DeepNLP/ICML-2024-Accepted-Papers huggingface dataset:
LangCell: Language-Cell Pre-training for Cell Identity Understanding
Authors: Suyuan Zhao, Jiahuan Zhang, Yushuai Wu, Yizhen Luo, Zaiqing Nie

Cell identity encompasses various semantic aspects of a cell, including cell type, pathway information, disease information, and more, which are essential for biologists to gain insights into its biological characteristics. Understanding cell identity from the transcriptomic data, such as annotating cell types, has become an important task in bioinformatics. As these semantic aspects are determined by human experts, it is impossible for AI models to effectively carry out cell identity understanding tasks without the supervision signals provided by single-cell and label pairs. The single-cell pre-trained language models (PLMs) currently used for this task are trained only on a single modality, transcriptomics data, lack an understanding of cell identity knowledge. As a result, they have to be fine-tuned for downstream tasks and struggle when lacking labeled data with the desired semantic labels. To address this issue, we propose an innovative solution by constructing a unified representation of single-cell data and natural language during the pre-training phase, allowing the model to directly incorporate insights related to cell identity. More specifically, we introduce LangCell, the first Language-Cell pre-training framework. LangCell utilizes texts enriched with cell identity information to gain a profound comprehension of cross-modal knowledge. Results from experiments conducted on different benchmarks show that LangCell is the only single-cell PLM that can work effectively in zero-shot cell identity understanding scenarios, and also significantly outperforms existing models in few-shot and fine-tuning cell identity understanding scenarios.
Optimistic Multi-Agent Policy Gradient
Authors: Wenshuai Zhao, Yi Zhao, Zhiyuan Li, Juho Kannala, Joni Pajarinen

Relative overgeneralization (RO) occurs in cooperative multi-agent learning tasks when agents converge towards a suboptimal joint policy due to overfitting to suboptimal behaviors of other agents. No methods have been proposed for addressing RO in multi-agent policy gradient (MAPG) methods although these methods produce state-of-the-art results. To address this gap, we propose a general, yet simple, framework to enable optimistic updates in MAPG methods that alleviate the RO problem. Our approach involves clipping the advantage to eliminate negative values, thereby facilitating optimistic updates in MAPG. The optimism prevents individual agents from quickly converging to a local optimum. Additionally, we provide a formal analysis to show that the proposed method retains optimality at a fixed point. In extensive evaluations on a diverse set of tasks including the Multi-agent MuJoCo and Overcooked benchmarks, our method outperforms strong baselines on 13 out of 19 tested tasks and matches the performance on the rest.
Clifford-Steerable Convolutional Neural Networks
Authors: Maksim Zhdanov, David Ruhe, Maurice Weiler, Ana Lucic, Johannes Brandstetter, Patrick Forré

We present Clifford-Steerable Convolutional Neural Networks (CS-CNNs), a novel class of ${\operatorname{E}}(p, q)$-equivariant CNNs. CS-CNNs process multivector fields on pseudo-Euclidean spaces $\mathbb{R}^{p,q}$. They specialize, for instance, to ${\operatorname{E}}(3)$-equivariance on $\mathbb{R}^3$ and Poincaré-equivariance on Minkowski spacetime $\mathbb{R}^{1,3}$. Our approach is based on an implicit parametrization of ${\operatorname{O}}(p,q)$-steerable kernels via Clifford group equivariant neural networks. We significantly and consistently outperform baseline methods on fluid dynamics as well as relativistic electrodynamics forecasting tasks.
3D-VLA: A 3D Vision-Language-Action Generative World Model
Authors: Haoyu Zhen, Xiaowen Qiu, Peihao Chen, Jincheng Yang, Xin Yan, Yilun Du, Yining Hong, Chuang Gan

