Mingyang Zhou

Mingyang Zhou, Zichao Yan, Elliot Layne et al. · mila

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.

Mingyang Zhou, Licheng Yu, Amanpreet Singh et al. · meta-ai

Vision-and-Language (V+L) pre-training models have achieved tremendous success in recent years on various multi-modal benchmarks. However, the majority of existing models require pre-training on a large set of parallel image-text data, which is costly to collect, compared to image-only or text-only data. In this paper, we explore unsupervised Vision-and-Language pre-training (UVLP) to learn the cross-modal representation from non-parallel image and text datasets. We found two key factors that lead to good unsupervised V+L pre-training without parallel data: (i) joint image-and-text input (ii) overall image-text alignment (even for non-parallel data). Accordingly, we propose a novel unsupervised V+L pre-training curriculum for non-parallel texts and images. We first construct a weakly aligned image-text corpus via a retrieval-based approach, then apply a set of multi-granular alignment pre-training tasks, including region-to-tag, region-to-phrase, and image-to-sentence alignment, to bridge the gap between the two modalities. A comprehensive ablation study shows each granularity is helpful to learn a stronger pre-trained model. We adapt our pre-trained model to a set of V+L downstream tasks, including VQA, NLVR2, Visual Entailment, and RefCOCO+. Our model achieves the state-of-art performance in all these tasks under the unsupervised setting.

Mingyang Zhou, Grace Luo, Anna Rohrbach et al.

News Image Captioning requires describing an image by leveraging additional context from a news article. Previous works only coarsely leverage the article to extract the necessary context, which makes it challenging for models to identify relevant events and named entities. In our paper, we first demonstrate that by combining more fine-grained context that captures the key named entities (obtained via an oracle) and the global context that summarizes the news, we can dramatically improve the model's ability to generate accurate news captions. This begs the question, how to automatically extract such key entities from an image? We propose to use the pre-trained vision and language retrieval model CLIP to localize the visually grounded entities in the news article and then capture the non-visual entities via an open relation extraction model. Our experiments demonstrate that by simply selecting a better context from the article, we can significantly improve the performance of existing models and achieve new state-of-the-art performance on multiple benchmarks.

Kung-Hsiang Huang, Hou Pong Chan, Yi R. Fung et al.

Data visualization in the form of charts plays a pivotal role in data analysis, offering critical insights and aiding in informed decision-making. Automatic chart understanding has witnessed significant advancements with the rise of large foundation models in recent years. Foundation models, such as large language models, have revolutionized various natural language processing tasks and are increasingly being applied to chart understanding tasks. This survey paper provides a comprehensive overview of the recent developments, challenges, and future directions in chart understanding within the context of these foundation models. We review fundamental building blocks crucial for studying chart understanding tasks. Additionally, we explore various tasks and their evaluation metrics and sources of both charts and textual inputs. Various modeling strategies are then examined, encompassing both classification-based and generation-based approaches, along with tool augmentation techniques that enhance chart understanding performance. Furthermore, we discuss the state-of-the-art performance of each task and discuss how we can improve the performance. Challenges and future directions are addressed, highlighting the importance of several topics, such as domain-specific charts, lack of efforts in developing evaluation metrics, and agent-oriented settings. This survey paper serves as a comprehensive resource for researchers and practitioners in the fields of natural language processing, computer vision, and data analysis, providing valuable insights and directions for future research in chart understanding leveraging large foundation models. The studies mentioned in this paper, along with emerging new research, will be continually updated at: https://github.com/khuangaf/Awesome-Chart-Understanding.

Kung-Hsiang Huang, Mingyang Zhou, Hou Pong Chan et al.

Recent advancements in large vision-language models (LVLMs) have led to significant progress in generating natural language descriptions for visual content and thus enhancing various applications. One issue with these powerful models is that they sometimes produce texts that are factually inconsistent with the visual input. While there has been some effort to mitigate such inconsistencies in natural image captioning, the factuality of generated captions for structured document images, such as charts, has not received as much scrutiny, posing a potential threat to information reliability in critical applications. This work delves into the factuality aspect by introducing a comprehensive typology of factual errors in generated chart captions. A large-scale human annotation effort provides insight into the error patterns and frequencies in captions crafted by various chart captioning models, ultimately forming the foundation of a novel dataset, CHOCOLATE. Our analysis reveals that even state-of-the-art models, including GPT-4V, frequently produce captions laced with factual inaccuracies. In response to this challenge, we establish the new task of Chart Caption Factual Error Correction and introduce CHARTVE, a model for visual entailment that outperforms proprietary and open-source LVLMs in evaluating factual consistency. Furthermore, we propose C2TFEC, an interpretable two-stage framework that excels at correcting factual errors. This work inaugurates a new domain in factual error correction for chart captions, presenting a novel evaluation mechanism, and demonstrating an effective approach to ensuring the factuality of generated chart captions. The code and data as well as the continuously updated benchmark can be found at: https://khuangaf.github.io/CHOCOLATE/.

