Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis; improving peptide and protein identification and quantification; characterizing protein-protein interactions and protein complexes; advancing spatial and perturbation proteomics; integrating multi-omics data; and ultimately enabling AI-empowered virtual cells.

The advent of Multimodal Large Language Models, leveraging the power of Large Language Models, has recently demonstrated superior multimodal understanding and reasoning abilities, heralding a new era for artificial general intelligence. However, achieving AGI necessitates more than just comprehension and reasoning. A crucial capability required is effective planning in diverse scenarios, which involves making reasonable decisions based on complex environments to solve real-world problems. Despite its importance, the planning abilities of current MLLMs in varied scenarios remain underexplored. In this paper, we introduce EgoPlan-Bench2, a rigorous and comprehensive benchmark designed to assess the planning capabilities of MLLMs across a wide range of real-world scenarios. EgoPlan-Bench2 encompasses everyday tasks spanning 4 major domains and 24 detailed scenarios, closely aligned with human daily life. EgoPlan-Bench2 is constructed through a semi-automatic process utilizing egocentric videos, complemented by manual verification. Grounded in a first-person perspective, it mirrors the way humans approach problem-solving in everyday life. We evaluate 21 competitive MLLMs and provide an in-depth analysis of their limitations, revealing that they face significant challenges in real-world planning. To further improve the planning proficiency of current MLLMs, we propose a training-free approach using multimodal Chain-of-Thought (CoT) prompting through investigating the effectiveness of various multimodal prompts in complex planning. Our approach enhances the performance of GPT-4V by 10.24 on EgoPlan-Bench2 without additional training. Our work not only sheds light on the current limitations of MLLMs in planning, but also provides insights for future enhancements in this critical area. We have made data and code available at https://qiulu66.github.io/egoplanbench2/.

Recent developments in Large Language Models pre-trained on extensive corpora have shown significant success in various natural language processing tasks with minimal fine-tuning. This success offers new promise for robotics, which has long been constrained by the high cost of action-labeled data. We ask: given the abundant video data containing interaction-related knowledge available as a rich "corpus", can a similar generative pre-training approach be effectively applied to enhance robot learning? The key challenge is to identify an effective representation for autoregressive pre-training that benefits robot manipulation tasks. Inspired by the way humans learn new skills through observing dynamic environments, we propose that effective robotic learning should emphasize motion-related knowledge, which is closely tied to low-level actions and is hardware-agnostic, facilitating the transfer of learned motions to actual robot actions. To this end, we introduce Moto, which converts video content into latent Motion Token sequences by a Latent Motion Tokenizer, learning a bridging "language" of motion from videos in an unsupervised manner. We pre-train Moto-GPT through motion token autoregression, enabling it to capture diverse visual motion knowledge. After pre-training, Moto-GPT demonstrates the promising ability to produce semantically interpretable motion tokens, predict plausible motion trajectories, and assess trajectory rationality through output likelihood. To transfer learned motion priors to real robot actions, we implement a co-fine-tuning strategy that seamlessly bridges latent motion token prediction and real robot control. Extensive experiments show that the fine-tuned Moto-GPT exhibits superior robustness and efficiency on robot manipulation benchmarks, underscoring its effectiveness in transferring knowledge from video data to downstream visual manipulation tasks.

Large foundation models pretrained on raw web-scale data are not readily deployable without additional step of extensive alignment to human preferences. Such alignment is typically done by collecting large amounts of pairwise comparisons from humans ("Do you prefer output A or B?") and learning a reward model or a policy with the Bradley-Terry-Luce (BTL) model as a proxy for a human's underlying implicit preferences. These methods generally suffer from assuming a universal preference shared by all humans, which lacks the flexibility of adapting to plurality of opinions and preferences. In this work, we propose PAL, a framework to model human preference complementary to existing pretraining strategies, which incorporates plurality from the ground up. We propose using the ideal point model as a lens to view alignment using preference comparisons. Together with our novel reformulation and using mixture modeling, our framework captures the plurality of population preferences while simultaneously learning a common preference latent space across different preferences, which can few-shot generalize to new, unseen users. Our approach enables us to use the penultimate-layer representation of large foundation models and simple MLP layers to learn reward functions that are on-par with the existing large state-of-the-art reward models, thereby enhancing efficiency of reward modeling significantly. We show that PAL achieves competitive reward model accuracy compared to strong baselines on 1) Language models with Summary dataset ; 2) Image Generative models with Pick-a-Pic dataset ; 3) A new semisynthetic heterogeneous dataset generated using Anthropic Personas. Finally, our experiments also highlight the shortcoming of current preference datasets that are created using rigid rubrics which wash away heterogeneity, and call for more nuanced data collection approaches.

Unsupervised Reinforcement Learning (RL) provides a promising paradigm for learning useful behaviors via reward-free per-training. Existing methods for unsupervised RL mainly conduct empowerment-driven skill discovery or entropy-based exploration. However, empowerment often leads to static skills, and pure exploration only maximizes the state coverage rather than learning useful behaviors. In this paper, we propose a novel unsupervised RL framework via an ensemble of skills, where each skill performs partition exploration based on the state prototypes. Thus, each skill can explore the clustered area locally, and the ensemble skills maximize the overall state coverage. We adopt state-distribution constraints for the skill occupancy and the desired cluster for learning distinguishable skills. Theoretical analysis is provided for the state entropy and the resulting skill distributions. Based on extensive experiments on several challenging tasks, we find our method learns well-explored ensemble skills and achieves superior performance in various downstream tasks compared to previous methods.

