Miracle-dz/UniFAR-FTUs huggingface dataset:
Lo-Hi: Practical ML Drug Discovery Benchmark

Finding new drugs is getting harder and harder. One of the hopes of drug discovery is to use machine learning models to predict molecular properties. That is why models for molecular property prediction are being developed and tested on benchmarks such as MoleculeNet. However, existing benchmarks are unrealistic and are too different from applying the models in practice. We have created a new practical \emph{Lo-Hi} benchmark consisting of two tasks: Lead Optimization (Lo) and Hit Identification (Hi), corresponding to the real drug discovery process. For the Hi task, we designed a novel molecular splitting algorithm that solves the Balanced Vertex Minimum $k$-Cut problem. We tested state-of-the-art and classic ML models, revealing which works better under practical settings. We analyzed modern benchmarks and showed that they are unrealistic and overoptimistic. Review: https://openreview.net/forum? id=H2Yb28qGLV Lo-Hi benchmark: https://github.com/SteshinSS/lohi_neurips2023 Lo-Hi splitter library: https://github.com/SteshinSS/lohi_splitter
SUBP: Soft Uniform Block Pruning for 1xN Sparse CNNs Multithreading Acceleration

The study of sparsity in Convolutional Neural Networks (CNNs) has become widespread to compress and accelerate models in environments with limited resources. By constraining N consecutive weights along the output channel to be group-wise non-zero, the recent network with 1$\times$N sparsity has received tremendous popularity for its three outstanding advantages: 1) A large amount of storage space saving by a \emph{Block Sparse Row} matrix. 2) Excellent performance at a high sparsity. 3) Significant speedups on CPUs with Advanced Vector Extensions. Recent work requires selecting and fine-tuning 1$\times$N sparse weights based on dense pre-trained weights, leading to the problems such as expensive training cost and memory access, sub-optimal model quality, as well as unbalanced workload across threads (different sparsity across output channels). To overcome them, this paper proposes a novel \emph{\textbf{S}oft \textbf{U}niform \textbf{B}lock \textbf{P}runing} (SUBP) approach to train a uniform 1$\times$N sparse structured network from scratch. Specifically, our approach tends to repeatedly allow pruned blocks to regrow to the network based on block angular redundancy and importance sampling in a uniform manner throughout the training process. It not only makes the model less dependent on pre-training, reduces the model redundancy and the risk of pruning the important blocks permanently but also achieves balanced workload. Empirically, on ImageNet, comprehensive experiments across various CNN architectures show that our SUBP consistently outperforms existing 1$\times$N and structured sparsity methods based on pre-trained models or training from scratch. Source codes and models are available at \url{https://github.com/JingyangXiang/SUBP}.
Resolvent expansions of 3D magnetic Schroedinger operators and Pauli operators

We obtain asymptotic resolvent expansions at the threshold of the essential spectrum for magnetic Schr\"odinger and Pauli operators in dimension three. These operators are treated as perturbations of the Laplace operator in $L^2(\mathbb{R}^3)$ and $L^2(\mathbb{R}^3;\mathbb{C}^2)$, respectively. The main novelty of our approach is to show that the relative perturbations, which are first order differential operators, can be factorized in suitably chosen auxiliary spaces. This allows us to derive the desired asymptotic expansions of the resolvents around zero. We then calculate their leading and sub-leading terms explicitly. Analogous factorization schemes for more general perturbations, including e.g.~finite rank perturbations, are discussed as well.
Routing Arena: A Benchmark Suite for Neural Routing Solvers

