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Here, we present the outcomes from the second Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry, which engaged participants across global hybrid locations, resulting in 34 team submissions. The submissions spanned seven key application areas and demonstrated the diverse utility of LLMs for applications in (1) molecular and material property prediction; (2) molecular and material design; (3) automation and novel interfaces; (4) scientific communication and education; (5) research data management and automation; (6) hypothesis generation and evaluation; and (7) knowledge extraction and reasoning from scientific literature. Each team submission is presented in a summary table with links to the code and as brief papers in the appendix. Beyond team results, we discuss the hackathon event and its hybrid format, which included physical hubs in Toronto, Montreal, San Francisco, Berlin, Lausanne, and Tokyo, alongside a global online hub to enable local and virtual collaboration. Overall, the event highlighted significant improvements in LLM capabilities since the previous year's hackathon, suggesting continued expansion of LLMs for applications in materials science and chemistry research. These outcomes demonstrate the dual utility of LLMs as both multipurpose models for diverse machine learning tasks and platforms for rapid prototyping custom applications in scientific research., Comment: Updating author information, the submission remains largely unchanged. 98 pages total

Federated learning is a distributed machine learning paradigm designed to protect user data privacy, which has been successfully implemented across various scenarios. In traditional federated learning, the entire parameter set of local models is updated and averaged in each training round. Although this full network update method maximizes knowledge acquisition and sharing for each model layer, it prevents the layers of the global model from cooperating effectively to complete the tasks of each client, a challenge we refer to as layer mismatch. This mismatch problem recurs after every parameter averaging, consequently slowing down model convergence and degrading overall performance. To address the layer mismatch issue, we introduce the FedPart method, which restricts model updates to either a single layer or a few layers during each communication round. Furthermore, to maintain the efficiency of knowledge acquisition and sharing, we develop several strategies to select trainable layers in each round, including sequential updating and multi-round cycle training. Through both theoretical analysis and experiments, our findings demonstrate that the FedPart method significantly surpasses conventional full network update strategies in terms of convergence speed and accuracy, while also reducing communication and computational overheads., Comment: 27 pages, 8 figures, accepted by NeurIPS 2024

Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. The binding affinity, which refers to the strength of this interaction, is central to many important problems in bioinformatics such as drug design. An extensive amount of work has been devoted to predicting binding affinity over the past decades due to its significance. In this paper, we review all significant recent works, focusing on the methods, features, and benchmark datasets. We have observed a rising trend in the use of traditional machine learning and deep learning models for predicting binding affinity, accompanied by an increasing amount of data on proteins and small drug-like molecules. While prediction results are constantly improving, we also identify several open questions and potential directions that remain unexplored in the field. This paper could serve as an excellent starting point for machine learning researchers who wish to engage in the study of binding affinity, or for anyone with general interests in machine learning, drug discovery, and bioinformatics.

3D Gaussian Splatting (3DGS) has gained significant attention for its application in dense Simultaneous Localization and Mapping (SLAM), enabling real-time rendering and high-fidelity mapping. However, existing 3DGS-based SLAM methods often suffer from accumulated tracking errors and map drift, particularly in large-scale environments. To address these issues, we introduce GLC-SLAM, a Gaussian Splatting SLAM system that integrates global optimization of camera poses and scene models. Our approach employs frame-to-model tracking and triggers hierarchical loop closure using a global-to-local strategy to minimize drift accumulation. By dividing the scene into 3D Gaussian submaps, we facilitate efficient map updates following loop corrections in large scenes. Additionally, our uncertainty-minimized keyframe selection strategy prioritizes keyframes observing more valuable 3D Gaussians to enhance submap optimization. Experimental results on various datasets demonstrate that GLC-SLAM achieves superior or competitive tracking and mapping performance compared to state-of-the-art dense RGB-D SLAM systems.