Hao Liao, Wei Zhang, Zhanyi Huang et al.

In the past decade, significant strides in deep learning have led to numerous groundbreaking applications. Despite these advancements, the understanding of the high generalizability of deep learning, especially in such an over-parametrized space, remains limited. For instance, in deep neural networks (DNNs), their internal representations, decision-making mechanism, absence of overfitting in an over-parametrized space, superior generalizability, etc., remain less understood. Successful applications are often considered as empirical rather than scientific achievement. This paper delves into the loss landscape of DNNs through the lens of spin glass in statistical physics, a system characterized by a complex energy landscape with numerous metastable states, as a novel perspective in understanding how DNNs work. We investigated the loss landscape of single hidden layer neural networks activated by Rectified Linear Unit (ReLU) function, and introduced several protocols to examine the analogy between DNNs and spin glass. Specifically, we used (1) random walk in the parameter space of DNNs to unravel the structures in their loss landscape; (2) a permutation-interpolation protocol to study the connection between copies of identical regions in the loss landscape due to the permutation symmetry in the hidden layers; (3) hierarchical clustering to reveal the hierarchy among trained solutions of DNNs, reminiscent of the so-called Replica Symmetry Breaking (RSB) phenomenon (i.e. the Parisi solution) in spin glass; (4) finally, we examine the relationship between the ruggedness of DNN's loss landscape and its generalizability, showing an improvement of flattened minima.

Wenlong Shi, Jianxun Lian, Mingqi Wu et al.

Large language models (LLMs) increasingly serve as interactive social agents, yet their ability to maintain coherent and authentic persona-level role-playing remains limited, particularly in realistic social scenarios. Existing research predominantly focuses on character-level settings and relies on static evaluation formats, failing to capture the complexity of everyday social interactions. In this work, we present PersonaArena, a dynamic simulation framework for evaluating and improving persona-level role-playing in LLMs. PersonaArena leverages a large, filtered corpus of user-generated social content to construct a nuanced persona bank, and elicits multi-turn, context-rich interactions within simulated social environments. Our framework features a multi-agent debating judge for holistic and unbiased assessment. Through extensive experiments, we demonstrate that PersonaArena enables rigorous evaluation and enhancement of LLMs' role-playing capabilities, advancing the development of more authentic and socially adept AI agents.

Hao Liao, Wensheng Lu, Jianxun Lian et al.

Large Language Models (LLMs) have shown promise for generative recommender systems due to their transformative capabilities in user interaction. However, ensuring they do not recommend out-of-domain (OOD) items remains a challenge. We study two distinct methods to address this issue: RecLM-ret, a retrieval-based method, and RecLM-cgen, a constrained generation method. Both methods integrate seamlessly with existing LLMs to ensure in-domain recommendations. Comprehensive experiments on three recommendation datasets demonstrate that RecLM-cgen consistently outperforms RecLM-ret and existing LLM-based recommender models in accuracy while eliminating OOD recommendations, making it the preferred method for adoption. Additionally, RecLM-cgen maintains strong generalist capabilities and is a lightweight plug-and-play module for easy integration into LLMs, offering valuable practical benefits for the community. Source code is available at https://github.com/microsoft/RecAI

Chia-Hsuan Lee, Mingyang Zhou, Renkun Ni et al.

Preference optimization methods such as DPO and KTO are widely used for aligning language models, yet little is understood about what properties of preference data drive downstream reasoning gains. We ask: what aspects of a preference pair improve a reasoning model's performance on general reasoning tasks? We investigate two distinct notions of quality delta in preference data: generator-level delta, arising from the differences in capability between models that generate chosen and rejected reasoning traces, and sample-level delta, arising from differences in judged quality differences within an individual preference pair. To study generator-level delta, we vary the generator's scale and model family, and to study sample-level delta, we employ an LLM-as-a-judge to rate the quality of generated traces along multiple reasoning-quality dimensions. We find that increasing generator-level delta steadily improves performance on out-of-domain reasoning tasks and filtering data by sample-level delta can enable more data-efficient training. Our results suggest a twofold recipe for improving reasoning performance through preference optimization: maximize generator-level delta when constructing preference pairs and exploit sample-level delta to select the most informative training examples.

