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Applications · Genetics, Cell Biology, Health, etc

Zhenyi Zhang, Tiejun Li, Peijie Zhou

Reconstructing dynamics using samples from sparsely time-resolved snapshots is an important problem in both natural sciences and machine learning. Here, we introduce a new deep learning approach for solving regularized unbalanced optimal transport (RUOT) and inferring continuous unbalanced stochastic dynamics from observed snapshots. Based on the RUOT form, our method models these dynamics without requiring prior knowledge of growth and death processes or additional information, allowing them to be learned directly from data. Theoretically, we explore the connections between the RUOT and Schrödinger bridge problem and discuss the key challenges and potential solutions. The effectiveness of our method is demonstrated with a synthetic gene regulatory network, high-dimensional Gaussian Mixture Model, and single-cell RNA-seq data from blood development. Compared with other methods, our approach accurately identifies growth and transition patterns, eliminates false transitions, and constructs the Waddington developmental landscape. Our code is available at: [https://github.com/zhenyiizhang/DeepRUOT](https://github.com/zhenyiizhang/DeepRUOT).

Runzhe Wu, Ayush Sekhari, Akshay Krishnamurthy, Wen Sun

We study computationally and statistically efficient Reinforcement Learning algorithms for the *linear Bellman Complete* setting. This setting uses linear function approximation to capture value functions and unifies existing models like linear Markov Decision Processes (MDP) and Linear Quadratic Regulators (LQR). While it is known from the prior works that this setting is statistically tractable, it remained open whether a computationally efficient algorithm exists. Our work provides a computationally efficient algorithm for the linear Bellman complete setting that works for MDPs with large action spaces, random initial states, and random rewards but relies on the underlying dynamics to be deterministic. Our approach is based on randomization: we inject random noise into least squares regression problems to perform optimistic value iteration. Our key technical contribution is to carefully design the noise to only act in the null space of the training data to ensure optimism while circumventing a subtle error amplification issue.

Deep Learning · Large Language Models

Maojia Song, Shang Hong Sim, Rishabh Bhardwaj, Hai Leong Chieu, Navonil Majumder, Soujanya Poria

LLMs are an integral component of retrieval-augmented generation (RAG) systems. While many studies focus on evaluating the overall quality of end-to-end RAG systems, there is a gap in understanding the appropriateness of LLMs for the RAG task. To address this, we introduce Trust-Score, a holistic metric that evaluates the trustworthiness of LLMs within the RAG framework. Our results show that various prompting methods, such as in-context learning, fail to effectively adapt LLMs to the RAG task as measured by Trust-Score. Consequently, we propose Trust-Align, a method to align LLMs for improved Trust-Score performance. 26 out of 27 models aligned using Trust-Align substantially outperform competitive baselines on ASQA, QAMPARI, and ELI5. Specifically, in LLaMA-3-8b, Trust-Align outperforms FRONT on ASQA (↑12.56), QAMPARI (↑36.04), and ELI5 (↑17.69). Trust-Align also significantly enhances models’ ability to correctly refuse and provide quality citations. We also demonstrate the effectiveness of Trust-Align across different open-weight models, including the LLaMA series (1b to 8b), Qwen-2.5 series (0.5b to 7b), and Phi3.5 (3.8b). We release our code at https://github.com/declare-lab/trust-align.

Siyu Chen, Beining Wu, Miao Lu, Zhuoran Yang, Tianhao Wang

In this work, we tackle the following question: Can neural networks trained with gradient-based methods achieve the optimal statistical-computational tradeoff in learning Gaussian single-index models? Prior research has shown that any polynomial-time algorithm under the statistical query (SQ) framework requires $\Omega(d^{s^\star/2}\lor d)$ samples, where $s^\star$ is the generative exponent representing the intrinsic difficulty of learning the underlying model.However, it remains unknown whether neural networks can achieve this sample complexity. Inspired by prior techniques such as label transformation and landscape smoothing for learning single-index models, we propose a unified gradient-based algorithm for training a two-layer neural network in polynomial time.Our method is adaptable to a variety of loss and activation functions, covering a broad class of existing approaches.We show that our algorithm learns a feature representation that strongly aligns with the unknown signal $\theta^\star$, with sample complexity $\tilde O (d^{s^\star/2} \lor d)$, matching the SQ lower bound up to a polylogarithmic factor for all generative exponents $s^\star\geq 1$.Furthermore, we extend our approach to the setting where $\theta^\star$ is $k$-sparse for $k = o(\sqrt{d})$ by introducing a novel weight perturbation technique that leverages the sparsity structure. We derive a corresponding SQ lower bound of order $\tilde\Omega(k^{s^\star})$, matched by our method up to a polylogarithmic factor.Our framework, especially the weight perturbation technique, is of independent interest, and suggests potential gradient-based solutions to other problems such as sparse tensor PCA.