In personalized federated learning (PFL), it is widely recognized that achieving both high model generalization and effective personalization poses a significant challenge due to their conflicting nature. As a result, existing PFL methods can only manage a trade-off between these two objectives. This raises an interesting question: Is it feasible to develop a model capable of achieving both objectives simultaneously? Our paper presents an affirmative answer, and the key lies in the observation that deep models inherently exhibit hierarchical architectures, which produce representations with various levels of generalization and personalization at different stages. A straightforward approach stemming from this observation is to select multiple representations from these layers and combine them to concurrently achieve generalization and personalization. However, the number of candidate representations is commonly huge, which makes this method infeasible due to high computational costs.To address this problem, we propose DualFed, a new method that can directly yield dual representations correspond to generalization and personalization respectively, thereby simplifying the optimization task. Specifically, DualFed inserts a personalized projection network between the encoder and classifier. The pre-projection representations are able to capture generalized information shareable across clients, and the post-projection representations are effective to capture task-specific information on local clients. This design minimizes the mutual interference between generalization and personalization, thereby achieving a win-win situation. Extensive experiments show that DualFed can outperform other FL methods. Code is available at https://github.com/GuogangZhu/DualFed., Comment: Accepted by ACM MutltiMedia 2024

Personalized Federated Learning (PFL) is a commonly used framework that allows clients to collaboratively train their personalized models. PFL is particularly useful for handling situations where data from different clients are not independent and identically distributed (non-IID). Previous research in PFL implicitly assumes that clients can gain more benefits from those with similar data distributions. Correspondingly, methods such as personalized weight aggregation are developed to assign higher weights to similar clients during training. We pose a question: can a client benefit from other clients with dissimilar data distributions and if so, how? This question is particularly relevant in scenarios with a high degree of non-IID, where clients have widely different data distributions, and learning from only similar clients will lose knowledge from many other clients. We note that when dealing with clients with similar data distributions, methods such as personalized weight aggregation tend to enforce their models to be close in the parameter space. It is reasonable to conjecture that a client can benefit from dissimilar clients if we allow their models to depart from each other. Based on this idea, we propose DiversiFed which allows each client to learn from clients with diversified data distribution in personalized federated learning. DiversiFed pushes personalized models of clients with dissimilar data distributions apart in the parameter space while pulling together those with similar distributions. In addition, to achieve the above effect without using prior knowledge of data distribution, we design a loss function that leverages the model similarity to determine the degree of attraction and repulsion between any two models. Experiments on several datasets show that DiversiFed can benefit from dissimilar clients and thus outperform the state-of-the-art methods., Comment: 14 pages, 9 figures

In traditional Federated Learning approaches like FedAvg, the global model underperforms when faced with data heterogeneity. Personalized Federated Learning (PFL) enables clients to train personalized models to fit their local data distribution better. However, we surprisingly find that the feature extractor in FedAvg is superior to those in most PFL methods. More interestingly, by applying a linear transformation on local features extracted by the feature extractor to align with the classifier, FedAvg can surpass the majority of PFL methods. This suggests that the primary cause of FedAvg's inadequate performance stems from the mismatch between the locally extracted features and the classifier. While current PFL methods mitigate this issue to some extent, their designs compromise the quality of the feature extractor, thus limiting the full potential of PFL. In this paper, we propose a new PFL framework called FedPFT to address the mismatch problem while enhancing the quality of the feature extractor. FedPFT integrates a feature transformation module, driven by personalized prompts, between the global feature extractor and classifier. In each round, clients first train prompts to transform local features to match the global classifier, followed by training model parameters. This approach can also align the training objectives of clients, reducing the impact of data heterogeneity on model collaboration. Moreover, FedPFT's feature transformation module is highly scalable, allowing for the use of different prompts to tailor local features to various tasks. Leveraging this, we introduce a collaborative contrastive learning task to further refine feature extractor quality. Our experiments demonstrate that FedPFT outperforms state-of-the-art methods by up to 7.08%., Comment: 23 pages, 9 figures

