Yulun Wu

Yulun Wu, Robert A. Barton, Zichen Wang et al. · amazon-science, harvard

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.

Yulun Wu, Layne C. Price, Zichen Wang et al.

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.

Dichucheng Li, Yulun Wu, Qinyu Li et al.

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.

Dichucheng Li, Mingjin Che, Wenwu Meng et al.

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.

Shuang Chen, Yue Guo, Zhaochen Su et al.

Inspired by the remarkable reasoning capabilities of Deepseek-R1 in complex textual tasks, many works attempt to incentivize similar capabilities in Multimodal Large Language Models (MLLMs) by directly applying reinforcement learning (RL). However, they still struggle to activate complex reasoning. In this paper, rather than examining multimodal RL in isolation, we delve into current training pipelines and identify three crucial phenomena: 1) Effective cold start initialization is critical for enhancing MLLM reasoning. Intriguingly, we find that initializing with carefully selected text data alone can lead to performance surpassing many recent multimodal reasoning models, even before multimodal RL. 2) Standard GRPO applied to multimodal RL suffers from gradient stagnation, which degrades training stability and performance. 3) Subsequent text-only RL training, following the multimodal RL phase, further enhances multimodal reasoning. This staged training approach effectively balances perceptual grounding and cognitive reasoning development. By incorporating the above insights and addressing multimodal RL issues, we introduce ReVisual-R1, achieving a new state-of-the-art among open-source 7B MLLMs on challenging benchmarks including MathVerse, MathVision, WeMath, LogicVista, DynaMath, and challenging AIME2024 and AIME2025.

Yulun Wu, Louie McConnell, Claudia Iriondo

Estimating an individual's counterfactual outcomes under interventions 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 the 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 disentangled exogenous noise abduction 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.