Mintong Kang, Chejian Xu, Bo Li

Recent advancements in large audio-language models (LALMs) have enabled speech-based user interactions, significantly enhancing user experience and accelerating the deployment of LALMs in real-world applications. However, ensuring the safety of LALMs is crucial to prevent risky outputs that may raise societal concerns or violate AI regulations. Despite the importance of this issue, research on jailbreaking LALMs remains limited due to their recent emergence and the additional technical challenges they present compared to attacks on DNN-based audio models. Specifically, the audio encoders in LALMs, which involve discretization operations, often lead to gradient shattering, hindering the effectiveness of attacks relying on gradient-based optimizations. The behavioral variability of LALMs further complicates the identification of effective (adversarial) optimization targets. Moreover, enforcing stealthiness constraints on adversarial audio waveforms introduces a reduced, non-convex feasible solution space, further intensifying the challenges of the optimization process. To overcome these challenges, we develop AdvWave, the first jailbreak framework against LALMs. We propose a dual-phase optimization method that addresses gradient shattering, enabling effective end-to-end gradient-based optimization. Additionally, we develop an adaptive adversarial target search algorithm that dynamically adjusts the adversarial optimization target based on the response patterns of LALMs for specific queries. To ensure that adversarial audio remains perceptually natural to human listeners, we design a classifier-guided optimization approach that generates adversarial noise resembling common urban sounds. Extensive evaluations on multiple advanced LALMs demonstrate that AdvWave outperforms baseline methods, achieving a 40\% higher average jailbreak attack success rate. Both audio stealthiness metrics and human evaluations confirm that adversarial audio generated by AdvWave is indistinguishable from natural sounds. We believe AdvWave will inspire future research aiming to enhance the safety alignment of LALMs, supporting their responsible deployment in real-world scenarios.

Mintong Kang, Bo Li

As large language models (LLMs) become increasingly prevalent across various applications, it is critical to establish safety guardrails to moderate input/output content of LLMs and ensure compliance with safety policies. Existing guardrail models, such as OpenAI Mod and LlamaGuard, treat various safety categories (e.g., self-harm, self-harm/instructions) independently and fail to explicitly capture the intercorrelations among them. This has led to limitations such as ineffectiveness due to inadequate training on long-tail data from correlated safety categories, susceptibility to jailbreaking attacks, and inflexibility regarding new safety categories.To address these limitations, we propose $R^2$-Guard, a robust reasoning enabled LLM guardrail via knowledge-enhanced logical reasoning. Specifically, $R^2$-Guard comprises two parts: data-driven guardrail models and reasoning components. The data-driven guardrail models provide unsafety probabilities of moderated content on different safety categories.We then encode safety knowledge among different categories as first-order logical rules and embed them into a probabilistic graphic model (PGM) based reasoning component. The unsafety probabilities of different categories from data-driven guardrail models are sent to the reasoning component for final inference. We employ two types of PGMs: Markov logic networks (MLNs) and probabilistic circuits (PCs), and optimize PCs to achieve precision-efficiency balance via improved graph structure. We also propose different methods to optimize the weights of knowledge. To further perform stress tests for guardrail models, we employ a pairwise construction method to construct a new safety benchmark TwinSafety, which features principled categories and presents new challenges for moderation. We show that $R^2$-Guard is effective even given unrepresentative categories or challenging jailbreaking prompts. We demonstrate the effectiveness of $R^2$-Guard by comparisons with eight strong guardrail models on six standard moderation datasets, and demonstrate the robustness of $R^2$-Guard against four SOTA jailbreaking attacks. $R^2$-Guard significantly surpasses SOTA method LlamaGuard by 12.6% on standard moderation datasets and by 59.9% against jailbreaking attacks.We further reveal that $R^2$-Guard can effectively adapt to safety category updates by simply editing the PGM reasoning graph.

