Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Despite the development of several deep learning methods for predicting amino acid sequences (peptides) responsible for generating the observed mass spectra, training data biases hinder further advancements of \emph{de novo} peptide sequencing. Firstly, prior methods struggle to identify amino acids with Post-Translational Modifications (PTMs) due to their lower frequency in training data compared to canonical amino acids, further resulting in unsatisfactory peptide sequencing performance. Secondly, various noise and missing peaks in mass spectra reduce the reliability of training data (Peptide-Spectrum Matches, PSMs). To address these challenges, we propose AdaNovo, a novel and domain knowledge-inspired framework that calculates Conditional Mutual Information (CMI) between the mass spectra and amino acids or peptides, using CMI for robust training against above biases. Extensive experiments indicate that AdaNovo outperforms previous competitors on the widely-used 9-species benchmark, meanwhile yielding 3.6\% - 9.4\% improvements in PTMs identification. The supplements contain the code.

To address the challenges of sim-to-real gap and sample efficiency in reinforcement learning (RL), this work studies distributionally robust Markov decision processes (RMDPs) --- optimize the worst-case performance when the deployed environment is within an uncertainty set around some nominal MDP. Despite recent efforts, the sample complexity of RMDPs has remained largely undetermined. While the statistical implications of distributional robustness in RL have been explored in some specific cases, the generalizability of the existing findings remains unclear, especially in comparison to standard RL. Assuming access to a generative model that samples from the nominal MDP, we examine the sample complexity of RMDPs using a class of generalized $L_p$ norms as the'distance' function for the uncertainty set, under two commonly adopted $sa$-rectangular and $s$-rectangular conditions. Our results imply that RMDPs can be more sample-efficient to solve than standard MDPs using generalized $L_p$ norms in both $sa$- and $s$-rectangular cases, potentially inspiring more empirical research. We provide a near-optimal upper bound and a matching minimax lower bound for the $sa$-rectangular scenarios. For $s$-rectangular cases, we improve the state-of-the-art upper bound and also derive a lower bound using $L_\infty$ norm that verifies the tightness.

Large language models have shown an impressive societal impact owing to their excellent understanding and logical reasoning skills. However, such strong ability relies on a huge amount of computing resources, which makes it difficult to deploy LLMs on computing resource-constrained platforms. Currently, LLMs process each token equivalently, but we argue that not every word is equally important. Some words should not be allocated excessive computing resources, particularly for dispensable terms in simple questions. In this paper, we propose a novel dynamic inference paradigm for LLMs, namely D-LLMs, which adaptively allocate computing resources in token processing. We design a dynamic decision module for each transformer layer that decides whether a network unit should be executed or skipped. Moreover, we tackle the issue of adapting D-LLMs to real-world applications, specifically concerning the missing KV-cache when layers are skipped. To overcome this, we propose a simple yet effective eviction policy to exclude the skipped layers from subsequent attention calculations. The eviction policy not only enables D-LLMs to be compatible with prevalent applications but also reduces considerable storage resources.

We demonstrate that numerous machine learning algorithms are specific instances of one single paradigm: reciprocal learning. These instances range from active learning over multi-armed bandits to self-training. We show that all these algorithms not only learn parameters from data but also vice versa: They iteratively alter training data in a way that depends on the current model fit. We introduce reciprocal learning as a generalization of these algorithms using the language of decision theory. This allows us to study under what conditions they converge. The key is to guarantee that reciprocal learning contracts such that the Banach fixed-point theorem applies. In this way, we find that reciprocal learning converges at linear rates to an approximately optimal model under some assumptions on the loss function, if their predictions are probabilistic and the sample adaption is both non-greedy and either randomized or regularized. We interpret these findings and provide corollaries that relate them to active learning, self-training, and bandits.

Accurate environment dynamics modeling is crucial for obtaining effective state representations in visual reinforcement learning (RL) applications. However, when facing multiple input modalities, existing dynamics modeling methods (e.g., DeepMDP) usually stumble in addressing the complex and volatile relationship between different modalities. In this paper, we study the problem of efficient dynamics modeling for multi-modal visual RL. We find that under the existence of modality heterogeneity, modality-correlated and distinct features are equally important but play different roles in reflecting the evolution of environmental dynamics. Motivated by this fact, we propose Dissected Dynamics Modeling (DDM), a novel multi-modal dynamics modeling method for visual RL. Unlike existing methods, DDM explicitly distinguishes consistent and inconsistent information across modalities and treats them separately with a divide-and-conquer strategy. This is done by dispatching the features carrying different information into distinct dynamics modeling pathways, which naturally form a series of implicit regularizations along the learning trajectories. In addition, a reward predictive function is further introduced to filter task-irrelevant information in both modality-consistent and inconsistent features, ensuring information integrity while avoiding potential distractions. Extensive experiments show that DDM consistently achieves competitive performance in challenging multi-modal visual environments.