Neural Combinatorial Optimization has been researched actively in the last eight years. Even though many of the proposed Machine Learning based approaches are compared on the same datasets, the evaluation protocol exhibits essential flaws and the selection of baselines often neglects State-of-the-Art Operations Research approaches. To improve on both of these shortcomings, we propose the Routing Arena, a benchmark suite for Routing Problems that provides a seamless integration of consistent evaluation and the provision of baselines and benchmarks prevalent in the Machine Learning- and Operations Research field. The proposed evaluation protocol considers the two most important evaluation cases for different applications: First, the solution quality for an a priori fixed time budget and secondly the anytime performance of the respective methods. By setting the solution trajectory in perspective to a Best Known Solution and a Base Solver's solutions trajectory, we furthermore propose the Weighted Relative Average Performance (WRAP), a novel evaluation metric that quantifies the often claimed runtime efficiency of Neural Routing Solvers. A comprehensive first experimental evaluation demonstrates that the most recent Operations Research solvers generate state-of-the-art results in terms of solution quality and runtime efficiency when it comes to the vehicle routing problem. Nevertheless, some findings highlight the advantages of neural approaches and motivate a shift in how neural solvers should be conceptualized.
Understanding the Effects of RLHF on LLM Generalisation and Diversity

Large language models (LLMs) fine-tuned with reinforcement learning from human feedback (RLHF) have been used in some of the most widely deployed AI models to date, such as OpenAI's ChatGPT or Anthropic's Claude. While there has been significant work developing these methods, our understanding of the benefits and downsides of each stage in RLHF is still limited. To fill this gap, we present an extensive analysis of how each stage of the process (i.e. supervised fine-tuning (SFT), reward modelling, and RLHF) affects two key properties: out-of-distribution (OOD) generalisation and output diversity. OOD generalisation is crucial given the wide range of real-world scenarios in which these models are being used, while output diversity refers to the model's ability to generate varied outputs and is important for a variety of use cases. We perform our analysis across two base models on both summarisation and instruction following tasks, the latter being highly relevant for current LLM use cases. We find that RLHF generalises better than SFT to new inputs, particularly as the distribution shift between train and test becomes larger. However, RLHF significantly reduces output diversity compared to SFT across a variety of measures, implying a tradeoff in current LLM fine-tuning methods between generalisation and diversity. Our results provide guidance on which fine-tuning method should be used depending on the application, and show that more research is needed to improve the tradeoff between generalisation and diversity.
An Open-Loop Baseline for Reinforcement Learning Locomotion Tasks

In search of a simple baseline for Deep Reinforcement Learning in locomotion tasks, we propose a model-free open-loop strategy. By leveraging prior knowledge and the elegance of simple oscillators to generate periodic joint motions, it achieves respectable performance in five different locomotion environments, with a number of tunable parameters that is a tiny fraction of the thousands typically required by DRL algorithms. We conduct two additional experiments using open-loop oscillators to identify current shortcomings of these algorithms. Our results show that, compared to the baseline, DRL is more prone to performance degradation when exposed to sensor noise or failure. Furthermore, we demonstrate a successful transfer from simulation to reality using an elastic quadruped, where RL fails without randomization or reward engineering. Overall, the proposed baseline and associated experiments highlight the existing limitations of DRL for robotic applications, provide insights on how to address them, and encourage reflection on the costs of complexity and generality.
Nonlinear Correct and Smooth for Semi-Supervised Learning

Graph-based semi-supervised learning (GSSL) has been used successfully in various applications. Existing methods leverage the graph structure and labeled samples for classification. Label Propagation (LP) and Graph Neural Networks (GNNs) both iteratively pass messages on graphs, where LP propagates node labels through edges and GNN aggregates node features from the neighborhood. Recently, combining LP and GNN has led to improved performance. However, utilizing labels and features jointly in higher-order graphs has not been explored. Therefore, we propose Nonlinear Correct and Smooth (NLCS), which improves the existing post-processing approach by incorporating non-linearity and higher-order representation into the residual propagation to handle intricate node relationships effectively. Systematic evaluations show that our method achieves remarkable average improvements of 13.71% over base prediction and 2.16% over the state-of-the-art post-processing method on six commonly used datasets. Comparisons and analyses show our method effectively utilizes labels and features jointly in higher-order graphs to resolve challenging graph relationships.
Spin-Vibronic Dynamics in Open-Shell Systems beyond the Spin Hamiltonian Formalism