Deep Learning · Generative Models and Autoencoders

Marianne Arriola, Aaron Gokaslan, Justin Chiu, Zhihan Yang, Zhixuan Qi, Jiaqi Han, Subham Sahoo, Volodymyr Kuleshov

Diffusion language models offer unique benefits over autoregressive models due to their potential for parallelized generation and controllability, yet they lag in likelihood modeling and are limited to fixed-length generation. In this work, we introduce a class of block diffusion language models that interpolate between discrete denoising diffusion and autoregressive models. Block diffusion overcomes key limitations of both approaches by supporting flexible-length generation and improving inference efficiency with KV caching and parallel token sampling. We propose a recipe for building effective block diffusion models that includes an efficient training algorithm, estimators of gradient variance, and data-driven noise schedules to minimize the variance. Block diffusion sets a new state-of-the-art performance among diffusion models on language modeling benchmarks and enables generation of arbitrary-length sequences. We provide the code, along with the model weights and blog post on the project page: https://m-arriola.com/bd3lms/

Ricardo Dominguez-Olmedo, Florian Eddie Dorner, Moritz Hardt

We study a fundamental problem in the evaluation of large language models that we call training on the test task. Unlike wrongful practices like training on the test data, leakage, or data contamination, training on the test task is not a malpractice. Rather, the term describes a growing set of techniques to include task-relevant data in the pretraining stage of a language model. We demonstrate that training on the test task confounds both relative model evaluations and claims about emergent capabilities. We argue that the seeming superiority of one model family over another may be explained by a different degree of training on the test task. To this end, we propose an effective method to adjust for the effect of training on the test task on benchmark evaluations. Put simply, to fine-tune each model under comparison on the same task-relevant data before evaluation. Lastly, we show that instances of emergent behavior disappear gradually as models train on the test task. Our work promotes a new perspective on the evaluation of large language models with broad implications for benchmarking and the study of emergent capabilities.

Haitao Lin, Guojiang Zhao, Odin Zhang, Yufei Huang, Lirong Wu, Cheng Tan, Zicheng Liu, Zhifeng Gao, Stan Z Li

Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. However, a lack of systematic understanding persists due to the diverse settings, complex implementation, difficult reproducibility, and task singularity. Firstly, the absence of standardization can lead to unfair comparisons and inconclusive insights. To address this dilemma, we propose CBGBench, a comprehensive benchmark for SBDD, that unifies the task as a generative graph completion, analogous to fill-in-the-blank of the 3D complex binding graph. By categorizing existing methods based on their attributes, CBGBench facilitates a modular and extensible framework that implements cutting-edge methods. Secondly, a single de novo molecule generation task can hardly reflect their capabilities. To broaden the scope, we adapt these models to a range of tasks essential in drug design, considered sub-tasks within the graph fill-in-the-blank tasks. These tasks include the generative designation of de novo molecules, linkers, fragments, scaffolds, and sidechains, all conditioned on the structures of protein pockets. Our evaluations are conducted with fairness, encompassing comprehensive perspectives on interaction, chemical properties, geometry authenticity, and substructure validity. We further provide insights with analysis from empirical studies. Our results indicate that there is potential for further improvements on many tasks, with optimization in network architectures, and effective incorporation of chemical prior knowledge. Finally, to lower the barrier to entry and facilitate further developments in the field, we also provide a single [codebase](https://github.com/EDAPINENUT/CBGBench) that unifies the discussed models, data pre-processing, training, sampling, and evaluation.

Applications · Computer Vision

Huayu Chen, Hang Su, Peize Sun, Jun Zhu

Classifier-Free Guidance (CFG) is a critical technique for enhancing the sample quality of visual generative models. However, in autoregressive (AR) multi-modal generation, CFG introduces design inconsistencies between language and visual content, contradicting the design philosophy of unifying different modalities for visual AR. Motivated by language model alignment methods, we propose Condition Contrastive Alignment (CCA) to facilitate guidance-free AR visual generation. Unlike guidance methods that alter the sampling process to achieve the ideal sampling distribution, CCA directly fine-tunes pretrained models to fit the same distribution target. Experimental results show that CCA can significantly enhance the guidance-free performance of all tested models with just one epoch of fine-tuning (1% of pretraining epochs) on the pretraining dataset. This largely removes the need for guided sampling in AR visual generation and cuts the sampling cost by half. Moreover, by adjusting training parameters, CCA can achieve trade-offs between sample diversity and fidelity similar to CFG. This experimentally confirms the strong theoretical connection between language-targeted alignment and visual-targeted guidance methods, unifying two previously independent research fields.