To address data heterogeneity, the key strategy of Personalized Federated Learning (PFL) is to decouple general knowledge (shared among clients) and client-specific knowledge, as the latter can have a negative impact on collaboration if not removed. Existing PFL methods primarily adopt a parameter partitioning approach, where the parameters of a model are designated as one of two types: parameters shared with other clients to extract general knowledge and parameters retained locally to learn client-specific knowledge. However, as these two types of parameters are put together like a jigsaw puzzle into a single model during the training process, each parameter may simultaneously absorb both general and client-specific knowledge, thus struggling to separate the two types of knowledge effectively. In this paper, we introduce FedDecomp, a simple but effective PFL paradigm that employs parameter additive decomposition to address this issue. Instead of assigning each parameter of a model as either a shared or personalized one, FedDecomp decomposes each parameter into the sum of two parameters: a shared one and a personalized one, thus achieving a more thorough decoupling of shared and personalized knowledge compared to the parameter partitioning method. In addition, as we find that retaining local knowledge of specific clients requires much lower model capacity compared with general knowledge across all clients, we let the matrix containing personalized parameters be low rank during the training process. Moreover, a new alternating training strategy is proposed to further improve the performance. Experimental results across multiple datasets and varying degrees of data heterogeneity demonstrate that FedDecomp outperforms state-of-the-art methods up to 4.9\%. The code is available at https://github.com/XinghaoWu/FedDecomp., Comment: Accepted by ACM MM 2024

The objective of drug discovery is to identify chemical compounds that possess specific pharmaceutical properties toward a binding target. Existing large language models (LLMS) can achieve high token matching scores in terms of likelihood for molecule generation. However, relying solely on LLM decoding often results in the generation of molecules that are either invalid due to a single misused token, or suboptimal due to unbalanced exploration and exploitation as a consequence of the LLMs prior experience. Here we propose ERP, Entropy-Reinforced Planning for Transformer Decoding, which employs an entropy-reinforced planning algorithm to enhance the Transformer decoding process and strike a balance between exploitation and exploration. ERP aims to achieve improvements in multiple properties compared to direct sampling from the Transformer. We evaluated ERP on the SARS-CoV-2 virus (3CLPro) and human cancer cell target protein (RTCB) benchmarks and demonstrated that, in both benchmarks, ERP consistently outperforms the current state-of-the-art algorithm by 1-5 percent, and baselines by 5-10 percent, respectively. Moreover, such improvement is robust across Transformer models trained with different objectives. Finally, to further illustrate the capabilities of ERP, we tested our algorithm on three code generation benchmarks and outperformed the current state-of-the-art approach as well. Our code is publicly available at: https://github.com/xuefeng-cs/ERP., Comment: Published in ICML2024

Federated Semi-Supervised Learning (FSSL) leverages both labeled and unlabeled data on clients to collaboratively train a model.In FSSL, the heterogeneous data can introduce prediction bias into the model, causing the model's prediction to skew towards some certain classes. Existing FSSL methods primarily tackle this issue by enhancing consistency in model parameters or outputs. However, as the models themselves are biased, merely constraining their consistency is not sufficient to alleviate prediction bias. In this paper, we explore this bias from a Bayesian perspective and demonstrate that it principally originates from label prior bias within the training data. Building upon this insight, we propose a debiasing method for FSSL named FedDB. FedDB utilizes the Average Prediction Probability of Unlabeled Data (APP-U) to approximate the biased prior.During local training, FedDB employs APP-U to refine pseudo-labeling through Bayes' theorem, thereby significantly reducing the label prior bias. Concurrently, during the model aggregation, FedDB uses APP-U from participating clients to formulate unbiased aggregate weights, thereby effectively diminishing bias in the global model. Experimental results show that FedDB can surpass existing FSSL methods. The code is available at https://github.com/GuogangZhu/FedDB., Comment: Accepted by IJCAI 2024

This paper studies Learning from Imperfect Human Feedback (LIHF), addressing the potential irrationality or imperfect perception when learning from comparative human feedback. Building on evidences that human's imperfection decays over time (i.e., humans learn to improve), we cast this problem as a concave-utility continuous-action dueling bandit but under a restricted form of corruption: i.e., the corruption scale is decaying over time as $t^{\rho-1}$ for some "imperfection rate" $\rho \in [0, 1]$. With $T$ as the total number of iterations, we establish a regret lower bound of $ \Omega(\max\{\sqrt{T}, T^{\rho}\}) $ for LIHF, even when $\rho$ is known. For the same setting, we develop the Robustified Stochastic Mirror Descent for Imperfect Dueling (RoSMID) algorithm, which achieves nearly optimal regret $\tilde{\mathcal{O}}(\max\{\sqrt{T}, T^{\rho}\})$. Core to our analysis is a novel framework for analyzing gradient-based algorithms for dueling bandit under corruption, and we demonstrate its general applicability by showing how this framework can be easily applied to obtain corruption-robust guarantees for other popular gradient-based dueling bandit algorithms. Our theoretical results are validated by extensive experiments.

