MiceBoneChallenge: Micro-CT public dataset and six solutions for automatic growth plate detection in micro-CT mice bone scans

Detecting and quantifying bone changes in micro-CT scans of rodents is a common task in preclinical drug development studies. However, this task is manual, time-consuming and subject to inter- and intra-observer variability. In 2024, Anonymous Company organized an internal challenge to develop models for automatic bone quantification. We prepared and annotated a high-quality dataset of 3D $\mu$CT bone scans from $83$ mice. The challenge attracted over $80$ AI scientists from around the globe who formed $23$ teams. The participants were tasked with developing a solution to identify the plane where the bone growth happens, which is essential for fully automatic segmentation of trabecular bone. As a result, six computer vision solutions were developed that can accurately identify the location of the growth plate plane. The solutions achieved the mean absolute error of $1.91\pm0.87$ planes from the ground truth on the test set, an accuracy level acceptable for practical use by a radiologist. The annotated 3D scans dataset along with the six solutions and source code, is being made public, providing researchers with opportunities to develop and benchmark their own approaches. The code, trained models, and the data will be shared.

Knowledge Graph Based Agent for Complex, Knowledge-Intensive QA in Medicine

Biomedical knowledge is uniquely complex and structured, requiring distinct reasoning strategies compared to other scientific disciplines like physics or chemistry. Biomedical scientists do not rely on a single approach to reasoning; instead, they use various strategies, including rule-based, prototype-based, and case-based reasoning. This diversity calls for flexible approaches that accommodate multiple reasoning strategies while leveraging in-domain knowledge. We introduce KGARevion, a knowledge graph (KG) based agent designed to address the complexity of knowledge-intensive medical queries. Upon receiving a query, KGARevion generates relevant triplets by using the knowledge base of the LLM. These triplets are then verified against a grounded KG to filter out erroneous information and ensure that only accurate, relevant data contribute to the final answer. Unlike RAG-based models, this multi-step process ensures robustness in reasoning while adapting to different models of medical reasoning. Evaluations on four gold-standard medical QA datasets show that KGARevion improves accuracy by over 5.2%, outperforming 15 models in handling complex medical questions. To test its capabilities, we curated three new medical QA datasets with varying levels of semantic complexity, where KGARevion achieved a 10.4% improvement in accuracy.

Joint RGB-Spectral Decomposition Model Guided Image Enhancement in Mobile Photography

The integration of miniaturized spectrometers into mobile devices offers new avenues for image quality enhancement and facilitates novel downstream tasks. However, the broader application of spectral sensors in mobile photography is hindered by the inherent complexity of spectral images and the constraints of spectral imaging capabilities. To overcome these challenges, we propose a joint RGB-Spectral decomposition model guided enhancement framework, which consists of two steps: joint decomposition and prior-guided enhancement. Firstly, we leverage the complementarity between RGB and Low-resolution Multi-Spectral Images (Lr-MSI) to predict shading, reflectance, and material semantic priors. Subsequently, these priors are seamlessly integrated into the established HDRNet to promote dynamic range enhancement, color mapping, and grid expert learning, respectively. Additionally, we construct a high-quality Mobile-Spec dataset to support our research, and our experiments validate the effectiveness of Lr-MSI in the tone enhancement task. This work aims to establish a solid foundation for advancing spectral vision in mobile photography. The code is available at \url{https://github.com/CalayZhou/JDM-HDRNet}.

Deep Temporal Sequence Classification and Mathematical Modeling for Cell Tracking in Dense 3D Microscopy Videos of Bacterial Biofilms

Automatic cell tracking in dense environments is plagued by inaccurate correspondences and misidentification of parent-offspring relationships. In this paper, we introduce a novel cell tracking algorithm named DenseTrack, which integrates deep learning with mathematical model-based strategies to effectively establish correspondences between consecutive frames and detect cell division events in crowded scenarios. We formulate the cell tracking problem as a deep learning-based temporal sequence classification task followed by solving a constrained one-to-one matching optimization problem exploiting the classifier's confidence scores. Additionally, we present an eigendecomposition-based cell division detection strategy that leverages knowledge of cellular geometry. The performance of the proposed approach has been evaluated by tracking densely packed cells in 3D time-lapse image sequences of bacterial biofilm development. The experimental results on simulated as well as experimental fluorescence image sequences suggest that the proposed tracking method achieves superior performance in terms of both qualitative and quantitative evaluation measures compared to recent state-of-the-art cell tracking approaches.