Diffusion models can learn strong image priors from underlying data distribution and use them to solve inverse problems,but the training process is computationally expensive and requires lots of data.Such bottlenecks prevent most existing works from being feasible for high-dimensional and high-resolution data such as 3D images.This paper proposes a method to learn an efficient data prior for the entire image by training diffusion models only on patches of images.Specifically, we propose a patch-based position-aware diffusion inverse solver, called PaDIS, where we obtain the score function of the whole image through scores of patches and their positional encoding and utilize this as the prior for solving inverse problems.First of all, we show that this diffusion model achieves an improved memory efficiency and data efficiencywhile still maintaining the capability to generate entire images via positional encoding.Additionally, the proposed PaDIS model is highly flexible and can be plugged in with different diffusion inverse solvers (DIS).We demonstrate that the proposed PaDIS approach enables solving various inverse problems in both natural and medical image domains, including CT reconstruction, deblurring, and superresolution, given only patch-based priors.Notably, PaDIS outperforms previous DIS methods trained on entire image priors in the case of limited training data, demonstrating the data efficiency of our proposed approach by learning patch-based prior.

While neural networks (NNs) have a large potential as autonomous controllers for Cyber-Physical Systems, verifying the safety of neural network based control systems (NNCSs) poses significant challenges for the practical use of NNs-- especially when safety is needed for unbounded time horizons. One reason for this is the intractability of analyzing NNs, ODEs and hybrid systems. To this end, we introduce VerSAILLE (Verifiably Safe AI via Logically Linked Envelopes): The first general approach that allows reusing control theory literature for NNCS verification. By joining forces, we can exploit the efficiency of NN verification tools while retaining the rigor of differential dynamic logic (dL). Based on a provably safe control envelope in dL, we derive a specification for the NN which is proven with NN verification tools. We show that a proof of the NN's adherence to the specification is then mirrored by a dL proof on the infinite-time safety of the NNCS.The NN verification properties resulting from hybrid systems typically contain nonlinear arithmetic over formulas with arbitrary logical structure while efficient NN verification tools merely support linear constraints. To overcome this divide, we present Mosaic: An efficient, sound and complete verification approach for polynomial real arithmetic properties on piece-wise linear NNs.

Providing functionality through articulation and interaction with objects is a key objective in 3D generation. We introduce MIDGArD (Modular Interpretable Diffusion over Graphs for Articulated Designs), a novel diffusion-based framework for articulated 3D asset generation. MIDGArD improves over foundational work in the field by enhancing quality, consistency, and controllability in the generation process. This is achieved through MIDGArD's modular approach that separates the problem into two primary components: structure generation and shape generation. The structure generation module of MIDGArD aims at producing coherent articulation features from noisy or incomplete inputs. It acts on the object's structural and kinematic attributes, represented as features of a graph that are being progressively denoised to issue coherent and interpretable articulation solutions. This denoised graph then serves as an advanced conditioning mechanism for the shape generation module, a 3D generative model that populates each link of the articulated structure with consistent 3D meshes. Experiments show the superiority of MIDGArD on the quality, consistency, and interpretability of the generated assets. Importantly, the generated models are fully simulatable, i.e., can be seamlessly integrated into standard physics engines such as MuJoCo, broadening MIDGArD's applicability to fields such as digital content creation, meta realities, and robotics.

Large language models (LLMs) are vulnerable to adversarial attacks that can bypass their safety guardrails. In many domains, adversarial training has proven to be one of the most promising methods to reliably improve robustness against such attacks. Yet, in the context of LLMs, current methods for adversarial training are hindered by the high computational costs required to perform discrete adversarial attacks at each training iteration. We address this problem by instead calculating adversarial attacks in the continuous embedding space of the LLM, which is orders of magnitudes more efficient. We propose a fast adversarial training algorithm (C-AdvUL) composed of two losses: the first makes the model robust on continuous embedding attacks computed on an adversarial behaviour dataset; the second ensures the usefulness of the final model by fine-tuning on utility data. Moreover, we introduce C-AdvIPO, an adversarial variant of IPO that does not require utility data for adversarially robust alignment. Our empirical evaluation on five models from different families (Gemma, Phi3, Mistral, Zephyr, Llama2) and at different scales (2B, 3.8B, 7B) shows that both algorithms substantially enhance LLM robustness against discrete attacks (GCG, AutoDAN, PAIR), while maintaining utility. Our results demonstrate that robustness to continuous perturbations can extrapolate to discrete threat models. Thereby, we present a path toward scalable adversarial training algorithms for robustly aligning LLMs.

High-quality preference datasets are essential for training reward models that can effectively guide large language models (LLMs) in generating high-quality responses aligned with human preferences.As LLMs become stronger and better aligned, permissively licensed preference datasets, such as Open Assistant, HH-RLHF, and HelpSteer need to be updated to remain effective for reward modeling.Methods that distil preference data from proprietary LLMs such as GPT-4 have restrictions on commercial usage imposed by model providers.To improve upon both generated responses and attribute labeling quality, we release HelpSteer2, a permissively licensed preference dataset (CC-BY-4.0). Using a powerful Nemotron-4-340B base model trained on HelpSteer2, we are able to achieve the SOTA score (92.0%) on Reward-Bench's primary dataset, outperforming currently listed open and proprietary models, as of June 12th, 2024.Notably, HelpSteer2 consists of only ten thousand response pairs, an order of magnitude fewer than existing preference datasets (e.g., HH-RLHF), which makes it highly efficient for training reward models. Our extensive experiments demonstrate that reward models trained with HelpSteer2 are effective in aligning LLMs. Additionally, we propose SteerLM 2.0, a model alignment approach that can effectively make use of the rich multi-attribute score predicted by our reward models.