Automating Exploratory Proteomics Research via Language Models

With the development of artificial intelligence, its contribution to science is evolving from simulating a complex problem to automating entire research processes and producing novel discoveries. Achieving this advancement requires both specialized general models grounded in real-world scientific data and iterative, exploratory frameworks that mirror human scientific methodologies. In this paper, we present PROTEUS, a fully automated system for scientific discovery from raw proteomics data. PROTEUS uses large language models (LLMs) to perform hierarchical planning, execute specialized bioinformatics tools, and iteratively refine analysis workflows to generate high-quality scientific hypotheses. The system takes proteomics datasets as input and produces a comprehensive set of research objectives, analysis results, and novel biological hypotheses without human intervention. We evaluated PROTEUS on 12 proteomics datasets collected from various biological samples (e.g. immune cells, tumors) and different sample types (single-cell and bulk), generating 191 scientific hypotheses. These were assessed using both automatic LLM-based scoring on 5 metrics and detailed reviews from human experts. Results demonstrate that PROTEUS consistently produces reliable, logically coherent results that align well with existing literature while also proposing novel, evaluable hypotheses. The system's flexible architecture facilitates seamless integration of diverse analysis tools and adaptation to different proteomics data types. By automating complex proteomics analysis workflows and hypothesis generation, PROTEUS has the potential to considerably accelerate the pace of scientific discovery in proteomics research, enabling researchers to efficiently explore large-scale datasets and uncover biological insights.

Dissertation: On the Theoretical Foundation of Model Comparison and Evaluation for Recommender System

Recommender systems have become increasingly important with the rise of the web as a medium for electronic and business transactions. One of the key drivers of this technology is the ease with which users can provide feedback about their likes and dislikes through simple clicks of a mouse. This feedback is commonly collected in the form of ratings, but can also be inferred from a user's browsing and purchasing history. Recommender systems utilize users' historical data to infer customer interests and provide personalized recommendations. The basic principle of recommendations is that significant dependencies exist between user- and item-centric activity, which can be learned in a data-driven manner to make accurate predictions. Collaborative filtering is one family of recommendation algorithms that uses ratings from multiple users to predict missing ratings or uses binary click information to predict potential clicks. However, recommender systems can be more complex and incorporate auxiliary data such as content-based attributes, user interactions, and contextual information.

GDDA: Semantic OOD Detection on Graphs under Covariate Shift via Score-Based Diffusion Models

Out-of-distribution (OOD) detection poses a significant challenge for Graph Neural Networks (GNNs), particularly in open-world scenarios with varying distribution shifts. Most existing OOD detection methods on graphs primarily focus on identifying instances in test data domains caused by either semantic shifts (changes in data classes) or covariate shifts (changes in data features), while leaving the simultaneous occurrence of both distribution shifts under-explored. In this work, we address both types of shifts simultaneously and introduce a novel challenge for OOD detection on graphs: graph-level semantic OOD detection under covariate shift. In this scenario, variations between the training and test domains result from the concurrent presence of both covariate and semantic shifts, where only graphs associated with unknown classes are identified as OOD samples (OODs). To tackle this challenge, we propose a novel two-phase framework called Graph Disentangled Diffusion Augmentation (GDDA). The first phase focuses on disentangling graph representations into domain-invariant semantic factors and domain-specific style factors. In the second phase, we introduce a novel distribution-shift-controlled score-based generative diffusion model that generates latent factors outside the training semantic and style spaces. Additionally, auxiliary pseudo-in-distribution (InD) and pseudo-OOD graph representations are employed to enhance the effectiveness of the energy-based semantic OOD detector. Extensive empirical studies on three benchmark datasets demonstrate that our approach outperforms state-of-the-art baselines.