LLMs Assist NLP Researchers: Critique Paper (Meta-)Reviewing

This work is motivated by two key trends. On one hand, large language models (LLMs) have shown remarkable versatility in various generative tasks such as writing, drawing, and question answering, significantly reducing the time required for many routine tasks. On the other hand, researchers, whose work is not only time-consuming but also highly expertise-demanding, face increasing challenges as they have to spend more time reading, writing, and reviewing papers. This raises the question: how can LLMs potentially assist researchers in alleviating their heavy workload? This study focuses on the topic of LLMs assist NLP Researchers, particularly examining the effectiveness of LLM in assisting paper (meta-)reviewing and its recognizability. To address this, we constructed the ReviewCritique dataset, which includes two types of information: (i) NLP papers (initial submissions rather than camera-ready) with both human-written and LLM-generated reviews, and (ii) each review comes with "deficiency" labels and corresponding explanations for individual segments, annotated by experts. Using ReviewCritique, this study explores two threads of research questions: (i) "LLMs as Reviewers", how do reviews generated by LLMs compare with those written by humans in terms of quality and distinguishability? (ii) "LLMs as Metareviewers", how effectively can LLMs identify potential issues, such as Deficient or unprofessional review segments, within individual paper reviews? To our knowledge, this is the first work to provide such a comprehensive analysis.

Advancing Tool-Augmented Large Language Models: Integrating Insights from Errors in Inference Trees

Tool-augmented large language models (LLMs) leverage tools, often in the form of APIs, to enhance their reasoning capabilities on complex tasks, thus taking on the role of intelligent agents interacting with the real world. The recently introduced ToolLLaMA model by Qin et al. [2024] utilizes the depth-first search-based decision tree (DFSDT) method for reasoning with $16000+$ real-world APIs, which effectively improves the planning and inferencing performance of tool-augmented LLMs compared to traditional chain reasoning approaches. However, their approach only employs successful paths from decision trees (also called inference trees) for supervised fine-tuning (SFT) during training, which does not fully exploit the advantages of the tree of thought. In this study, we propose an inference trajectory optimization framework based on the preference data extracted from decision trees to address this limitation. We first introduce a novel method for constructing preference data from the tree of thought, capitalizing on the failed explorations previously overlooked in the trees. Specifically, we generate an effective step-wise preference dataset, named ToolPreference, for tool use based on the ToolBench dataset. In the subsequent training phase, we first fine-tune the LLM with tool-usage expert trajectories and then use these step-wise preference pairs for direct preference optimization (DPO) to update the policy of the LLM, resulting in our ToolPrefer-LLaMA (TP-LLaMA) model. Our experiments demonstrate that by obtaining insights from errors in inference trees, TP-LLaMA significantly outperforms the baselines across almost all test scenarios by a large margin and exhibits better generalization capabilities with unseen APIs. At the same time, TP-LLaMA has also demonstrated superior reasoning efficiency compared to the baselines, making it more suitable for complex tool-usage reasoning tasks.

