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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, facial images) and covariates are relatively limited. In this case, to predict one's outcomes under counterfactual treatments, it is crucial to leverage individual information contained in its high-dimensional observed outcome in addition to the covariates. Prior works using variational inference in counterfactual generative modeling have been focusing on neural adaptations and model variants within the conditional variational autoencoder formulation, which we argue is fundamentally ill-suited to the notion of counterfactual in causal inference. In this work, we present a novel variational Bayesian causal inference framework and its theoretical backings to properly handle counterfactual generative modeling tasks, through which we are able to conduct counterfactual supervision end-to-end during training without any counterfactual samples, and encourage latent disentanglement that aids the correct identification of causal effect in counterfactual generations. In experiments, we demonstrate the advantage of our framework compared to state-of-the-art models in counterfactual generative modeling on multiple benchmarks.

Organ transplantation serves as the primary therapeutic strategy for end-stage organ failures. However, allograft rejection is a common complication of organ transplantation. Histological assessment is essential for the timely detection and diagnosis of transplant rejection and remains the gold standard. Nevertheless, the traditional histochemical staining process is time-consuming, costly, and labor-intensive. Here, we present a panel of virtual staining neural networks for lung and heart transplant biopsies, which digitally convert autofluorescence microscopic images of label-free tissue sections into their brightfield histologically stained counterparts, bypassing the traditional histochemical staining process. Specifically, we virtually generated Hematoxylin and Eosin (H&E), Masson's Trichrome (MT), and Elastic Verhoeff-Van Gieson (EVG) stains for label-free transplant lung tissue, along with H&E and MT stains for label-free transplant heart tissue. Subsequent blind evaluations conducted by three board-certified pathologists have confirmed that the virtual staining networks consistently produce high-quality histology images with high color uniformity, closely resembling their well-stained histochemical counterparts across various tissue features. The use of virtually stained images for the evaluation of transplant biopsies achieved comparable diagnostic outcomes to those obtained via traditional histochemical staining, with a concordance rate of 82.4% for lung samples and 91.7% for heart samples. Moreover, virtual staining models create multiple stains from the same autofluorescence input, eliminating structural mismatches observed between adjacent sections stained in the traditional workflow, while also saving tissue, expert time, and staining costs., Comment: 21 Pages, 5 Figures

We propose Deep Longitudinal Targeted Minimum Loss-based Estimation (Deep LTMLE), a novel approach to estimate the counterfactual mean of outcome under dynamic treatment policies in longitudinal problem settings. Our approach utilizes a transformer architecture with heterogeneous type embedding trained using temporal-difference learning. After obtaining an initial estimate using the transformer, following the targeted minimum loss-based likelihood estimation (TMLE) framework, we statistically corrected for the bias commonly associated with machine learning algorithms. Furthermore, our method also facilitates statistical inference by enabling the provision of 95% confidence intervals grounded in asymptotic statistical theory. Simulation results demonstrate our method's superior performance over existing approaches, particularly in complex, long time-horizon scenarios. It remains effective in small-sample, short-duration contexts, matching the performance of asymptotically efficient estimators. To demonstrate our method in practice, we applied our method to estimate counterfactual mean outcomes for standard versus intensive blood pressure management strategies in a real-world cardiovascular epidemiology cohort study.

We present the design and implementation of a tool for semi-automatic verification of functional specifications of operating system modules. Such verification tasks are traditionally done in interactive theorem provers, where the functionalities of the module are specified at abstract and concrete levels using data such as structures, algebraic datatypes, arrays, maps and so on. In this work, we provide encodings to SMT for these commonly occurring data types. This allows verification conditions to be reduced into a form suitable for SMT solvers. The use of SMT solvers combined with a tactic language allows semi-automatic verification of the specification. We apply the tool to verify functional specification for key parts of the uC-OS/II operating system, based on earlier work giving full verification of the system in Coq. We demonstrate a large reduction in the amount of human effort due to increased level of automation.

Recently, neural implicit functions have demonstrated remarkable results in the field of multi-view reconstruction. However, most existing methods are tailored for dense views and exhibit unsatisfactory performance when dealing with sparse views. Several latest methods have been proposed for generalizing implicit reconstruction to address the sparse view reconstruction task, but they still suffer from high training costs and are merely valid under carefully selected perspectives. In this paper, we propose a novel sparse view reconstruction framework that leverages on-surface priors to achieve highly faithful surface reconstruction. Specifically, we design several constraints on global geometry alignment and local geometry refinement for jointly optimizing coarse shapes and fine details. To achieve this, we train a neural network to learn a global implicit field from the on-surface points obtained from SfM and then leverage it as a coarse geometric constraint. To exploit local geometric consistency, we project on-surface points onto seen and unseen views, treating the consistent loss of projected features as a fine geometric constraint. The experimental results with DTU and BlendedMVS datasets in two prevalent sparse settings demonstrate significant improvements over the state-of-the-art methods., Comment: Accepted by AAAI 2024. Project page: https://alvin528.github.io/NeuSurf/