Yang Tian, Sizhe Yang, Jia Zeng, Ping Wang, Dahua Lin, Hao Dong, Jiangmiao Pang

Current efforts to learn scalable policies in robotic manipulation primarily fall into two categories: one focuses on "action," which involves behavior cloning from extensive collections of robotic data, while the other emphasizes "vision," enhancing model generalization by pre-training representations or generative models, also referred to as world models, using large-scale visual datasets. This paper presents an end-to-end paradigm that predicts actions using inverse dynamics models conditioned on the robot's forecasted visual states, named Predictive Inverse Dynamics Models (PIDM). By closing the loop between vision and action, the end-to-end PIDM can be a better scalable action learner. In practice, we use Transformers to process both visual states and actions, naming the model Seer. It is initially pre-trained on large-scale robotic datasets, such as DROID, and can be adapted to real-world scenarios with a little fine-tuning data. Thanks to large-scale, end-to-end training and the continuous synergy between vision and action at each execution step, Seer significantly outperforms state-of-the-art methods across both simulation and real-world experiments. It achieves improvements of 13% on the LIBERO-LONG benchmark, 22% on CALVIN ABC-D, and 43% in real-world tasks. Notably, it demonstrates superior generalization for novel objects, lighting conditions, and environments under high-intensity disturbances. Code and models will be publicly available.

Deep Learning · Large Language Models

Xiao Yu, Baolin Peng, Vineeth Vajipey, Hao Cheng, Michel Galley, Jianfeng Gao, Zhou Yu

Autonomous agents have demonstrated significant potential in automating complex multistep decision-making tasks. However, even state-of-the-art vision-language models (VLMs), such as GPT-4o, still fall short of human-level performance, particularly in intricate web environments and long-horizon planning tasks. To address these limitations, we introduce Reflective Monte Carlo Tree Search (R-MCTS), a novel test-time algorithm designed to enhance the ability of AI agents, e.g., powered by GPT-4o, to explore decision space on the fly.R-MCTS extends traditional MCTS by 1) incorporating contrastive reflection, allowing agents to learn from past interactions and dynamically improve their search efficiency; and 2) using multi-agent debate to provide reliable state evaluation. Moreover, we improve the agent's performance by fine-tuning GPT-4o through self-learning, using R-MCTS generated tree traversals without any human-provided labels. On the challenging VisualWebArena benchmark, our GPT-4o-based R-MCTS agent achieves a 6% to 30% relative improvement across various tasks compared to the previous state-of-the-art. Additionally, we show that the knowledge gained from test-time search can be effectively transferred back to GPT-4o via fine-tuning. The fine-tuned GPT-4o matches 97\% of R-MCTS's performance while reducing compute usage by a factor of four at test time. Furthermore, qualitative results reveal that the fine-tuned GPT-4o model demonstrates the ability to explore the environment, evaluate a state, and backtrack to viable ones when it detects that the current state cannot lead to success. Moreover, our work demonstrates the compute scaling properties in both training - data collection with R-MCTS - and testing time. These results suggest a promising research direction to enhance VLMs' reasoning and planning capabilities for agentic applications via test-time search and self-learning.

Optimization · Everything Else

Joshua Russell, Ignacio Gavier, Devdhar Patel, Edward Rietman, Hava Siegelmann

Neural networks are known to be universal computers for Boolean functions. Recent advancements in hardware have significantly reduced matrix multiplication times, making neural network simulation both fast and efficient. Consequently, functions defined by complex Boolean networks are increasingly viable candidates for simulation through their neural network representation. Prior research has introduced a general method for deriving neural network representations of Boolean networks. However, the resulting neural networks are often suboptimal in terms of the number of neurons and connections, leading to slower simulation performance. Optimizing them while preserving functional equivalence --lossless optimization-- is an NP-hard problem, and current methods only provide lossy solutions. In this paper, we present a deterministic algorithm to optimize such neural networks in terms of neurons and connections while preserving functional equivalence. Moreover, to accelerate the compression of the neural network, we introduce an objective-aware algorithm that exploits representations that are shared among subproblems of the overall optimization. We demonstrate experimentally that we are able to reduce connections and neurons by up to 70% and 60%, respectively, in comparison to state-of-the-art. We also find that our objective-aware algorithm results in consistent speedups in optimization time, achieving up to 34.3x and 5.9x speedup relative to naive and caching solutions, respectively. Our methods are of practical relevance to applications such as high-throughput circuit simulation and placing neurosymbolic systems on the same hardware architecture.