Zhenqian Shen, Mingyang Zhou, Yongqi Zhang et al.

Motivation: Emerging drug-drug interaction (DDI) prediction is crucial for new drugs but is hindered by distribution changes between known and new drugs in real-world scenarios. Current evaluation often neglects these changes, relying on unrealistic i.i.d. split due to the absence of drug approval data. Results: We propose DDI-Ben, a benchmarking framework for emerging DDI prediction under distribution changes. DDI-Ben introduces a distribution change simulation framework that leverages distribution changes between drug sets as a surrogate for real-world distribution changes of DDIs, and is compatible with various drug split strategies. Through extensive benchmarking on ten representative methods, we show that most existing approaches suffer substantial performance degradation under distribution changes. Our analysis further indicates that large language model (LLM) based methods and the integration of drug-related textual information offer promising robustness against such degradation. To support future research, we release the benchmark datasets with simulated distribution changes. Overall, DDI-Ben highlights the importance of explicitly addressing distribution changes and provides a foundation for developing more resilient methods for emerging DDI prediction. Availability and implementation: Our code and data are available at https://github.com/LARS-research/DDI-Bench.

Wensheng Lu, Jianxun Lian, Wei Zhang et al.

Inspired by the exceptional general intelligence of Large Language Models (LLMs), researchers have begun to explore their application in pioneering the next generation of recommender systems - systems that are conversational, explainable, and controllable. However, existing literature primarily concentrates on integrating domain-specific knowledge into LLMs to enhance accuracy, often neglecting the ability to follow instructions. To address this gap, we initially introduce a collection of supervised learning tasks, augmented with labels derived from a conventional recommender model, aimed at explicitly improving LLMs' proficiency in adhering to recommendation-specific instructions. Subsequently, we develop a reinforcement learning-based alignment procedure to further strengthen LLMs' aptitude in responding to users' intentions and mitigating formatting errors. Through extensive experiments on two real-world datasets, our method markedly advances the capability of LLMs to comply with instructions within recommender systems, while sustaining a high level of accuracy performance.

Qimin Zhong, Hao Liao, Haiming Qin et al.

Whether Large Language Models (LLMs) develop coherent internal world models remains a core debate. While conventional Next-Token Prediction (NTP) focuses on one-step-ahead supervision, Multi-Token Prediction (MTP) has shown promise in learning more structured representations. In this work, we provide a theoretical perspective analyzing the gradient inductive bias of MTP, supported by empirical evidence, showing that MTP promotes the convergence toward internal belief states by inducing representational contractivity via gradient coupling. However, we reveal that standard MTP often suffers from structural hallucinations, where discrete token supervision encourages illegal shortcuts in latent space that violate environmental constraints. To address this, we propose a novel method Latent Semantic Enhancement MTP (LSE-MTP), which anchors predictions to ground-truth hidden state trajectories. Experiments on synthetic graphs and real-world Manhattan Taxi Ride show that LSE-MTP effectively bridges the gap between discrete tokens and continuous state representations, enhancing representation alignment, reducing structural hallucinations, and improving robustness to perturbations.

Mingyang Zhou, Quanming Yao, Lun Du et al.

Reproducing machine learning papers is essential for scientific progress but remains challenging for both humans and automated agents. Existing agent-based methods often struggle to fully and accurately reproduce implementation details such as mathematical formulas and algorithmic logic. Previous studies show that reflection with explicit feedback improves agent performance. However, current paper reproduction methods fail to effectively adopt this strategy. This gap mainly arises from the diverse paper patterns, complex method modules, and varied configurations encountered in research papers. Motivated by how humans use systematic checklists to efficiently debug complex code, we propose \textbf{RePro}, a \textbf{Re}flective Paper-to-Code \textbf{Repro}duction framework that automatically extracts a paper's fingerprint, referring to a comprehensive set of accurate and atomic criteria serving as high-quality supervisory signals. The framework first generates code based on the extracted information, and then leverages the fingerprint within iterative verification and refinement loop. This approach systematically detects discrepancies and produces targeted revisions to align generated code with the paper's implementation details. Extensive experiments on the PaperBench Code-Dev benchmark have been conducted, RePro achieves 13.0\% performance gap over baselines, and it correctly revises complex logical and mathematical criteria in reflecting, on which the effectiveness is obvious.