While reinforcement learning (RL) has shown promising performance, its sample complexity continues to be a substantial hurdle, restricting its broader application across a variety of domains. Imitation learning (IL) utilizes oracles to improve sample efficiency, yet it is often constrained by the quality of the oracles deployed. which actively interleaves between IL and RL based on an online estimate of their performance. RPI draws on the strengths of IL, using oracle queries to facilitate exploration, an aspect that is notably challenging in sparse-reward RL, particularly during the early stages of learning. As learning unfolds, RPI gradually transitions to RL, effectively treating the learned policy as an improved oracle. This algorithm is capable of learning from and improving upon a diverse set of black-box oracles. Integral to RPI are Robust Active Policy Selection (RAPS) and Robust Policy Gradient (RPG), both of which reason over whether to perform state-wise imitation from the oracles or learn from its own value function when the learner's performance surpasses that of the oracles in a specific state. Empirical evaluations and theoretical analysis validate that RPI excels in comparison to existing state-of-the-art methodologies, demonstrating superior performance across various benchmark domains.

Personalized federated learning (PFL) reduces the impact of non-independent and identically distributed (non-IID) data among clients by allowing each client to train a personalized model when collaborating with others. A key question in PFL is to decide which parameters of a client should be localized or shared with others. In current mainstream approaches, all layers that are sensitive to non-IID data (such as classifier layers) are generally personalized. The reasoning behind this approach is understandable, as localizing parameters that are easily influenced by non-IID data can prevent the potential negative effect of collaboration. However, we believe that this approach is too conservative for collaboration. For example, for a certain client, even if its parameters are easily influenced by non-IID data, it can still benefit by sharing these parameters with clients having similar data distribution. This observation emphasizes the importance of considering not only the sensitivity to non-IID data but also the similarity of data distribution when determining which parameters should be localized in PFL. This paper introduces a novel guideline for client collaboration in PFL. Unlike existing approaches that prohibit all collaboration of sensitive parameters, our guideline allows clients to share more parameters with others, leading to improved model performance. Additionally, we propose a new PFL method named FedCAC, which employs a quantitative metric to evaluate each parameter's sensitivity to non-IID data and carefully selects collaborators based on this evaluation. Experimental results demonstrate that FedCAC enables clients to share more parameters with others, resulting in superior performance compared to state-of-the-art methods, particularly in scenarios where clients have diverse distributions., Comment: Accepted by ICCV2023

Personalized federated learning (PFL) is a popular framework that allows clients to have different models to address application scenarios where clients' data are in different domains. The typical model of a client in PFL features a global encoder trained by all clients to extract universal features from the raw data and personalized layers (e.g., a classifier) trained using the client's local data. Nonetheless, due to the differences between the data distributions of different clients (aka, domain gaps), the universal features produced by the global encoder largely encompass numerous components irrelevant to a certain client's local task. Some recent PFL methods address the above problem by personalizing specific parameters within the encoder. However, these methods encounter substantial challenges attributed to the high dimensionality and non-linearity of neural network parameter space. In contrast, the feature space exhibits a lower dimensionality, providing greater intuitiveness and interpretability as compared to the parameter space. To this end, we propose a novel PFL framework named FedPick. FedPick achieves PFL in the low-dimensional feature space by selecting task-relevant features adaptively for each client from the features generated by the global encoder based on its local data distribution. It presents a more accessible and interpretable implementation of PFL compared to those methods working in the parameter space. Extensive experimental results show that FedPick could effectively select task-relevant features for each client and improve model performance in cross-domain FL., Comment: 13 pages, 13 figures