Yuda Song, Hanlin Zhang, Carson Eisenach, Sham Kakade, Dean Foster, Udaya Ghai

Self-improvement is a mechanism in Large Language Model (LLM) pre-training, post-training and test-time inference. We explore a framework where the model verifies its own outputs, filters or reweights data based on this verification, and distills the filtered data. Despite several empirical successes, a fundamental understanding is still lacking. In this work, we initiate a comprehensive, modular and controlled study on LLM self-improvement. We provide a mathematical formulation for self-improvement, which is largely governed by a quantity which we formalize as the **generation-verification gap**. Through experiments with various model families and tasks, we discover a scaling phenomenon of self-improvement -- a variant of the generation-verification gap scales monotonically with the model pre-training flops. We also examine when self-improvement is possible, an iterative self-improvement procedure, and ways to improve its performance. Our findings not only advance understanding of LLM self-improvement with practical implications, but also open numerous avenues for future research into its capabilities and boundaries.

Optimization · Learning for Optimization

Xinsong Feng, Zihan Yu, Yanhai Xiong, Haipeng Chen

Reinforcement learning (RL) has emerged as a promising tool for combinatorial optimization (CO) problems due to its ability to learn fast, effective, and generalizable solutions. Nonetheless, existing works mostly focus on one-shot deterministic CO, while sequential stochastic CO (SSCO) has rarely been studied despite its broad applications such as adaptive influence maximization (IM) and infectious disease intervention. In this paper, we study the SSCO problem where we first decide the budget (e.g., number of seed nodes in adaptive IM) allocation for all time steps, and then select a set of nodes for each time step. The few existing studies on SSCO simplify the problems by assuming a uniformly distributed budget allocation over the time horizon, yielding suboptimal solutions. We propose a generic hierarchical RL (HRL) framework called wake-sleep option (WS-option), a two-layer option-based framework that simultaneously decides adaptive budget allocation on the higher layer and node selection on the lower layer. WS-option starts with a coherent formulation of the two-layer Markov decision processes (MDPs), capturing the interdependencies between the two layers of decisions. Building on this, WS-option employs several innovative designs to balance the model's training stability and computational efficiency, preventing the vicious cyclic interference issue between the two layers. Empirical results show that WS-option exhibits significantly improved effectiveness and generalizability compared to traditional methods. Moreover, the learned model can be generalized to larger graphs, which significantly reduces the overhead of computational resources.

Gregor Bachmann, Sotiris Anagnostidis, Albert Pumarola, Markos Georgopoulos, Artsiom Sanakoyeu, Yuming Du, Edgar Schoenfeld, Ali Thabet, Jonas Kohler

The performance of large language models (LLMs) is closely linked to their underlying size, leading to ever-growing networks and hence slower inference. Speculative decoding has been proposed as a technique to accelerate autoregressive generation, leveraging a fast draft model to propose candidate tokens, which are then verified in parallel based on their likelihood under the target model. While this approach guarantees to reproduce the target output, it incurs a substantial penalty: many high-quality draft tokens are rejected, even when they represent objectively valid continuations. Indeed, we show that even powerful draft models such as GPT-4o, as well as human text cannot achieve high acceptance rates under the standard verification scheme. This severely limits the speedup potential of current speculative decoding methods, as an early rejection becomes overwhelmingly likely when solely relying on alignment of draft and target.We thus ask the following question: Can we adapt verification to recognize correct, but non-aligned replies? To this end, we draw inspiration from the LLM-as-a-judge framework, which demonstrated that LLMs are able to rate answers in a versatile way. We carefully design a dataset coined TokenCourt to elicit the same capability in the target model by training a compact module on top of the embeddings to produce ``judgements" of the current continuation. We showcase our strategy on the Llama-3.1 family, where our 8B/405B-Judge achieves a speedup of $9\times$ over Llama-405B, while maintaining its quality on a large range of benchmarks. These benefits remain present even in optimized inference frameworks, where our method reaches up to $141$ tokens/s for 8B/70B-Judge and $129$ tokens/s for 8B/405B on $2$ and $8$ H100s respectively.