Qimin Zhong, Hao Liao, Siwei Wang et al.

Large Language Models (LLMs) have achieved impressive performance across diverse tasks but continue to struggle with learning transitive relations, a cornerstone for complex planning. To address this issue, we investigate the Multi-Token Prediction (MTP) paradigm and its impact to transitive relation learning. We theoretically analyze the MTP paradigm using a Transformer architecture composed of a shared output head and a transfer layer. Our analysis reveals that the transfer layer gradually learns the multi-step adjacency information, which in turn enables the backbone model to capture unobserved transitive reachability relations beyond those directly present in the training data, albeit with some inevitable noise in adjacency estimation. Building on this foundation, we propose two strategies to enhance the transfer layer and overall learning quality: Next-Token Injection (NTI) and a Transformer-based transfer layer. Our experiments on both synthetic graphs and the Blocksworld planning benchmark validate our theoretical findings and demonstrate that the improvements significantly enhance the model's path-planning capability. These findings deepen our understanding of how Transformers with MTP learn in complex planning tasks, and provide practical strategies to overcome the transitivity bottleneck, paving the way toward structurally aware and general-purpose planning models.

Mingyang Zhou, Yi R. Fung, Long Chen et al.

Building cross-model intelligence that can understand charts and communicate the salient information hidden behind them is an appealing challenge in the vision and language(V+L) community. The capability to uncover the underlined table data of chart figures is a critical key to automatic chart understanding. We introduce ChartT5, a V+L model that learns how to interpret table information from chart images via cross-modal pre-training on plot table pairs. Specifically, we propose two novel pre-training objectives: Masked Header Prediction (MHP) and Masked Value Prediction (MVP) to facilitate the model with different skills to interpret the table information. We have conducted extensive experiments on chart question answering and chart summarization to verify the effectiveness of the proposed pre-training strategies. In particular, on the ChartQA benchmark, our ChartT5 outperforms the state-of-the-art non-pretraining methods by over 8% performance gains.

Mingyang Zhou, Mahasweta Chakraborti, Sijia Qian et al.

Sharing of anti-vaccine posts on social media, including misinformation posts, has been shown to create confusion and reduce the publics confidence in vaccines, leading to vaccine hesitancy and resistance. Recent years have witnessed the fast rise of such anti-vaccine posts in a variety of linguistic and visual forms in online networks, posing a great challenge for effective content moderation and tracking. Extending previous work on leveraging textual information to understand vaccine information, this paper presents Insta-VAX, a new multi-modal dataset consisting of a sample of 64,957 Instagram posts related to human vaccines. We applied a crowdsourced annotation procedure verified by two trained expert judges to this dataset. We then bench-marked several state-of-the-art NLP and computer vision classifiers to detect whether the posts show anti-vaccine attitude and whether they contain misinformation. Extensive experiments and analyses demonstrate the multimodal models can classify the posts more accurately than the uni-modal models, but still need improvement especially on visual context understanding and external knowledge cooperation. The dataset and classifiers contribute to monitoring and tracking of vaccine discussions for social scientific and public health efforts in combating the problem of vaccine misinformation.

Mingyang Zhou, Luowei Zhou, Shuohang Wang et al.

Vision-and-language pre-training has achieved impressive success in learning multimodal representations between vision and language. To generalize this success to non-English languages, we introduce UC2, the first machine translation-augmented framework for cross-lingual cross-modal representation learning. To tackle the scarcity problem of multilingual captions for image datasets, we first augment existing English-only datasets with other languages via machine translation (MT). Then we extend the standard Masked Language Modeling and Image-Text Matching training objectives to multilingual setting, where alignment between different languages is captured through shared visual context (i.e, using image as pivot). To facilitate the learning of a joint embedding space of images and all languages of interest, we further propose two novel pre-training tasks, namely Masked Region-to-Token Modeling (MRTM) and Visual Translation Language Modeling (VTLM), leveraging MT-enhanced translated data. Evaluation on multilingual image-text retrieval and multilingual visual question answering benchmarks demonstrates that our proposed framework achieves new state-of-the-art on diverse non-English benchmarks while maintaining comparable performance to monolingual pre-trained models on English tasks.

Kaihui Liang, Austin Chau, Yu Li et al.

