measuring the discrepancies among media outlets and further dissecting the origins of thematic differences suffer from small sample sizes and limited scope and granularity. In this study, we use a large dataset of 1.8 million news headlines from major U.S. media outlets spanning from 2014 to 2022 to thoroughly track and dissect the fine-grained thematic discrepancy in U.S. news media. We employ multiple correspondence analysis (MCA) to quantify the fine-grained thematic discrepancy related to four prominent topics - domestic politics, economic issues, social issues, and foreign affairs in order to derive a more holistic analysis. Additionally, we compare the most frequent $n$-grams in media headlines to provide further qualitative insights into our analysis. Our findings indicate that on domestic politics and social issues, the discrepancy can be attributed to a certain degree of media bias. Meanwhile, the discrepancy in reporting foreign affairs is largely attributed to the diversity in individual journalistic styles. Finally, U.S. media outlets show consistency and high similarity in their coverage of economic issues., Comment: Accepted for publication in Proceedings of the Workshop on News Media and Computational Journalism (MEDIATE), AAAI International Conference on Web and Social Media (ICWSM), 2023

We first adopt a human-guided machine learning framework to develop a new dataset for hyperpartisan news title detection with 2,200 manually labeled and 1.8 million machine-labeled titles that were posted from 2014 to the present by nine representative media organizations across three media bias groups - Left, Central, and Right in an active learning manner. A fine-tuned transformer-based language model achieves an overall accuracy of 0.84 and an F1 score of 0.78 on an external validation set. Next, we conduct a computational analysis to quantify the extent and dynamics of partisanship in news titles. While some aspects are as expected, our study reveals new or nuanced differences between the three media groups. We find that overall the Right media tends to use proportionally more hyperpartisan titles. Roughly around the 2016 Presidential Election, the proportions of hyperpartisan titles increased across all media bias groups, with the Left media exhibiting the most significant relative increase. We identify three major topics including foreign issues, political systems, and societal issues that are suggestive of hyperpartisanship in news titles using logistic regression models and the Shapley values. Through an analysis of the topic distribution, we find that societal issues gradually gain more attention from all media groups. We further apply a lexicon-based language analysis tool to the titles of each topic and quantify the linguistic distance between any pairs of the three media groups, uncovering three distinct patterns., Comment: Accepted for publication in ICWSM 2024

Since the term "Cyber threat hunting" was introduced in 2016, there have been a rising trend of proactive defensive measure to create more cyber security. This research will look into peer reviewed literature on the subject of cyber threat hunting. Our study shows an increase in the field with methods of machine learning.\\ Keywords: Cyber threat, Cyber security, threat hunting , security system, data driven, Intel, analytic driven, TTPs

Representation learning for proteins has primarily focused on the global understanding of protein sequences regardless of their length. However, shorter proteins (known as peptides) take on distinct structures and functions compared to their longer counterparts. Unfortunately, there are not as many naturally occurring peptides available to be sequenced and therefore less peptide-specific data to train with. In this paper, we propose a new peptide data augmentation scheme, where we train peptide language models on artificially constructed peptides that are small contiguous subsets of longer, wild-type proteins; we refer to the training peptides as "chopped proteins". We evaluate the representation potential of models trained with chopped proteins versus natural peptides and find that training language models with chopped proteins results in more generalized embeddings for short protein sequences. These peptide-specific models also retain information about the original protein they were derived from better than language models trained on full-length proteins. We compare masked language model training objectives to three novel peptide-specific training objectives: next-peptide prediction, contrastive peptide selection and evolution-weighted MLM. We demonstrate improved zero-shot learning performance for a deep mutational scan peptides benchmark.

