Disentangling the Complex Multiplexed DIA Spectra in De Novo Peptide Sequencing

Data-Independent Acquisition (DIA) was introduced to improve sensitivity to cover all peptides in a range rather than only sampling high-intensity peaks as in Data-Dependent Acquisition (DDA) mass spectrometry. However, it is not very clear how useful DIA data is for de novo peptide sequencing as the DIA data are marred with coeluted peptides, high noises, and varying data quality. We present a new deep learning method DIANovo, and address each of these difficulties, and improves the previous established system DeepNovo-DIA by from 25% to 81%, averaging 48%, for amino acid recall, and by from 27% to 89%, averaging 57%, for peptide recall, by equipping the model with a deeper understanding of coeluted DIA spectra. This paper also provides criteria about when DIA data could be used for de novo peptide sequencing and when not to by providing a comparison between DDA and DIA, in both de novo and database search mode. We find that while DIA excels with narrow isolation windows on older-generation instruments, it loses its advantage with wider windows. However, with Orbitrap Astral, DIA consistently outperforms DDA due to narrow window mode enabled. We also provide a theoretical explanation of this phenomenon, emphasizing the critical role of the signal-to-noise profile in the successful application of de novo sequencing.

Towards Cross-domain Few-shot Graph Anomaly Detection

Few-shot graph anomaly detection (GAD) has recently garnered increasing attention, which aims to discern anomalous patterns among abundant unlabeled test nodes under the guidance of a limited number of labeled training nodes. Existing few-shot GAD approaches typically adopt meta-training methods trained on richly labeled auxiliary networks to facilitate rapid adaptation to target networks that possess sparse labels. However, these proposed methods often assume that the auxiliary and target networks exist in the same data distributions-an assumption rarely holds in practical settings. This paper explores a more prevalent and complex scenario of cross-domain few-shot GAD, where the goal is to identify anomalies within sparsely labeled target graphs using auxiliary graphs from a related, yet distinct domain. The challenge here is nontrivial owing to inherent data distribution discrepancies between the source and target domains, compounded by the uncertainties of sparse labeling in the target domain. In this paper, we propose a simple and effective framework, termed CDFS-GAD, specifically designed to tackle the aforementioned challenges. CDFS-GAD first introduces a domain-adaptive graph contrastive learning module, which is aimed at enhancing cross-domain feature alignment. Then, a prompt tuning module is further designed to extract domain-specific features tailored to each domain. Moreover, a domain-adaptive hypersphere classification loss is proposed to enhance the discrimination between normal and anomalous instances under minimal supervision, utilizing domain-sensitive norms. Lastly, a self-training strategy is introduced to further refine the predicted scores, enhancing its reliability in few-shot settings. Extensive experiments on twelve real-world cross-domain data pairs demonstrate the effectiveness of the proposed CDFS-GAD framework in comparison to various existing GAD methods.

How Far Are We to GPT-4V? Closing the Gap to Commercial Multimodal Models with Open-Source Suites

In this report, we introduce InternVL 1.5, an open-source multimodal large language model (MLLM) to bridge the capability gap between open-source and proprietary commercial models in multimodal understanding. We introduce three simple improvements: (1) Strong Vision Encoder: we explored a continuous learning strategy for the large-scale vision foundation model -- InternViT-6B, boosting its visual understanding capabilities, and making it can be transferred and reused in different LLMs. (2) Dynamic High-Resolution: we divide images into tiles ranging from 1 to 40 of 448$\times$448 pixels according to the aspect ratio and resolution of the input images, which supports up to 4K resolution input. (3) High-Quality Bilingual Dataset: we carefully collected a high-quality bilingual dataset that covers common scenes, document images, and annotated them with English and Chinese question-answer pairs, significantly enhancing performance in OCR- and Chinese-related tasks. We evaluate InternVL 1.5 through a series of benchmarks and comparative studies. Compared to both open-source and proprietary models, InternVL 1.5 shows competitive performance, achieving state-of-the-art results in 8 of 18 benchmarks. Code has been released at https://github.com/OpenGVLab/InternVL.