We propose 3Deformer, a general-purpose framework for interactive 3D shape editing. Given a source 3D mesh with semantic materials, and a user-specified semantic image, 3Deformer can accurately edit the source mesh following the shape guidance of the semantic image, while preserving the source topology as rigid as possible. Recent studies of 3D shape editing mostly focus on learning neural networks to predict 3D shapes, which requires high-cost 3D training datasets and is limited to handling objects involved in the datasets. Unlike these studies, our 3Deformer is a non-training and common framework, which only requires supervision of readily-available semantic images, and is compatible with editing various objects unlimited by datasets. In 3Deformer, the source mesh is deformed utilizing the differentiable renderer technique, according to the correspondences between semantic images and mesh materials. However, guiding complex 3D shapes with a simple 2D image incurs extra challenges, that is, the deform accuracy, surface smoothness, geometric rigidity, and global synchronization of the edited mesh should be guaranteed. To address these challenges, we propose a hierarchical optimization architecture to balance the global and local shape features, and propose further various strategies and losses to improve properties of accuracy, smoothness, rigidity, and so on. Extensive experiments show that our 3Deformer is able to produce impressive results and reaches the state-of-the-art level.

Reinforcement learning (RL) has made significant strides in various complex domains. However, identifying an effective policy via RL often necessitates extensive exploration. Imitation learning aims to mitigate this issue by using expert demonstrations to guide exploration. In real-world scenarios, one often has access to multiple suboptimal black-box experts, rather than a single optimal oracle. These experts do not universally outperform each other across all states, presenting a challenge in actively deciding which oracle to use and in which state. We introduce MAPS and MAPS-SE, a class of policy improvement algorithms that perform imitation learning from multiple suboptimal oracles. In particular, MAPS actively selects which of the oracles to imitate and improve their value function estimates, and MAPS-SE additionally leverages an active state exploration criterion to determine which states one should explore. We provide a comprehensive theoretical analysis and demonstrate that MAPS and MAPS-SE enjoy sample efficiency advantage over the state-of-the-art policy improvement algorithms. Empirical results show that MAPS-SE significantly accelerates policy optimization via state-wise imitation learning from multiple oracles across a broad spectrum of control tasks in the DeepMind Control Suite. Our code is publicly available at: https://github.com/ripl/maps.

Federated learning (FL) is a new paradigm for distributed machine learning that allows a global model to be trained across multiple clients without compromising their privacy. Although FL has demonstrated remarkable success in various scenarios, recent studies mainly utilize shallow and small neural networks. In our research, we discover a significant performance decline when applying the existing FL framework to deeper neural networks, even when client data are independently and identically distributed (i.i.d.). Our further investigation shows that the decline is due to the continuous accumulation of dissimilarities among client models during the layer-by-layer back-propagation process, which we refer to as "divergence accumulation." As deeper models involve a longer chain of divergence accumulation, they tend to manifest greater divergence, subsequently leading to performance decline. Both theoretical derivations and empirical evidence are proposed to support the existence of divergence accumulation and its amplified effects in deeper models. To address this issue, we propose several technical guidelines based on reducing divergence, such as using wider models and reducing the receptive field. These approaches can greatly improve the accuracy of FL on deeper models. For example, the application of these guidelines can boost the ResNet101 model's performance by as much as 43\% on the Tiny-ImageNet dataset., Comment: 16 pages, 8 figures

Open-vocabulary Video Instance Segmentation (OpenVIS) can simultaneously detect, segment, and track arbitrary object categories in a video, without being constrained to categories seen during training. In this work, we propose InstFormer, a carefully designed framework for the OpenVIS task that achieves powerful open-vocabulary capabilities through lightweight fine-tuning with limited-category data. InstFormer begins with the open-world mask proposal network, encouraged to propose all potential instance class-agnostic masks by the contrastive instance margin loss. Next, we introduce InstCLIP, adapted from pre-trained CLIP with Instance Guidance Attention, which encodes open-vocabulary instance tokens efficiently. These instance tokens not only enable open-vocabulary classification but also offer strong universal tracking capabilities. Furthermore, to prevent the tracking module from being constrained by the training data with limited categories, we propose the universal rollout association, which transforms the tracking problem into predicting the next frame's instance tracking token. The experimental results demonstrate the proposed InstFormer achieve state-of-the-art capabilities on a comprehensive OpenVIS evaluation benchmark, while also achieves competitive performance in fully supervised VIS task.