Recent vision-language-action (VLA) models rely on 2D inputs, lacking integration with the broader realm of the 3D physical world. Furthermore, they perform action prediction by learning a direct mapping from perception to action, neglecting the vast dynamics of the world and the relations between actions and dynamics. In contrast, human beings are endowed with world models that depict imagination about future scenarios to plan action accordingly. To this end, we propose 3D-VLA by introducing a new family of embodied foundation models that seamlessly link 3D perception, reasoning, and action through a generative world model. Specifically, 3D-VLA is built on top of a 3D-based large language model (LLM) and a set of action tokens is introduced to engage with the embodied environment. Furthermore, to inject generation abilities into the model, we train the embodied diffusion models and align them into the LLM for predicting the goal image and point cloud. To train our 3D-VLA, we curate a large-scale 3D embodied instruction dataset by extracting vast 3D-related information from existing robotics datasets. Our experiments on held-in datasets demonstrate that 3D-VLA significantly improves the reasoning, multimodality generation and planning capabilities in embodied environments, showcasing its potential in real-world applications.
How Does Goal Relabeling Improve Sample Efficiency?
Authors: Sirui Zheng, Chenjia Bai, Zhuoran Yang, Zhaoran Wang

Hindsight experience replay and goal relabeling are successful in reinforcement learning (RL) since they enable agents to learn from failures. Despite their successes, we lack a theoretical understanding, such as (i) why hindsight experience replay improves sample efficiency and (ii) how to design a relabeling method that achieves sample efficiency. To this end, we construct an example to show the information-theoretical improvement in sample efficiency achieved by goal relabeling. Our example reveals that goal relabeling can enhance sample efficiency and exploit the rich information in observations through better hypothesis elimination. Based on these insights, we develop an RL algorithm called GOALIVE. To analyze the sample complexity of GOALIVE, we introduce a complexity measure, the goal-conditioned Bellman-Eluder (GOAL-BE) dimension, which characterizes the sample complexity of goal-conditioned RL problems. Compared to the Bellman-Eluder dimension, the goal-conditioned version offers an exponential improvement in the best case. To the best of our knowledge, our work provides the first characterization of the theoretical improvement in sample efficiency achieved by goal relabeling.
PRISE: LLM-Style Sequence Compression for Learning Temporal Action Abstractions in Control
Authors: Ruijie Zheng, Ching-An Cheng, Hal Daumé Iii, Furong Huang, Andrey Kolobov

Temporal action abstractions, along with belief state representations, are a powerful knowledge sharing mechanism for sequential decision making. In this work, we propose a novel view that treats inducing temporal action abstractions as a sequence compression problem. To do so, we bring a subtle but critical component of LLM training pipelines – input tokenization via byte pair encoding (BPE) – to bear on the seemingly distant task of learning skills of variable time span in continuous control domains. We introduce an approach called Primitive Sequence Encoding (PRISE) that combines continuous action quantization with BPE to learn powerful action abstractions. We empirically show that high-level skills discovered by PRISE from a multitask set of robotic manipulation demonstrations significantly boost the learning performance of behavior cloning on downstream tasks.
Exploiting Negative Samples: A Catalyst for Cohort Discovery in Healthcare Analytics
Authors: Kaiping Zheng, Horng-Ruey Chua, Melanie Herschel, H. V. Jagadish, Beng Chin Ooi, James Wei Luen Yip

In healthcare analytics, addressing binary diagnosis or prognosis tasks presents unique challenges due to the inherent asymmetry between positive and negative samples. While positive samples, indicating patients with a disease, are defined based on stringent medical criteria, negative samples are defined in an open-ended manner and remain underexplored in prior research. To bridge this gap, we propose an innovative approach to facilitate cohort discovery within negative samples, leveraging a Shapley-based exploration of interrelationships between these samples, which holds promise for uncovering valuable insights concerning the studied disease, and related comorbidity and complications. We quantify each sample’s contribution using data Shapley values, subsequently constructing the Negative Sample Shapley Field to model the distribution of all negative samples. Next, we transform this field through manifold learning, preserving the essential data structure information while imposing an isotropy constraint in data Shapley values. Within this transformed space, we pinpoint cohorts of medical interest via density-based clustering. We empirically evaluate the effectiveness of our approach on the real-world electronic medical records from National University Hospital in Singapore, yielding clinically valuable insights aligned with existing knowledge, and benefiting medical research and clinical decision-making.
Constrained Exploration via Reflected Replica Exchange Stochastic Gradient Langevin Dynamics
Authors: Haoyang Zheng, Hengrong Du, Qi Feng, Wei Deng, Guang Lin