ODE-DPS: ODE-based Diffusion Posterior Sampling for Inverse Problems in Partial Differential Equation

In recent years we have witnessed a growth in mathematics for deep learning, which has been used to solve inverse problems of partial differential equations (PDEs). However, most deep learning-based inversion methods either require paired data or necessitate retraining neural networks for modifications in the conditions of the inverse problem, significantly reducing the efficiency of inversion and limiting its applicability. To overcome this challenge, in this paper, leveraging the score-based generative diffusion model, we introduce a novel unsupervised inversion methodology tailored for solving inverse problems arising from PDEs. Our approach operates within the Bayesian inversion framework, treating the task of solving the posterior distribution as a conditional generation process achieved through solving a reverse-time stochastic differential equation. Furthermore, to enhance the accuracy of inversion results, we propose an ODE-based Diffusion Posterior Sampling inversion algorithm. The algorithm stems from the marginal probability density functions of two distinct forward generation processes that satisfy the same Fokker-Planck equation. Through a series of experiments involving various PDEs, we showcase the efficiency and robustness of our proposed method.

Capturing Shock Waves by Relaxation Neural Networks

In this paper, we put forward a neural network framework to solve the nonlinear hyperbolic systems. This framework, named relaxation neural networks(RelaxNN), is a simple and scalable extension of physics-informed neural networks(PINN). It is shown later that a typical PINN framework struggles to handle shock waves that arise in hyperbolic systems' solutions. This ultimately results in the failure of optimization that is based on gradient descent in the training process. Relaxation systems provide a smooth asymptotic to the discontinuity solution, under the expectation that macroscopic problems can be solved from a microscopic perspective. Based on relaxation systems, the RelaxNN framework alleviates the conflict of losses in the training process of the PINN framework. In addition to the remarkable results demonstrated in numerical simulations, most of the acceleration techniques and improvement strategies aimed at the standard PINN framework can also be applied to the RelaxNN framework.

MixRED: A Mix-lingual Relation Extraction Dataset

Relation extraction is a critical task in the field of natural language processing with numerous real-world applications. Existing research primarily focuses on monolingual relation extraction or cross-lingual enhancement for relation extraction. Yet, there remains a significant gap in understanding relation extraction in the mix-lingual (or code-switching) scenario, where individuals intermix contents from different languages within sentences, generating mix-lingual content. Due to the lack of a dedicated dataset, the effectiveness of existing relation extraction models in such a scenario is largely unexplored. To address this issue, we introduce a novel task of considering relation extraction in the mix-lingual scenario called MixRE and constructing the human-annotated dataset MixRED to support this task. In addition to constructing the MixRED dataset, we evaluate both state-of-the-art supervised models and large language models (LLMs) on MixRED, revealing their respective advantages and limitations in the mix-lingual scenario. Furthermore, we delve into factors influencing model performance within the MixRE task and uncover promising directions for enhancing the performance of both supervised models and LLMs in this novel task.

A Scoping Review of Energy-Efficient Driving Behaviors and Applied State-of-the-Art AI Methods

The transportation sector remains a major contributor to greenhouse gas emissions. The understanding of energy-efficient driving behaviors and utilization of energy-efficient driving strategies are essential to reduce vehicles' fuel consumption. However, there is no comprehensive investigation into energy-efficient driving behaviors and strategies. Furthermore, many state-of-the-art AI models have been applied for the analysis of eco-friendly driving styles, but no overview is available. To fill the gap, this paper conducts a thorough literature review on ecological driving behaviors and styles and analyzes the driving factors influencing energy consumption and state-of-the-art methodologies. With a thorough scoping review process, the methodological and related data are compared. The results show that the factors that impact driving behaviors can be summarized into eleven features including speed, acceleration, deceleration, pedal, and so on. This paper finds that supervised/unsupervised learning algorithms and reinforcement learning frameworks have been popularly used to model the vehicle's energy consumption with multi-dimensional data. Furthermore, the literature shows that the driving data are collected from either simulators or real-world experiments, and the real-world data are mainly stored and transmitted by meters, controller area networks, onboard data services, smartphones, and additional sensors installed in the vehicle. Based on driving behavior factors, driver characteristics, and safety rules, this paper recommends nine energy-efficient driving styles including four guidelines for the drivers' selection and adjustment of the vehicle parameters, three recommendations for the energy-efficient driving styles in different driving scenarios, and two subjective suggestions for different types of drivers and employers.