DiP-GO: A Diffusion Pruner via Few-step Gradient Optimization

Diffusion models have achieved remarkable progress in the field of image generation due to their outstanding capabilities. However, these models require substantial computing resources because of the multi-step denoising process during inference. While traditional pruning methods have been employed to optimize these models, the retraining process necessitates large-scale training datasets and extensive computational costs to maintain generalization ability, making it neither convenient nor efficient. Recent studies attempt to utilize the similarity of features across adjacent denoising stages to reduce computational costs through simple and static strategies. However, these strategies cannot fully harness the potential of the similar feature patterns across adjacent timesteps. In this work, we propose a novel pruning method that derives an efficient diffusion model via a more intelligent and differentiable pruner. At the core of our approach is casting the model pruning process into a SubNet search process. Specifically, we first introduce a SuperNet based on standard diffusion via adding some backup connections built upon the similar features. We then construct a plugin pruner network and design optimization losses to identify redundant computation. Finally, our method can identify an optimal SubNet through few-step gradient optimization and a simple post-processing procedure. We conduct extensive experiments on various diffusion models including Stable Diffusion series and DiTs. Our DiP-GO approach achieves 4.4 x speedup for SD-1.5 without any loss of accuracy, significantly outperforming the previous state-of-the-art methods.

Satori: Towards Proactive AR Assistant with Belief-Desire-Intention User Modeling

Augmented Reality assistance are increasingly popular for supporting users with tasks like assembly and cooking. However, current practice typically provide reactive responses initialized from user requests, lacking consideration of rich contextual and user-specific information. To address this limitation, we propose a novel AR assistance system, Satori, that models both user states and environmental contexts to deliver proactive guidance. Our system combines the Belief-Desire-Intention (BDI) model with a state-of-the-art multi-modal large language model (LLM) to infer contextually appropriate guidance. The design is informed by two formative studies involving twelve experts. A sixteen within-subject study find that Satori achieves performance comparable to an designer-created Wizard-of-Oz (WoZ) system without relying on manual configurations or heuristics, thereby enhancing generalizability, reusability and opening up new possibilities for AR assistance.

Summit Vitals: Multi-Camera and Multi-Signal Biosensing at High Altitudes

Video photoplethysmography (vPPG) is an emerging method for non-invasive and convenient measurement of physiological signals, utilizing two primary approaches: remote video PPG (rPPG) and contact video PPG (cPPG). Monitoring vitals in high-altitude environments, where heart rates tend to increase and blood oxygen levels often decrease, presents significant challenges. To address these issues, we introduce the SUMS dataset comprising 80 synchronized non-contact facial and contact finger videos from 10 subjects during exercise and oxygen recovery scenarios, capturing PPG, respiration rate (RR), and SpO2. This dataset is designed to validate video vitals estimation algorithms and compare facial rPPG with finger cPPG. Additionally, fusing videos from different positions (i.e., face and finger) reduces the mean absolute error (MAE) of SpO2 predictions by 7.6\% and 10.6\% compared to only face and only finger, respectively. In cross-subject evaluation, we achieve an MAE of less than 0.5 BPM for HR estimation and 2.5\% for SpO2 estimation, demonstrating the precision of our multi-camera fusion techniques. Our findings suggest that simultaneous training on multiple indicators, such as PPG and blood oxygen, can reduce MAE in SpO2 estimation by 17.8\%.

Resultant: Incremental Effectiveness on Likelihood for Unsupervised Out-of-Distribution Detection

Unsupervised out-of-distribution (U-OOD) detection is to identify OOD data samples with a detector trained solely on unlabeled in-distribution (ID) data. The likelihood function estimated by a deep generative model (DGM) could be a natural detector, but its performance is limited in some popular "hard" benchmarks, such as FashionMNIST (ID) vs. MNIST (OOD). Recent studies have developed various detectors based on DGMs to move beyond likelihood. However, despite their success on "hard" benchmarks, most of them struggle to consistently surpass or match the performance of likelihood on some "non-hard" cases, such as SVHN (ID) vs. CIFAR10 (OOD) where likelihood could be a nearly perfect detector. Therefore, we appeal for more attention to incremental effectiveness on likelihood, i.e., whether a method could always surpass or at least match the performance of likelihood in U-OOD detection. We first investigate the likelihood of variational DGMs and find its detection performance could be improved in two directions: i) alleviating latent distribution mismatch, and ii) calibrating the dataset entropy-mutual integration. Then, we apply two techniques for each direction, specifically post-hoc prior and dataset entropy-mutual calibration. The final method, named Resultant, combines these two directions for better incremental effectiveness compared to either technique alone. Experimental results demonstrate that the Resultant could be a new state-of-the-art U-OOD detector while maintaining incremental effectiveness on likelihood in a wide range of tasks.