Replica exchange stochastic gradient Langevin dynamics (reSGLD) is an effective sampler for non-convex learning in large-scale datasets. However, the simulation may encounter stagnation issues when the high-temperature chain delves too deeply into the distribution tails. To tackle this issue, we propose reflected reSGLD (r2SGLD): an algorithm tailored for constrained non-convex exploration by utilizing reflection steps within a bounded domain. Theoretically, we observe that reducing the diameter of the domain enhances mixing rates, exhibiting a quadratic behavior. Empirically, we test its performance through extensive experiments, including identifying dynamical systems with physical constraints, simulations of constrained multi-modal distributions, and image classification tasks. The theoretical and empirical findings highlight the crucial role of constrained exploration in improving the simulation efficiency.
GPT-4V(ision) is a Generalist Web Agent, if Grounded
Authors: Boyuan Zheng, Boyu Gou, Jihyung Kil, Huan Sun, Yu Su

The recent development on large multimodal models (LMMs), especially GPT-4V(ision) and Gemini, has been quickly expanding the capability boundaries of multimodal models beyond traditional tasks like image captioning and visual question answering. In this work, we explore the potential of LMMs like GPT-4V as a generalist web agent that can follow natural language instructions to complete tasks on any given website. We propose SEEACT, a generalist web agent that harnesses the power of LMMs for integrated visual understanding and acting on the web. We evaluate on the recent MIND2WEB benchmark. In addition to standard offline evaluation on cached websites, we enable a new online evaluation setting by developing a tool that allows running web agents on live websites. We show that GPT-4V presents a great potential for web agents—it can successfully complete 51.1% of the tasks on live websites if we manually ground its textual plans into actions on the websites. This substantially outperforms text-only LLMs like GPT-4 or smaller models (FLAN-T5 and BLIP-2) specifically fine-tuned for web agents. However, grounding still remains a major challenge. Existing LMM grounding strategies like set-of-mark prompting turns out to be not effective for web agents, and the best grounding strategy we develop in this paper leverages both the HTML structure and visuals. Yet, there is still a substantial gap with oracle grounding, leaving ample room for further improvement. All code, data, and evaluation tools are available at https://github.com/OSU-NLP-Group/SeeAct.
Characteristic Guidance: Non-linear Correction for Diffusion Model at Large Guidance Scale
Authors: Candi Zheng, Yuan Lan

Popular guidance for denoising diffusion probabilistic model (DDPM) linearly combines distinct conditional models together to provide enhanced control over samples. However, this approach overlooks nonlinear effects that become significant when guidance scale is large. To address this issue, we propose characteristic guidance, a guidance method that provides first-principle non-linear correction for classifier-free guidance. Such correction forces the guided DDPMs to respect the Fokker-Planck (FP) equation of diffusion process, in a way that is training-free and compatible with existing sampling methods. Experiments show that characteristic guidance enhances semantic characteristics of prompts and mitigate irregularities in image generation, proving effective in diverse applications ranging from simulating magnet phase transitions to latent space sampling.
Premier-TACO is a Few-Shot Policy Learner: Pretraining Multitask Representation via Temporal Action-Driven Contrastive Loss
Authors: Ruijie Zheng, Yongyuan Liang, Xiyao Wang, Shuang Ma, Hal Daumé Iii, Huazhe Xu, John Langford, Praveen Palanisamy, Kalyan Shankar Basu, Furong Huang

We present Premier-TACO, a multitask feature representation learning approach designed to improve few-shot policy learning efficiency in sequential decision-making tasks. Premier-TACO leverages a subset of multitask offline datasets for pretraining a general feature representation, which captures critical environmental dynamics and is fine-tuned using minimal expert demonstrations. It advances the temporal action contrastive learning (TACO) objective, known for state-of-the-art results in visual control tasks, by incorporating a novel negative example sampling strategy. This strategy is crucial in significantly boosting TACO’s computational efficiency, making large-scale multitask offline pretraining feasible. Our extensive empirical evaluation in a diverse set of continuous control benchmarks including Deepmind Control Suite, MetaWorld, and LIBERO demonstrate Premier-TACO’s effective- ness in pretraining visual representations, significantly enhancing few-shot imitation learning of novel tasks.
ESM All-Atom: Multi-Scale Protein Language Model for Unified Molecular Modeling
Authors: Kangjie Zheng, Siyu Long, Tianyu Lu, Junwei Yang, Xinyu Dai, Ming Zhang, Zaiqing Nie, Wei-Ying Ma, Hao Zhou