Projection-Free Variance Reduction Methods for Stochastic Constrained Multi-Level Compositional Optimization

This paper investigates projection-free algorithms for stochastic constrained multi-level optimization. In this context, the objective function is a nested composition of several smooth functions, and the decision set is closed and convex. Existing projection-free algorithms for solving this problem suffer from two limitations: 1) they solely focus on the gradient mapping criterion and fail to match the optimal sample complexities in unconstrained settings; 2) their analysis is exclusively applicable to non-convex functions, without considering convex and strongly convex objectives. To address these issues, we introduce novel projection-free variance reduction algorithms and analyze their complexities under different criteria. For gradient mapping, our complexities improve existing results and match the optimal rates for unconstrained problems. For the widely-used Frank-Wolfe gap criterion, we provide theoretical guarantees that align with those for single-level problems. Additionally, by using a stage-wise adaptation, we further obtain complexities for convex and strongly convex functions. Finally, numerical experiments on different tasks demonstrate the effectiveness of our methods.

Adaptive Variance Reduction for Stochastic Optimization under Weaker Assumptions

This paper explores adaptive variance reduction methods for stochastic optimization based on the STORM technique. Existing adaptive extensions of STORM rely on strong assumptions like bounded gradients and bounded function values, or suffer an additional $\mathcal{O}(\log T)$ term in the convergence rate. To address these limitations, we introduce a novel adaptive STORM method that achieves an optimal convergence rate of $\mathcal{O}(T^{-1/3})$ for non-convex functions with our newly designed learning rate strategy. Compared with existing approaches, our method requires weaker assumptions and attains the optimal convergence rate without the additional $\mathcal{O}(\log T)$ term. We also extend the proposed technique to stochastic compositional optimization, obtaining the same optimal rate of $\mathcal{O}(T^{-1/3})$. Furthermore, we investigate the non-convex finite-sum problem and develop another innovative adaptive variance reduction method that achieves an optimal convergence rate of $\mathcal{O}(n^{1/4} T^{-1/2} )$, where $n$ represents the number of component functions. Numerical experiments across various tasks validate the effectiveness of our method.

Universal Online Convex Optimization with $1$ Projection per Round

To address the uncertainty in function types, recent progress in online convex optimization (OCO) has spurred the development of universal algorithms that simultaneously attain minimax rates for multiple types of convex functions. However, for a $T$-round online problem, state-of-the-art methods typically conduct $O(\log T)$ projections onto the domain in each round, a process potentially time-consuming with complicated feasible sets. In this paper, inspired by the black-box reduction of Cutkosky and Orabona (2018), we employ a surrogate loss defined over simpler domains to develop universal OCO algorithms that only require $1$ projection. Embracing the framework of prediction with expert advice, we maintain a set of experts for each type of functions and aggregate their predictions via a meta-algorithm. The crux of our approach lies in a uniquely designed expert-loss for strongly convex functions, stemming from an innovative decomposition of the regret into the meta-regret and the expert-regret. Our analysis sheds new light on the surrogate loss, facilitating a rigorous examination of the discrepancy between the regret of the original loss and that of the surrogate loss, and carefully controlling meta-regret under the strong convexity condition. In this way, with only $1$ projection per round, we establish optimal regret bounds for general convex, exponentially concave, and strongly convex functions simultaneously. Furthermore, we enhance the expert-loss to exploit the smoothness property, and demonstrate that our algorithm can attain small-loss regret for multiple types of convex and smooth functions.

Learning Off-policy with Model-based Intrinsic Motivation For Active Online Exploration

Recent advancements in deep reinforcement learning (RL) have demonstrated notable progress in sample efficiency, spanning both model-based and model-free paradigms. Despite the identification and mitigation of specific bottlenecks in prior works, the agent's exploration ability remains under-emphasized in the realm of sample-efficient RL. This paper investigates how to achieve sample-efficient exploration in continuous control tasks. We introduce an RL algorithm that incorporates a predictive model and off-policy learning elements, where an online planner enhanced by a novelty-aware terminal value function is employed for sample collection. Leveraging the forward predictive error within a latent state space, we derive an intrinsic reward without incurring parameters overhead. This reward establishes a solid connection to model uncertainty, allowing the agent to effectively overcome the asymptotic performance gap. Through extensive experiments, our method shows competitive or even superior performance compared to prior works, especially the sparse reward cases.