Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Many deep learning methods have been developed for de novo peptide sequencing task, i.e., predicting the peptide sequence for the observed mass spectrum. However, two key challenges seriously hinder the further advancement of this important task. Firstly, since there is no consensus for the evaluation datasets, the empirical results in different research papers are often not comparable, leading to unfair comparison. Secondly, the current methods are usually limited to amino acid-level or peptide-level precision and recall metrics. In this work, we present the first unified benchmark NovoBench for de novo peptide sequencing, which comprises diverse mass spectrum data, integrated models, and comprehensive evaluation metrics. Recent impressive methods, including DeepNovo, PointNovo, Casanovo, InstaNovo, AdaNovo and π-HelixNovo are integrated into our framework. In addition to amino acid-level and peptide-level precision and recall, we evaluate the models' performance in terms of identifying post-tranlational modifications (PTMs), efficiency and robustness to peptide length, noise peaks and missing fragment ratio, which are important influencing factors while seldom be considered. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development.

As many practical fields transition to provide personalized decisions, data is increasingly relevant to support the evaluation of candidate plans and policies (e.g., guidelines for the treatment of disease, government directives, etc.). In the machine learning literature, significant efforts have been put into developing machinery to predict the effectiveness of policies efficiently. The challenge is that, in practice, the effectiveness of a candidate policy is not always identifiable, i.e., not uniquely estimable from the combination of the available data and assumptions about the domain at hand (e.g., encoded in a causal graph). In this paper, we develop graphical characterizations and estimation tools to bound the effect of policies given a causal graph and observational data collected in non-identifiable settings. Specifically, our contributions are two-fold: (1) we derive analytical bounds for general probabilistic and conditional policies that are tighter than existing results, (2) we develop an estimation framework to estimate bounds from finite samples, applicable in higher-dimensional spaces and continuously-valued data. We further show that the resulting estimators have favourable statistical properties such as fast convergence and robustness to model misspecification.

Safety and trustworthiness are indispensable requirements for real-world applications of AI systems using large language models (LLMs).

For embodied agents to infer representations of the underlying 3D physical world they inhabit, they should efficiently combine multisensory cues from numerous trials, e.g., by looking at and touching objects. Despite its importance, multisensory 3D scene representation learning has received less attention compared to the unimodal setting. In this paper, we propose the Generative Multisensory Network (GMN) for learning latent representations of 3D scenes which are partially observable through multiple sensory modalities. We also introduce a novel method, called the Amortized Product-of-Experts, to improve the computational efficiency and the robustness to unseen combinations of modalities at test time. Experimental results demonstrate that the proposed model can efficiently infer robust modality-invariant 3D-scene representations from arbitrary combinations of modalities and perform accurate cross-modal generation. To perform this exploration, we also develop the Multisensory Embodied 3D-Scene Environment (MESE).

Existing video multi-modal sentiment analysis mainly focuses on the sentiment expression of people within the video, yet often neglects the induced sentiment of viewers while watching the videos. Induced sentiment of viewers is essential for inferring the public response to videos and has broad application in analyzing public societal sentiment, effectiveness of advertising and other areas. The micro videos and the related comments provide a rich application scenario for viewers' induced sentiment analysis. In light of this, we introduces a novel research task, Multimodal Sentiment Analysis for Comment Response of Video Induced(MSA-CRVI), aims to infer opinions and emotions according to comments response to micro video. Meanwhile, we manually annotate a dataset named Comment Sentiment toward to Micro Video (CSMV) to support this research. It is the largest video multi-modal sentiment dataset in terms of scale and video duration to our knowledge, containing 107, 267 comments and 8, 210 micro videos with a video duration of 68.83 hours. To infer the induced sentiment of comment should leverage the video content, we propose the Video Content-aware Comment Sentiment Analysis (VC-CSA) method as a baseline to address the challenges inherent in this new task. Extensive experiments demonstrate that our method is showing significant improvements over other established baselines.

Offline policy evaluation (OPE) allows us to evaluate and estimate a new sequential decision-making policy's performance by leveraging historical interaction data collected from other policies. Evaluating a new policy online without a confident estimate of its performance can lead to costly, unsafe, or hazardous outcomes, especially in education and healthcare. Several OPE estimators have been proposed in the last decade, many of which have hyperparameters and require training. Unfortunately, choosing the best OPE algorithm for each task and domain is still unclear. In this paper, we propose a new algorithm that adaptively blends a set of OPE estimators given a dataset without relying on an explicit selection using a statistical procedure. We prove that our estimator is consistent and satisfies several desirable properties for policy evaluation. Additionally, we demonstrate that when compared to alternative approaches, our estimator can be used to select higher-performing policies in healthcare and robotics. Our work contributes to improving ease of use for a general-purpose, estimator-agnostic, off-policy evaluation framework for offline RL.

Constructing and maintaining useful representations of sensory experience is essential for reasoning about ones environment. High-level associative (topological) maps can be useful for efficient planning and are easily constructed from experience. Conversely, embedding new experiences within a metric structure allows them to be integrated with existing ones and novel associations to be implicitly inferred. Neurobiologically, the synaptic associations between hippocampal place cells and entorhinal grid cells are thought to represent associative and metric structures, respectively. Learning the place-grid cell associations can therefore be interpreted as learning a mapping between these two spaces. Here, we show how this map could be constructed by probabilistic message-passing through the hippocampalentorhinal system, where messages are scheduled to reduce the propagation of redundant information. We propose that this offline inference corresponds to coordinated hippocampal-entorhinal replay during sharp wave ripples. Our results also suggest that the metric map will contain local distortions that reflect the inferred structure of the environment according to associative experience, explaining observed grid deformations.

We present Saliency-driven Experience Replay - SER - a biologically-plausible approach based on replicating human visual saliency to enhance classification models in continual learning settings. Inspired by neurophysiological evidence that the primary visual cortex does not contribute to object manifold untangling for categorization and that primordial saliency biases are still embedded in the modern brain, we propose to employ auxiliary saliency prediction features as a modulation signal to drive and stabilize the learning of a sequence of non-i.i.d.

As the key component in multimodal large language models (MLLMs), the ability of the visual encoder greatly affects MLLM's understanding on diverse image content. Although some large-scale pretrained vision encoders such as vision encoders in CLIP and DINOv2 have brought promising performance, we found that there is still no single vision encoder that can dominate various image content understanding, e.g., the CLIP vision encoder leads to outstanding results on general image understanding but poor performance on document or chart content. To alleviate the bias of CLIP vision encoder, we first delve into the inherent behavior of different pre-trained vision encoders and then propose the MoVA, a powerful and novel MLLM, adaptively routing and fusing task-specific vision experts with a coarse-to-fine mechanism. In the coarse-grained stage, we design a contextaware expert routing strategy to dynamically select the most suitable vision experts according to the user instruction, input image, and expertise of vision experts.

How to decode human vision through neural signals has attracted a long-standing interest in neuroscience and machine learning. Modern contrastive learning and generative models improved the performance of visual decoding and reconstruction based on functional Magnetic Resonance Imaging (fMRI). However, the high cost and low temporal resolution of fMRI limit their applications in brain-computer interfaces (BCIs), prompting a high need for visual decoding based on electroencephalography (EEG). In this study, we present an end-to-end EEG-based visual reconstruction zero-shot framework, consisting of a tailored brain encoder, called the Adaptive Thinking Mapper (ATM), which projects neural signals from different sources into the shared subspace as the clip embedding, and a two-stage multi-pipe EEG-to-image generation strategy. In stage one, EEG is embedded to align the highlevel clip embedding, and then the prior diffusion model refines EEG embedding into image priors.