The ellipsoid embedding function of a symplectic four-manifold measures the amount by which its symplectic form must be scaled in order for it to admit an embedding of an ellipsoid of varying eccentricity. This function generalizes the Gromov width and ball packing numbers. In the one continuous family of symplectic four-manifolds that has been analyzed, one-point blowups of the complex projective plane, there is an open dense set of symplectic forms whose ellipsoid embedding functions are completely described by finitely many obstructions, while there is simultaneously a Cantor set of symplectic forms for which an infinite number of obstructions are needed. In the latter case, we say that the embedding function has an infinite staircase. In this paper we identify a new infinite staircase when the target is a four-dimensional polydisk, extending a countable family identified by Usher in 2019. Our work computes the function on infinitely many intervals and thereby indicates a method of proof for a conjecture of Usher., Comment: 55 pages, 16 figures. v2: abstract shortened and slightly edited, expository sections S2.2, S4.1, and S4.4 edited for clarity, acknowledgements and bibliography edited. v3: several changes throughout the paper, specifically Conjecture 1.2.1. To appear in Involve

Predicting the responses of a cell under perturbations may bring important benefits to drug discovery and personalized therapeutics. In this work, we propose a novel graph variational Bayesian causal inference framework to predict a cell's gene expressions under counterfactual perturbations (perturbations that this cell did not factually receive), leveraging information representing biological knowledge in the form of gene regulatory networks (GRNs) to aid individualized cellular response predictions. Aiming at a data-adaptive GRN, we also developed an adjacency matrix updating technique for graph convolutional networks and used it to refine GRNs during pre-training, which generated more insights on gene relations and enhanced model performance. Additionally, we propose a robust estimator within our framework for the asymptotically efficient estimation of marginal perturbation effect, which is yet to be carried out in previous works. With extensive experiments, we exhibited the advantage of our approach over state-of-the-art deep learning models for individual response prediction.

Estimating an individual's potential outcomes under counterfactual treatments is a challenging task for traditional causal inference and supervised learning approaches when the outcome is high-dimensional (e.g. gene expressions, impulse responses, human faces) and covariates are relatively limited. In this case, to construct one's outcome under a counterfactual treatment, it is crucial to leverage individual information contained in its observed factual outcome on top of the covariates. We propose a deep variational Bayesian framework that rigorously integrates two main sources of information for outcome construction under a counterfactual treatment: one source is the individual features embedded in the high-dimensional factual outcome; the other source is the response distribution of similar subjects (subjects with the same covariates) that factually received this treatment of interest.

Quantum algorithms can enhance machine learning in different aspects. In 2014, Rebentrost $et~al.$ constructed a least squares quantum support vector machine (LS-QSVM), in which the Swap Test plays a crucial role in realizing the classification. However, as the output states of a previous test cannot be reused for a new test in the Swap Test, the quantum algorithm LS-QSVM has to be repeated in preparing qubits, manipulating operations, and carrying out the measurement. This paper proposes a QSVM based on the generalized quantum amplitude estimation (AE-QSVM) which gets rid of the constraint of repetitive processes and saves the quantum resources. At first, AE-QSVM is trained by using the quantum singular value decomposition. Then, a query sample is classified by using the generalized quantum amplitude estimation in which high accuracy can be achieved by adding auxiliary qubits instead of repeating the algorithm. The complexity of AE-QSVM is reduced to $O(\kappa^{3}\varepsilon^{-3}(log(mn)+1))$ with an accuracy $\varepsilon$, where $m$ is the number of training vectors, $n$ is the dimension of the feature space, and $\kappa$ is the condition number. Experiments demonstrate that AE-QSVM is advantageous in terms of training matrix, the number of iterations, space complexity, and time complexity., Comment: 10 pages,4 figures

Image-based characterization and disease understanding involve integrative analysis of morphological, spatial, and topological information across biological scales. The development of graph convolutional networks (GCNs) has created the opportunity to address this information complexity via graph-driven architectures, since GCNs can perform feature aggregation, interaction, and reasoning with remarkable flexibility and efficiency. These GCNs capabilities have spawned a new wave of research in medical imaging analysis with the overarching goal of improving quantitative disease understanding, monitoring, and diagnosis. Yet daunting challenges remain for designing the important image-to-graph transformation for multi-modality medical imaging and gaining insights into model interpretation and enhanced clinical decision support. In this review, we present recent GCNs developments in the context of medical image analysis including imaging data from radiology and histopathology. We discuss the fast-growing use of graph network architectures in medical image analysis to improve disease diagnosis and patient outcomes in clinical practice. To foster cross-disciplinary research, we present GCNs technical advancements, emerging medical applications, identify common challenges in the use of image-based GCNs and their extensions in model interpretation, large-scale benchmarks that promise to transform the scope of medical image studies and related graph-driven medical research.