Martin Klissarov, Mikael Henaff, Roberta Raileanu, Shagun Sodhani, Pascal Vincent, Amy Zhang, Pierre-Luc Bacon, Doina Precup, Marlos C. Machado, Pierluca D'Oro

Describing skills in natural language has the potential to provide an accessible way to inject human knowledge about decision-making into an AI system. We present MaestroMotif, a method for AI-assisted skill design, which yields high-performing and adaptable agents. MaestroMotif leverages the capabilities of Large Language Models (LLMs) to effectively create and reuse skills. It first uses an LLM's feedback to automatically design rewards corresponding to each skill, starting from their natural language description. Then, it employs an LLM's code generation abilities, together with reinforcement learning, for training the skills and combining them to implement complex behaviors specified in language. We evaluate MaestroMotif using a suite of complex tasks in the NetHack Learning Environment (NLE), demonstrating that it surpasses existing approaches in both performance and usability.

Hexu Zhao, Haoyang Weng, Daohan Lu, Ang Li, Jinyang Li, Aurojit Panda, Saining Xie

3D Gaussian Splatting (3DGS) is increasingly popular for 3D reconstruction due to its superior visual quality and rendering speed. However, 3DGS training currently occurs on a single GPU, limiting its ability to handle high-resolution and large-scale 3D reconstruction tasks due to memory constraints. We introduce Grendel, a distributed system designed to partition 3DGS parameters and parallelize computation across multiple GPUs. As each Gaussian affects a small, dynamic subset of rendered pixels, Grendel employs sparse all-to-all communication to transfer the necessary Gaussians to pixel partitions and performs dynamic load balancing. Unlike existing 3DGS systems that train using one camera view image at a time, Grendel supports batched training with multiple views. We explore various optimization hyperparameter scaling strategies and find that a simple sqrt(batch-size) scaling rule is highly effective. Evaluations using large-scale, high-resolution scenes show that Grendel enhances rendering quality by scaling up 3DGS parameters across multiple GPUs. On the 4K ``Rubble'' dataset, we achieve a test PSNR of 27.28 by distributing 40.4 million Gaussians across 16 GPU, compared to a PSNR of 26.28 using 11.2 million Gaussians on a single GPU. Grendel is an open-source project available at: https://github.com/nyu-systems/Grendel-GS

Deep Learning · Graph Neural Networks

Jingchu Gai, Yiheng Du, Bohang Zhang, Haggai Maron, Liwei Wang

Graph spectra are an important class of structural features on graphs that have shown promising results in enhancing Graph Neural Networks (GNNs). Despite their widespread practical use, the theoretical understanding of the power of spectral invariants --- particularly their contribution to GNNs --- remains incomplete. In this paper, we address this fundamental question through the lens of homomorphism expressivity, providing a comprehensive and quantitative analysis of the expressive power of spectral invariants. Specifically, we prove that spectral invariant GNNs can homomorphism-count exactly a class of specific tree-like graphs which we refer to as \emph{parallel trees}. We highlight the significance of this result in various contexts, including establishing a quantitative expressiveness hierarchy across different architectural variants, offering insights into the impact of GNN depth, and understanding the subgraph counting capabilities of spectral invariant GNNs. In particular, our results significantly extend \citet{arvind2024hierarchy} and settle their open questions. Finally, we generalize our analysis to higher-order GNNs and answer an open question raised by \citet{zhang2024expressive}.

Applications · Computer Vision

Hejia Chen, Haoxian Zhang, Shoulong Zhang, Xiaoqiang Liu, Sisi Zhuang, zhangyuan, Pengfei Wan, Di ZHANG, Shuai Li

Speech-driven 3D talking face method should offer both accurate lip synchronization and controllable expressions. Previous methods solely adopt discrete emotion labels to globally control expressions throughout sequences while limiting flexible fine-grained facial control within the spatiotemporal domain. We propose a diffusion-transformer-based 3D talking face generation model, Cafe-Talk, which simultaneously incorporates coarse- and fine-grained multimodal control conditions. Nevertheless, the entanglement of multiple conditions challenges achieving satisfying performance. To disentangle speech audio and fine-grained conditions, we employ a two-stage training pipeline. Specifically, Cafe-Talk is initially trained using only speech audio and coarse-grained conditions. Then, a proposed fine-grained control adapter gradually adds fine-grained instructions represented by action units (AUs), preventing unfavorable speech-lip synchronization. To disentangle coarse- and fine-grained conditions, we design a swap-label training mechanism, which enables the dominance of the fine-grained conditions. We also devise a mask-based CFG technique to regulate the occurrence and intensity of fine-grained control. In addition, a text-based detector is introduced with text-AU alignment to enable natural language user input and further support multimodal control. Extensive experimental results prove that Cafe-Talk achieves state-of-the-art lip synchronization and expressiveness performance and receives wide acceptance in fine-grained control in user studies.