Gunrock 2.0 is built on top of Gunrock with an emphasis on user adaptation. Gunrock 2.0 combines various neural natural language understanding modules, including named entity detection, linking, and dialog act prediction, to improve user understanding. Its dialog management is a hierarchical model that handles various topics, such as movies, music, and sports. The system-level dialog manager can handle question detection, acknowledgment, error handling, and additional functions, making downstream modules much easier to design and implement. The dialog manager also adapts its topic selection to accommodate different users' profile information, such as inferred gender and personality. The generation model is a mix of templates and neural generation models. Gunrock 2.0 is able to achieve an average rating of 3.73 at its latest build from May 29th to June 4th.

Hao Liao, Jiao Wu, Mingyang Zhou et al.

The goal of the ranking problem in networks is to rank nodes from best to worst, according to a chosen criterion. In this work, we focus on ranking the nodes according to their quality. The problem of ranking the nodes in bipartite networks is valuable for many real-world applications. For instance, high-quality products can be promoted on an online shop or highly reputed restaurants attract more people on venues review platforms. However, many classical ranking algorithms share a common drawback: they tend to rank older movies higher than newer movies, though some newer movies may have a high quality. This time bias originates from the fact that older nodes in a network tend to have more connections than newer ones. In the study, we develop a ranking method using a rebalance approach to diminish the time bias of the rankings in bipartite graphs.

Dian Yu, Michelle Cohn, Yi Mang Yang et al.

Gunrock is the winner of the 2018 Amazon Alexa Prize, as evaluated by coherence and engagement from both real users and Amazon-selected expert conversationalists. We focus on understanding complex sentences and having in-depth conversations in open domains. In this paper, we introduce some innovative system designs and related validation analysis. Overall, we found that users produce longer sentences to Gunrock, which are directly related to users' engagement (e.g., ratings, number of turns). Additionally, users' backstory queries about Gunrock are positively correlated to user satisfaction. Finally, we found dialog flows that interleave facts and personal opinions and stories lead to better user satisfaction.

Mingyang Zhou, Josh Arnold, Zhou Yu

Reinforcement learning (RL) is an effective approach to learn an optimal dialog policy for task-oriented visual dialog systems. A common practice is to apply RL on a neural sequence-to-sequence (seq2seq) framework with the action space being the output vocabulary in the decoder. However, it is difficult to design a reward function that can achieve a balance between learning an effective policy and generating a natural dialog response. This paper proposes a novel framework that alternatively trains a RL policy for image guessing and a supervised seq2seq model to improve dialog generation quality. We evaluate our framework on the GuessWhich task and the framework achieves the state-of-the-art performance in both task completion and dialog quality.

Mingyang Zhou, Runxiang Cheng, Yong Jae Lee et al.

We introduce a novel multimodal machine translation model that utilizes parallel visual and textual information. Our model jointly optimizes the learning of a shared visual-language embedding and a translator. The model leverages a visual attention grounding mechanism that links the visual semantics with the corresponding textual semantics. Our approach achieves competitive state-of-the-art results on the Multi30K and the Ambiguous COCO datasets. We also collected a new multilingual multimodal product description dataset to simulate a real-world international online shopping scenario. On this dataset, our visual attention grounding model outperforms other methods by a large margin.

Aaron Gerow, Mingyang Zhou, Stan Matwin et al.

Bipartite data is common in data engineering and brings unique challenges, particularly when it comes to clustering tasks that impose on strong structural assumptions. This work presents an unsupervised method for assessing similarity in bipartite data. Similar to some co-clustering methods, the method is based on regular equivalence in graphs. The algorithm uses spectral properties of a bipartite adjacency matrix to estimate similarity in both dimensions. The method is reflexive in that similarity in one dimension is used to inform similarity in the other. Reflexive regular equivalence can also use the structure of transitivities -- in a network sense -- the contribution of which is controlled by the algorithm's only free-parameter, $α$. The method is completely unsupervised and can be used to validate assumptions of co-similarity, which are required but often untested, in co-clustering analyses. Three variants of the method with different normalizations are tested on synthetic data. The method is found to be robust to noise and well-suited to asymmetric co-similar structure, making it particularly informative for cluster analysis and recommendation in bipartite data of unknown structure. In experiments, the convergence and speed of the algorithm are found to be stable for different levels of noise. Real-world data from a network of malaria genes are analyzed, where the similarity produced by the reflexive method is shown to out-perform other measures' ability to correctly classify genes.