Protein language models have demonstrated significant potential in the field of protein engineering. However, current protein language models primarily operate at the residue scale, which limits their ability to provide information at the atom level. This limitation prevents us from fully exploiting the capabilities of protein language models for applications involving both proteins and small molecules. In this paper, we propose ESM-AA (ESM All-Atom), a novel approach that enables atom-scale and residue-scale unified molecular modeling. ESM-AA achieves this by pre-training on multi-scale code-switch protein sequences and utilizing a multi-scale position encoding to capture relationships among residues and atoms. Experimental results indicate that ESM-AA surpasses previous methods in protein-molecule tasks, demonstrating the full utilization of protein language models. Further investigations reveal that through unified molecular modeling, ESM-AA not only gains molecular knowledge but also retains its understanding of proteins.
BAT: Learning to Reason about Spatial Sounds with Large Language Models
Authors: Zhisheng Zheng, Puyuan Peng, Ziyang Ma, Xie Chen, Eunsol Choi, David Harwath

Spatial sound reasoning is a fundamental human skill, enabling us to navigate and interpret our surroundings based on sound. In this paper we present BAT, which combines the spatial sound perception ability of a binaural acoustic scene analysis model with the natural language reasoning capabilities of a large language model (LLM) to replicate this innate ability. To address the lack of existing datasets of in-the-wild spatial sounds, we synthesized a binaural audio dataset using AudioSet and SoundSpaces 2.0. Next, we developed SpatialSoundQA, a spatial sound-based question-answering dataset, offering a range of QA tasks that train BAT in various aspects of spatial sound perception and reasoning. The acoustic front end encoder of BAT is a novel spatial audio encoder named Spatial Audio Spectrogram Transformer, or Spatial-AST, which by itself achieves strong performance across sound event detection, spatial localization, and distance estimation. By integrating Spatial-AST with LLaMA-2 7B model, BAT transcends standard Sound Event Localization and Detection (SELD) tasks, enabling the model to reason about the relationships between the sounds in its environment. Our experiments demonstrate BAT’s superior performance on both spatial sound perception and reasoning, showcasing the immense potential of LLMs in navigating and interpreting complex spatial audio environments.
Conformal Predictions under Markovian Data
Authors: Frédéric Zheng, Alexandre Proutiere

We study the split Conformal Prediction method when applied to Markovian data. We quantify the gap in terms of coverage induced by the correlations in the data (compared to exchangeable data). This gap strongly depends on the mixing properties of the underlying Markov chain, and we prove that it typically scales as $\sqrt{t_\mathrm{mix}\ln(n)/n}$ (where $t_\mathrm{mix}$ is the mixing time of the chain). We also derive upper bounds on the impact of the correlations on the size of the prediction set. Finally we present $K$-split CP, a method that consists in thinning the calibration dataset and that adapts to the mixing properties of the chain. Its coverage gap is reduced to $t_\mathrm{mix}/(n\ln(n))$ without really affecting the size of the prediction set. We finally test our algorithms on synthetic and real-world datasets.
Detecting and Identifying Selection Structure in Sequential Data
Authors: Yujia Zheng, Zeyu Tang, Yiwen Qiu, Bernhard Schölkopf, Kun Zhang