Vibronic coupling has a dramatic influence over a large number of molecular processes, ranging from photochemistry to spin relaxation and electronic transport. The simulation of vibronic coupling with multireference wave function methods has been largely applied to organic compounds, and only early efforts are available for open-shell systems such as transition metal and lanthanide complexes. In this work, we derive a numerical strategy to differentiate the molecular electronic Hamiltonian in the context of multireference ab initio methods and inclusive of spin–orbit coupling effects. We then provide a formulation of open quantum system dynamics able to predict the time evolution of the electron density matrix under the influence of a Markovian phonon bath up to fourth-order perturbation theory. We apply our method to Co(II) and Dy(III) molecular complexes exhibiting long spin relaxation times and successfully validate our strategy against the use of an effective spin Hamiltonian. Our study sheds light on the nature of vibronic coupling, the importance of electronic excited states in spin relaxation, and the need for high-level computational chemistry to quantify it.
Light-LOAM: A Lightweight LiDAR Odometry and Mapping Based on Graph-Matching

Simultaneous Localization and Mapping (SLAM) plays an important role in robot autonomy. Reliability and efficiency are the two most valued features for applying SLAM in robot applications. In this letter, we consider achieving a reliable LiDAR-based SLAM function in computation-limited platforms, such as quadrotor UAVs based on graph-based point cloud association. First, contrary to most works selecting salient features for point cloud registration, we propose a non-conspicuous feature selection strategy for reliability and robustness purposes. Then a two-stage correspondence selection method is used to register the point cloud, which includes a KD-tree-based coarse matching followed by a graph-based matching method that uses geometric consistency to vote out incorrect correspondences. Additionally, we propose an odometry approach where the weight optimizations are guided by vote results from the aforementioned geometric consistency graph. In this way, the optimization of LiDAR odometry rapidly converges and evaluates a fairly accurate transformation resulting in the back-end module efficiently finishing the mapping task. Finally, we evaluate our proposed framework on different datasets and real-world environments. Experiments show that our SLAM system achieves a comparative level or higher level of accuracy with more balanced computation efficiency compared with the mainstream LiDAR-based SLAM solutions.
Enhancing Predictive Capabilities in Data-Driven Dynamical Modeling with Automatic Differentiation: Koopman and Neural ODE Approaches

Data-driven approximations of the Koopman operator are promising for predicting the time evolution of systems characterized by complex dynamics. Among these methods, the approach known as extended dynamic mode decomposition with dictionary learning (EDMD-DL) has garnered significant attention. Here we present a modification of EDMD-DL that concurrently determines both the dictionary of observables and the corresponding approximation of the Koopman operator. This innovation leverages automatic differentiation to facilitate gradient descent computations through the pseudoinverse. We also address the performance of several alternative methodologies. We assess a 'pure' Koopman approach, which involves the direct time-integration of a linear, high-dimensional system governing the dynamics within the space of observables. Additionally, we explore a modified approach where the system alternates between spaces of states and observables at each time step -- this approach no longer satisfies the linearity of the true Koopman operator representation. For further comparisons, we also apply a state space approach (neural ODEs). We consider systems encompassing two and three-dimensional ordinary differential equation systems featuring steady, oscillatory, and chaotic attractors, as well as partial differential equations exhibiting increasingly complex and intricate behaviors. Our framework significantly outperforms EDMD-DL. Furthermore, the state space approach offers superior performance compared to the 'pure' Koopman approach where the entire time evolution occurs in the space of observables. When the temporal evolution of the Koopman approach alternates between states and observables at each time step, however, its predictions become comparable to those of the state space approach.
Beyond Text: A Deep Dive into Large Language Models' Ability on Understanding Graph Data