UMAD: University of Macau Anomaly Detection Benchmark Dataset

Anomaly detection is critical in surveillance systems and patrol robots by identifying anomalous regions in images for early warning. Depending on whether reference data are utilized, anomaly detection can be categorized into anomaly detection with reference and anomaly detection without reference. Currently, anomaly detection without reference, which is closely related to out-of-distribution (OoD) object detection, struggles with learning anomalous patterns due to the difficulty of collecting sufficiently large and diverse anomaly datasets with the inherent rarity and novelty of anomalies. Alternatively, anomaly detection with reference employs the scheme of change detection to identify anomalies by comparing semantic changes between a reference image and a query one. However, there are very few ADr works due to the scarcity of public datasets in this domain. In this paper, we aim to address this gap by introducing the UMAD Benchmark Dataset. To our best knowledge, this is the first benchmark dataset designed specifically for anomaly detection with reference in robotic patrolling scenarios, e.g., where an autonomous robot is employed to detect anomalous objects by comparing a reference and a query video sequences. The reference sequences can be taken by the robot along a specified route when there are no anomalous objects in the scene. The query sequences are captured online by the robot when it is patrolling in the same scene following the same route. Our benchmark dataset is elaborated such that each query image can find a corresponding reference based on accurate robot localization along the same route in the prebuilt 3D map, with which the reference and query images can be geometrically aligned using adaptive warping. Besides the proposed benchmark dataset, we evaluate the baseline models of ADr on this dataset.

Enhancing One-shot Pruned Pre-trained Language Models through Sparse-Dense-Sparse Mechanism

Pre-trained language models (PLMs) are engineered to be robust in contextual understanding and exhibit outstanding performance in various natural language processing tasks. However, their considerable size incurs significant computational and storage costs. Modern pruning strategies employ one-shot techniques to compress PLMs without the need for retraining on task-specific or otherwise general data; however, these approaches often lead to an indispensable reduction in performance. In this paper, we propose SDS, a Sparse-Dense-Sparse pruning framework to enhance the performance of the pruned PLMs from a weight distribution optimization perspective. We outline the pruning process in three steps. Initially, we prune less critical connections in the model using conventional one-shot pruning methods. Next, we reconstruct a dense model featuring a pruning-friendly weight distribution by reactivating pruned connections with sparse regularization. Finally, we perform a second pruning round, yielding a superior pruned model compared to the initial pruning. Experimental results demonstrate that SDS outperforms the state-of-the-art pruning techniques SparseGPT and Wanda under an identical sparsity configuration. For instance, SDS reduces perplexity by 9.13 on Raw-Wikitext2 and improves accuracy by an average of 2.05% across multiple zero-shot benchmarks for OPT-125M with 2:4 sparsity.

Open-FinLLMs: Open Multimodal Large Language Models for Financial Applications

Large language models (LLMs) have advanced financial applications, yet they often lack sufficient financial knowledge and struggle with tasks involving multi-modal inputs like tables and time series data. To address these limitations, we introduce \textit{Open-FinLLMs}, a series of Financial LLMs. We begin with FinLLaMA, pre-trained on a 52 billion token financial corpus, incorporating text, tables, and time-series data to embed comprehensive financial knowledge. FinLLaMA is then instruction fine-tuned with 573K financial instructions, resulting in FinLLaMA-instruct, which enhances task performance. Finally, we present FinLLaVA, a multimodal LLM trained with 1.43M image-text instructions to handle complex financial data types. Extensive evaluations demonstrate FinLLaMA's superior performance over LLaMA3-8B, LLaMA3.1-8B, and BloombergGPT in both zero-shot and few-shot settings across 19 and 4 datasets, respectively. FinLLaMA-instruct outperforms GPT-4 and other Financial LLMs on 15 datasets. FinLLaVA excels in understanding tables and charts across 4 multimodal tasks. Additionally, FinLLaMA achieves impressive Sharpe Ratios in trading simulations, highlighting its robust financial application capabilities. We will continually maintain and improve our models and benchmarks to support ongoing innovation in academia and industry.