In spectral theory, the multiplicity of nearly degenerate eigenvalues presents significant challenges. This paper introduces a new difference quotient formula to capture the behavior of nearly degenerate Laplacian eigenvalues resulting from domain perturbations. Additionally, we propose a novel numerical algorithm for rigorously estimating the difference quotient of these multiple eigenvalues in response to domain deformation, using a recently developed guaranteed computation method for eigenvalue problems. As an application, we solve the open problem of the simplicity of the second Dirichlet eigenvalue for nearly equilateral triangles, offering a partial solution to Conjecture 6.47 in A. Henrot's book ``Shape Optimization and Spectral Theory."

We report an AlGaInAs multiple quantum well integrated source of polarization controlled light consisting of a polarization mode converter PMC, differential phase shifter(DPS), and a side wall grating distributed-feedback DFB laser. We demonstrate an asymmetrical stepped-height ridge waveguide PMC to realize TE to TM polarization conversion and a symmetrical straight waveguide DPS to enable polarization rotation from approximately counterclockwise circular polarization to linear polarization. Based on the identical epitaxial layer scheme, all of the PMC, DPS, and DFB laser can be integrated monolithically using only a single step of metalorganic vapor phase epitaxy and two steps of III V material dry etching. For the DFB-PMC device, a high TE to TM polarization conversion efficiency 98% over a wide range of DFB injection currents is reported at 1555 nm wavelength. For the DFB-PMC-DPS device, a 60 degree rotation of the Stokes vector was obtained on the Poincar\'e sphere with a range of bias voltage from 0 V to -4.0 V at IDFB is 170 mA., Comment: arXiv admin note: text overlap with arXiv:2210.10519

For conforming finite element approximations of the Laplacian eigenfunctions, a fully computable guaranteed error bound in the $L^2$ norm sense is proposed. The bound is based on the a priori error estimate for the Galerkin projection of the conforming finite element method, and has an optimal speed of convergence for the eigenfunctions with the worst regularity. The resulting error estimate bounds the distance of spaces of exact and approximate eigenfunctions and, hence, is robust even in the case of multiple and tightly clustered eigenvalues. The accuracy of the proposed bound is illustrated by numerical examples. The demonstration code is available at https://ganjin.online/xfliu/EigenfunctionEstimation4FEM ., Comment: 24 pages, 7 figures, 3 tables. arXiv admin note: text overlap with arXiv:1904.07903

We report the first demonstration of a 1555 nm stepped-height ridge waveguide polarization mode converter monolithically integrated with a side wall grating distributed-feedback (DFB) laser using the identical epitaxial layer scheme. The device shows stable single longitudinal mode (SLM) operation with the output light converted from TE to TM polarization with an efficiency of >94% over a wide range of DFB injection currents (IDFB) from 140 mA to 190 mA. The highest TM mode purity of 98.2% was obtained at IDFB=180 mA. A particular advantage of this device is that only a single step of metalorganic vapor-phase epitaxy and two steps of III-V material dry etching are required for the whole integrated device fabrication, significantly reducing complexity and cost.

A computer-assisted proof is proposed for the Laplacian eigenvalue minimization problems over triangular domains under diameter constraints. The proof utilizes recently developed guaranteed computation methods for both eigenvalues and eigenfunctions of differential operators. The paper also provides an elementary and concise proof of the Hadamard shape derivative, which helps to validate the monotonicity of eigenvalue with respect to shape parameters. Besides the model homogeneous Dirichlet eigenvalue problem, the eigenvalue problem associated with a non-homogeneous Neumann boundary condition, which is related to the Crouzeix--Raviart interpolation error constant, is considered. The computer-assisted proof tells that among the triangles with the unit diameter, the equilateral triangle minimizes the first eigenvalue for each concerned eigenvalue problem.