Large language models (LLMs) have achieved impressive performance on many natural language processing tasks. However, their capabilities on graph-structured data remain relatively unexplored. In this paper, we conduct a series of experiments benchmarking leading LLMs on diverse graph prediction tasks spanning node, edge, and graph levels. We aim to assess whether LLMs can effectively process graph data and leverage topological structures to enhance performance, compared to specialized graph neural networks. Through varied prompt formatting and task/dataset selection, we analyze how well LLMs can interpret and utilize graph structures. By comparing LLMs' performance with specialized graph models, we offer insights into the strengths and limitations of employing LLMs for graph analytics. Our findings provide insights into LLMs' capabilities and suggest avenues for further exploration in applying them to graph analytics.
Contrastive Prompt Learning-based Code Search based on Interaction Matrix

Code search aims to retrieve the code snippet that highly matches the given query described in natural language. Recently, many code pre-training approaches have demonstrated impressive performance on code search. However, existing code search methods still suffer from two performance constraints: inadequate semantic representation and the semantic gap between natural language (NL) and programming language (PL). In this paper, we propose CPLCS, a contrastive prompt learning-based code search method based on the cross-modal interaction mechanism. CPLCS comprises:(1) PL-NL contrastive learning, which learns the semantic matching relationship between PL and NL representations; (2) a prompt learning design for a dual-encoder structure that can alleviate the problem of inadequate semantic representation; (3) a cross-modal interaction mechanism to enhance the fine-grained mapping between NL and PL. We conduct extensive experiments to evaluate the effectiveness of our approach on a real-world dataset across six programming languages. The experiment results demonstrate the efficacy of our approach in improving semantic representation quality and mapping ability between PL and NL.
39AR‐40Ar ages for the Apollo 15 green and yellow volcanic glasses

A technique using the laser microprobe to extract noble gases from individual small (100–750 μm in diameter), low potassium (≤0.09 wt % K2O), glassy samples was developed. This technique has an advantage in that an individual sample can be chemically characterized by an electron microprobe and then analyzed for its argon age, thus eliminating any ambiguities in the classification of the sample and the need for large quantities of samples. This technique was then used to study the argon isotopes and apparent 39Ar-40Ar ages of three varieties of volcanic glass from Apollo 15: yellow volcanic, green volcanic group A, and green volcanic group D. The apparent solidification age for the glasses are 3.62±0.07, 3.41±0.12, and 3.35±0.18 aeons, respectively. The ages for group A and D green glasses agree well with previously reported ages for aliquots of ‘bulk’ green glass. A value of 40Ar/36Arsw = 0.5 ± 0.5 was used to correct the data since a 40Ar/36Arsw versus 39ArK/36Arsw plot failed to identify a well-defined trapped component. No significant difference in the solidification age (>0.2 aeons) was found between the A and D groups of the volcanic green glasses. These ages for volcanic glasses are consistent with the prediction of Delano and Livi [1981] that Array II volcanic glasses are generally older (≥3.6 aeons) than Array I glasses. The average exposure ages for the Apollo 15 yellow volcanic and green volcanic (groups A and D) glasses from 15426 and 15427 were indistinguishable, with ages between 300 and 275 m.y.
Thought Propagation: An Analogical Approach to Complex Reasoning with Large Language Models

Large Language Models (LLMs) have achieved remarkable success in reasoning tasks with the development of prompting methods. However, existing prompting approaches cannot reuse insights of solving similar problems and suffer from accumulated errors in multi-step reasoning, since they prompt LLMs to reason \textit{from scratch}. To address these issues, we propose \textbf{\textit{Thought Propagation} (TP)}, which explores the analogous problems and leverages their solutions to enhance the complex reasoning ability of LLMs. These analogous problems are related to the input one, with reusable solutions and problem-solving strategies. Thus, it is promising to propagate insights of solving previous analogous problems to inspire new problem-solving. To achieve this, TP first prompts LLMs to propose and solve a set of analogous problems that are related to the input one. Then, TP reuses the results of analogous problems to directly yield a new solution or derive a knowledge-intensive plan for execution to amend the initial solution obtained from scratch. TP is compatible with existing prompting approaches, allowing plug-and-play generalization and enhancement in a wide range of tasks without much labor in task-specific prompt engineering. Experiments across three challenging tasks demonstrate TP enjoys a substantial improvement over the baselines by an average of 12\% absolute increase in finding the optimal solutions in Shortest-path Reasoning, 13\% improvement of human preference in Creative Writing, and 15\% enhancement in the task completion rate of LLM-Agent Planning.
Cold-start Bundle Recommendation via Popularity-based Coalescence and Curriculum Heating