We investigate the non-stationary stochastic linear bandit problem where the reward distribution evolves each round. Existing algorithms characterize the non-stationarity by the total variation budget $B_K$, which is the summation of the change of the consecutive feature vectors of the linear bandits over $K$ rounds. However, such a quantity only measures the non-stationarity with respect to the expectation of the reward distribution, which makes existing algorithms sub-optimal under the general non-stationary distribution setting. In this work, we propose algorithms that utilize the variance of the reward distribution as well as the $B_K$, and show that they can achieve tighter regret upper bounds. Specifically, we introduce two novel algorithms: Restarted Weighted$\text{OFUL}^+$ and Restarted $\text{SAVE}^+$. These algorithms address cases where the variance information of the rewards is known and unknown, respectively. Notably, when the total variance $V_K$ is much smaller than $K$, our algorithms outperform previous state-of-the-art results on non-stationary stochastic linear bandits under different settings. Experimental evaluations further validate the superior performance of our proposed algorithms over existing works.

The growing interest in Large Language Models (LLMs) for specialized applications has revealed a significant challenge: when tailored to specific domains, LLMs tend to experience catastrophic forgetting, compromising their general capabilities and leading to a suboptimal user experience. Additionally, crafting a versatile model for multiple domains simultaneously often results in a decline in overall performance due to confusion between domains. In response to these issues, we present the RolE Prompting Guided Multi-Domain Adaptation (REGA) strategy. This novel approach effectively manages multi-domain LLM adaptation through three key components: 1) Self-Distillation constructs and replays general-domain exemplars to alleviate catastrophic forgetting. 2) Role Prompting assigns a central prompt to the general domain and a unique role prompt to each specific domain to minimize inter-domain confusion during training. 3) Role Integration reuses and integrates a small portion of domain-specific data to the general-domain data, which are trained under the guidance of the central prompt. The central prompt is used for a streamlined inference process, removing the necessity to switch prompts for different domains. Empirical results demonstrate that REGA effectively alleviates catastrophic forgetting and inter-domain confusion. This leads to improved domain-specific performance compared to standard fine-tuned models, while still preserving robust general capabilities.

This paper introduces a novel operator, termed the Y operator, to elevate control performance in Actor-Critic(AC) based reinforcement learning for systems governed by stochastic differential equations(SDEs). The Y operator ingeniously integrates the stochasticity of a class of child-mother system into the Critic network's loss function, yielding substantial advancements in the control performance of RL algorithms.Additionally, the Y operator elegantly reformulates the challenge of solving partial differential equations for the state-value function into a parallel problem for the drift and diffusion functions within the system's SDEs.A rigorous mathematical proof confirms the operator's validity.This transformation enables the Y Operator-based Reinforcement Learning(YORL) framework to efficiently tackle optimal control problems in both model-based and data-driven systems.The superiority of YORL is demonstrated through linear and nonlinear numerical examples showing its enhanced performance over existing methods post convergence.

Multimodal Large Language Models (MLLMs), building upon the powerful Large Language Models (LLMs) with exceptional reasoning and generalization capability, have opened up new avenues for embodied task planning. MLLMs excel in their ability to integrate diverse environmental inputs, such as real-time task progress, visual observations, and open-form language instructions, which are crucial for executable task planning. In this work, we introduce a benchmark with human annotations, EgoPlan-Bench, to quantitatively investigate the potential of MLLMs as embodied task planners in real-world scenarios. Our benchmark is distinguished by realistic tasks derived from real-world videos, a diverse set of actions involving interactions with hundreds of different objects, and complex visual observations from varied environments. We evaluate various open-source MLLMs, revealing that these models have not yet evolved into embodied planning generalists (even GPT-4V). We further construct an instruction-tuning dataset EgoPlan-IT from videos of human-object interactions, to facilitate the learning of high-level task planning in intricate real-world situations. The experiment results demonstrate that the model tuned on EgoPlan-IT not only significantly improves performance on our benchmark, but also effectively acts as embodied planner in simulations.

In this paper, we present a fast, lightweight odometry method that uses the Doppler velocity measurements from a Frequency-Modulated Continuous-Wave (FMCW) lidar without data association. FMCW lidar is a recently emerging technology that enables per-return relative radial velocity measurements via the Doppler effect. Since the Doppler measurement model is linear with respect to the 6-degrees-of-freedom (DOF) vehicle velocity, we can formulate a linear continuous-time estimation problem for the velocity and numerically integrate for the 6-DOF pose estimate afterward. The caveat is that angular velocity is not observable with a single FMCW lidar. We address this limitation by also incorporating the angular velocity measurements from a gyroscope. This results in an extremely efficient odometry method that processes lidar frames at an average wall-clock time of 5.64ms on a single thread, well below the 10Hz operating rate of the lidar we tested. We show experimental results on real-world driving sequences and compare against state-of-the-art Iterative Closest Point (ICP)-based odometry methods, presenting a compelling trade-off between accuracy and computation. We also present an algebraic observability study, where we demonstrate in theory that the Doppler measurements from multiple FMCW lidars are capable of observing all 6 degrees of freedom (translational and angular velocity).