We argue that the selective inclusion of data points based on latent objectives is common in practical situations, such as music sequences. Since this selection process often distorts statistical analysis, previous work primarily views it as a bias to be corrected and proposes various methods to mitigate its effect. However, while controlling this bias is crucial, selection also offers an opportunity to provide a deeper insight into the hidden generation process, as it is a fundamental mechanism underlying what we observe. In particular, overlooking selection in sequential data can lead to an incomplete or overcomplicated inductive bias in modeling, such as assuming a universal autoregressive structure for all dependencies. Therefore, rather than merely viewing it as a bias, we explore the causal structure of selection in sequential data to delve deeper into the complete causal process. Specifically, we show that selection structure is identifiable without any parametric assumptions or interventional experiments. Moreover, even in cases where selection variables coexist with latent confounders, we still establish the nonparametric identifiability under appropriate structural conditions. Meanwhile, we also propose a provably correct algorithm to detect and identify selection structures as well as other types of dependencies. The framework has been validated empirically on both synthetic data and real-world music.
ContPhy: Continuum Physical Concept Learning and Reasoning from Videos
Authors: Zhicheng Zheng, Xin Yan, Zhenfang Chen, Jingzhou Wang, Qin Zhi Eddie Lim, Joshua B. Tenenbaum, Chuang Gan

We introduce the Continuum Physical Dataset (ContPhy), a novel benchmark for assessing machine physical commonsense. ContPhy complements existing physical reasoning benchmarks by encompassing the inference of diverse physical properties, such as mass and density, across various scenarios and predicting corresponding dynamics. We evaluated a range of AI models and found that they still struggle to achieve satisfactory performance on ContPhy, which shows that current AI models still lack physical commonsense for the continuum, especially soft-bodies, and illustrates the value of the proposed dataset. We also introduce an oracle model (ContPRO) that marries the particle-based physical dynamic models with the recent large language models, which enjoy the advantages of both models, precise dynamic predictions, and interpretable reasoning. ContPhy aims to spur progress in perception and reasoning within diverse physical settings, narrowing the divide between human and machine intelligence in understanding the physical world.
DPN: Decoupling Partition and Navigation for Neural Solvers of Min-max Vehicle Routing Problems
Authors: Zhi Zheng, Shunyu Yao, Zhenkun Wang, Tong Xialiang, Mingxuan Yuan, Ke Tang

The min-max vehicle routing problem (min-max VRP) traverses all given customers by assigning several routes and aims to minimize the length of the longest route. Recently, reinforcement learning (RL)-based sequential planning methods have exhibited advantages in solving efficiency and optimality. However, these methods fail to exploit the problem-specific properties in learning representations, resulting in less effective features for decoding optimal routes. This paper considers the sequential planning process of min-max VRPs as two coupled optimization tasks: customer partition for different routes and customer navigation in each route (i.e., partition and navigation). To effectively process min-max VRP instances, we present a novel attention-based Partition-and-Navigation encoder (P&N Encoder) that learns distinct embeddings for partition and navigation. Furthermore, we utilize an inherent symmetry in decoding routes and develop an effective agent-permutation-symmetric (APS) loss function. Experimental results demonstrate that the proposed Decoupling-Partition-Navigation (DPN) method significantly surpasses existing learning-based methods in both single-depot and multi-depot min-max VRPs. Our code is available at
On Prompt-Driven Safeguarding for Large Language Models
Authors: Chujie Zheng, Fan Yin, Hao Zhou, Fandong Meng, Jie Zhou, Kai-Wei Chang, Minlie Huang, Nanyun Peng

Prepending model inputs with safety prompts is a common practice for safeguarding large language models (LLMs) against queries with harmful intents. However, the underlying working mechanisms of safety prompts have not been unraveled yet, restricting the possibility of automatically optimizing them to improve LLM safety. In this work, we investigate how LLMs’ behavior (i.e., complying with or refusing user queries) is affected by safety prompts from the perspective of model representation. We find that in the representation space, the input queries are typically moved by safety prompts in a "higher-refusal" direction, in which models become more prone to refusing to provide assistance, even when the queries are harmless. On the other hand, LLMs are naturally capable of distinguishing harmful and harmless queries without safety prompts. Inspired by these findings, we propose a method for safety prompt optimization, namely DRO (Directed Representation Optimization). Treating a safety prompt as continuous, trainable embeddings, DRO learns to move the queries’ representations along or opposite the refusal direction, depending on their harmfulness. Experiments with eight LLMs on out-of-domain and jailbreak benchmarks demonstrate that DRO remarkably improves the safeguarding performance of human-crafted safety prompts, without compromising the models’ general performance.