How can we recommend cold-start bundles to users? The cold-start problem in bundle recommendation is crucial because new bundles are continuously created on the Web for various marketing purposes. Despite its importance, existing methods for cold-start item recommendation are not readily applicable to bundles. They depend overly on historical information, even for less popular bundles, failing to address the primary challenge of the highly skewed distribution of bundle interactions. In this work, we propose CoHeat (Popularity-based Coalescence and Curriculum Heating), an accurate approach for cold-start bundle recommendation. CoHeat first represents users and bundles through graph-based views, capturing collaborative information effectively. To estimate the user-bundle relationship more accurately, CoHeat addresses the highly skewed distribution of bundle interactions through a popularity-based coalescence approach, which incorporates historical and affiliation information based on the bundle's popularity. Furthermore, it effectively learns latent representations by exploiting curriculum learning and contrastive learning. CoHeat demonstrates superior performance in cold-start bundle recommendation, achieving up to 193% higher nDCG@20 compared to the best competitor.
From Innermost to Full Almost-Sure Termination of Probabilistic Term Rewriting

There are many evaluation strategies for term rewrite systems, but proving termination automatically is usually easiest for innermost rewriting. Several syntactic criteria exist when innermost termination implies full termination. We adapt these criteria to the probabilistic setting, e.g., we show when it suffices to analyze almost-sure termination (AST) w.r. t. innermost rewriting to prove full AST of probabilistic term rewrite systems (PTRSs). These criteria also apply to other notions of termination like positive AST. We implemented and evaluated our new contributions in the tool AProVE.
SimPLR: A Simple and Plain Transformer for Scaling-Efficient Object Detection and Segmentation

The ability to detect objects in images at varying scales has played a pivotal role in the design of modern object detectors. Despite considerable progress in removing hand-crafted components and simplifying the architecture with transformers, multi-scale feature maps and/or pyramid design remain a key factor for their empirical success. In this paper, we show that this reliance on either feature pyramids or an hierarchical backbone is unnecessary and a transformer-based detector with scale-aware attention enables the plain detector `SimPLR' whose backbone and detection head are both non-hierarchical and operate on single-scale features. We find through our experiments that SimPLR with scale-aware attention is plain and simple, yet competitive with multi-scale vision transformer alternatives. Compared to the multi-scale and single-scale state-of-the-art, our model scales much better with bigger capacity (self-supervised) models and more pre-training data, allowing us to report a consistently better accuracy and faster runtime for object detection, instance segmentation as well as panoptic segmentation. Code will be released.
Pressure-driven homogenization of lithium disilicate glasses

Lithium disilicate glasses and glass-ceramics are good potential candidates for biomedical applications and solid-state batteries, and serve as models of nucleation and crystal growth. Moreover, these glasses exhibit a phase separation that influences their nucleation and crystallization behavior. The atomistic mechanisms of the phase separation and their pressure dependence are unclear so far. Here, we used molecular dynamics simulations supported by experiments to assess the spatial heterogeneity of lithium disilicate glasses prepared under pressure. We show that the glass heterogeneity decreases with increasing the cooling pressure and almost disappears at pressures around 30 GPa. The origin of the heterogeneity is due to the attraction between Li cations to form clustering channels, which decreases with pressure. Through our results, we hope to provide valuable insights and guidance for making glass-ceramics with controlled crystallization.