Speech Emotion Recognition (SER) has become a growing focus of research in human-computer interaction. Spatiotemporal features play a crucial role in SER, yet current research lacks comprehensive spatiotemporal feature learning. This paper focuses on addressing this gap by proposing a novel approach. In this paper, we employ Convolutional Neural Network (CNN) with varying kernel sizes for spatial and temporal feature extraction. Additionally, we introduce Squeeze-and-Excitation (SE) modules to capture and fuse multi-scale features, facilitating effective information fusion for improved emotion recognition and a deeper understanding of the temporal evolution of speech emotion. Moreover, we employ skip connections and Spatial Dropout (SD) layers to prevent overfitting and increase the model's depth. Our method outperforms the previous state-of-the-art method, achieving an average UAR and WAR improvement of 1.62% and 1.32%, respectively, across six benchmark SER datasets. Further experiments demonstrated that our method can fully extract spatiotemporal features in low-resource conditions.

Instrument playing techniques (IPTs) constitute a pivotal component of musical expression. However, the development of automatic IPT detection methods suffers from limited labeled data and inherent class imbalance issues. In this paper, we propose to apply a self-supervised learning model pre-trained on large-scale unlabeled music data and finetune it on IPT detection tasks. This approach addresses data scarcity and class imbalance challenges. Recognizing the significance of pitch in capturing the nuances of IPTs and the importance of onset in locating IPT events, we investigate multi-task finetuning with pitch and onset detection as auxiliary tasks. Additionally, we apply a post-processing approach for event-level prediction, where an IPT activation initiates an event only if the onset output confirms an onset in that frame. Our method outperforms prior approaches in both frame-level and event-level metrics across multiple IPT benchmark datasets. Further experiments demonstrate the efficacy of multi-task finetuning on each IPT class., Comment: submitted to ICASSP 2024

Recent advances in general purpose pre-trained language models have shown great potential in commonsense reasoning. However, current works still perform poorly on standard commonsense reasoning benchmarks including the Com2Sense Dataset. We argue that this is due to a disconnect with current cutting-edge machine learning methods. In this work, we aim to bridge the gap by introducing current ML-based methods to improve general purpose pre-trained language models in the task of commonsense reasoning. Specifically, we experiment with and systematically evaluate methods including knowledge transfer, model ensemble, and introducing an additional pairwise contrastive objective. Our best model outperforms the strongest previous works by ~15\% absolute gains in Pairwise Accuracy and ~8.7\% absolute gains in Standard Accuracy.

Instrument playing technique (IPT) is a key element of musical presentation. However, most of the existing works for IPT detection only concern monophonic music signals, yet little has been done to detect IPTs in polyphonic instrumental solo pieces with overlapping IPTs or mixed IPTs. In this paper, we formulate it as a frame-level multi-label classification problem and apply it to Guzheng, a Chinese plucked string instrument. We create a new dataset, Guzheng\_Tech99, containing Guzheng recordings and onset, offset, pitch, IPT annotations of each note. Because different IPTs vary a lot in their lengths, we propose a new method to solve this problem using multi-scale network and self-attention. The multi-scale network extracts features from different scales, and the self-attention mechanism applied to the feature maps at the coarsest scale further enhances the long-range feature extraction. Our approach outperforms existing works by a large margin, indicating its effectiveness in IPT detection., Comment: Accepted to ICASSP 2023

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.

The Guzheng is a kind of traditional Chinese instruments with diverse playing techniques. Instrument playing techniques (IPT) play an important role in musical performance. However, most of the existing works for IPT detection show low efficiency for variable-length audio and provide no assurance in the generalization as they rely on a single sound bank for training and testing. In this study, we propose an end-to-end Guzheng playing technique detection system using Fully Convolutional Networks that can be applied to variable-length audio. Because each Guzheng playing technique is applied to a note, a dedicated onset detector is trained to divide an audio into several notes and its predictions are fused with frame-wise IPT predictions. During fusion, we add the IPT predictions frame by frame inside each note and get the IPT with the highest probability within each note as the final output of that note. We create a new dataset named GZ_IsoTech from multiple sound banks and real-world recordings for Guzheng performance analysis. Our approach achieves 87.97% in frame-level accuracy and 80.76% in note-level F1-score, outperforming existing works by a large margin, which indicates the effectiveness of our proposed method in IPT detection., Comment: Accepted to ISMIR 2022

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.

We developed Distilled Graph Attention Policy Network (DGAPN), a reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. The framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention (sGAT) mechanism that leverages self-attention over both node and edge attributes as well as encoding the spatial structure -- this capability is of considerable interest in synthetic biology and drug discovery. An attentional policy network is introduced to learn the decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with stability. Exploration is driven by the stochasticity of the action space design and the innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while reducing the complexity of paths to chemical synthesis.