Cobra Effect in Reference-Free Image Captioning Metrics

Evaluating the compatibility between textual descriptions and corresponding images represents a core endeavor within multi-modal research. In recent years, a proliferation of reference-free methods, leveraging visual-language pre-trained models (VLMs), has emerged. Empirical evidence has substantiated that these innovative approaches exhibit a higher correlation with human judgment, marking a significant advancement in the field. However, does a higher correlation with human evaluations alone sufficiently denote the complete of a metric? In response to this question, in this paper, we study if there are any deficiencies in reference-free metrics. Specifically, inspired by the Cobra Effect, we utilize metric scores as rewards to direct the captioning model toward generating descriptions that closely align with the metric's criteria. If a certain metric has flaws, it will be exploited by the model and reflected in the generated sentences. Our findings reveal that descriptions guided by these metrics contain significant flaws, e.g. incoherent statements and excessive repetition. Subsequently, we propose a novel method termed Self-Improving to rectify the identified shortcomings within these metrics. We employ GPT-4V as an evaluative tool to assess generated sentences and the result reveals that our approach achieves state-of-the-art (SOTA) performance. In addition, we also introduce a challenging evaluation benchmark called Flaws Caption to evaluate reference-free image captioning metrics comprehensively. Our code is available at https://github.com/aaronma2020/robust_captioning_metric

Identifying Best Practice Melting Patterns in Induction Furnaces: A Data-Driven Approach Using Time Series KMeans Clustering and Multi-Criteria Decision Making

Improving energy efficiency in industrial production processes is crucial for competitiveness, and compliance with climate policies. This paper introduces a data-driven approach to identify optimal melting patterns in induction furnaces. Through time-series K-means clustering the melting patterns could be classified into distinct clusters based on temperature profiles. Using the elbow method, 12 clusters were identified, representing the range of melting patterns. Performance parameters such as melting time, energy-specific performance, and carbon cost were established for each cluster, indicating furnace efficiency and environmental impact. Multiple criteria decision-making methods including Simple Additive Weighting, Multiplicative Exponential Weighting, Technique for Order of Preference by Similarity to Ideal Solution, modified TOPSIS, and VlseKriterijumska Optimizacija I Kompromisno Resenje were utilized to determine the best-practice cluster. The study successfully identified the cluster with the best performance. Implementing the best practice operation resulted in an 8.6 % reduction in electricity costs, highlighting the potential energy savings in the foundry.

Panoptic Video Scene Graph Generation

Towards building comprehensive real-world visual perception systems, we propose and study a new problem called panoptic scene graph generation (PVSG). PVSG relates to the existing video scene graph generation (VidSGG) problem, which focuses on temporal interactions between humans and objects grounded with bounding boxes in videos. However, the limitation of bounding boxes in detecting non-rigid objects and backgrounds often causes VidSGG to miss key details crucial for comprehensive video understanding. In contrast, PVSG requires nodes in scene graphs to be grounded by more precise, pixel-level segmentation masks, which facilitate holistic scene understanding. To advance research in this new area, we contribute the PVSG dataset, which consists of 400 videos (289 third-person + 111 egocentric videos) with a total of 150K frames labeled with panoptic segmentation masks as well as fine, temporal scene graphs. We also provide a variety of baseline methods and share useful design practices for future work.