Daily Papers

Understanding the inner workings of neural networks is essential for enhancing model performance and interpretability. Current research predominantly focuses on examining the connection between individual neurons and the model's final predictions. Which suffers from challenges in interpreting the internal workings of the model, particularly when neurons encode multiple unrelated features. In this paper, we propose a novel framework that transitions the focus from analyzing individual neurons to investigating groups of neurons, shifting the emphasis from neuron-output relationships to functional interaction between neurons. Our automated framework, NeurFlow, first identifies core neurons and clusters them into groups based on shared functional relationships, enabling a more coherent and interpretable view of the network's internal processes. This approach facilitates the construction of a hierarchical circuit representing neuron interactions across layers, thus improving interpretability while reducing computational costs. Our extensive empirical studies validate the fidelity of our proposed NeurFlow. Additionally, we showcase its utility in practical applications such as image debugging and automatic concept labeling, thereby highlighting its potential to advance the field of neural network explainability.

Exposing meaningful and interpretable neural interactions is critical to understanding neural circuits. Inferred neural interactions from neural signals primarily reflect functional interactions. In a long experiment, subject animals may experience different stages defined by the experiment, stimuli, or behavioral states, and hence functional interactions can change over time. To model dynamically changing functional interactions, prior work employs state-switching generalized linear models with hidden Markov models (i.e., HMM-GLMs). However, we argue they lack biological plausibility, as functional interactions are shaped and confined by the underlying anatomical connectome. Here, we propose a novel prior-informed state-switching GLM. We introduce both a Gaussian prior and a one-hot prior over the GLM in each state. The priors are learnable. We will show that the learned prior should capture the state-constant interaction, shedding light on the underlying anatomical connectome and revealing more likely physical neuron interactions. The state-dependent interaction modeled by each GLM offers traceability to capture functional variations across multiple brain states. Our methods effectively recover true interaction structures in simulated data, achieve the highest predictive likelihood with real neural datasets, and render interaction structures and hidden states more interpretable when applied to real neural data.

Large language models (LLMs) have gained significant attention in chemistry. However, most existing datasets center on molecular-level property prediction and overlook the role of fine-grained functional group (FG) information. Incorporating FG-level data can provide valuable prior knowledge that links molecular structures with textual descriptions, which can be used to build more interpretable, structure-aware LLMs for reasoning on molecule-related tasks. Moreover, LLMs can learn from such fine-grained information to uncover hidden relationships between specific functional groups and molecular properties, thereby advancing molecular design and drug discovery. Here, we introduce FGBench, a dataset comprising 625K molecular property reasoning problems with functional group information. Functional groups are precisely annotated and localized within the molecule, which ensures the dataset's interoperability thereby facilitating further multimodal applications. FGBench includes both regression and classification tasks on 245 different functional groups across three categories for molecular property reasoning: (1) single functional group impacts, (2) multiple functional group interactions, and (3) direct molecular comparisons. In the benchmark of state-of-the-art LLMs on 7K curated data, the results indicate that current LLMs struggle with FG-level property reasoning, highlighting the need to enhance reasoning capabilities in LLMs for chemistry tasks. We anticipate that the methodology employed in FGBench to construct datasets with functional group-level information will serve as a foundational framework for generating new question-answer pairs, enabling LLMs to better understand fine-grained molecular structure-property relationships. The dataset and evaluation code are available at https://github.com/xuanliugit/FGBench.

Code Large Language Models (CodeLLMs) have ushered in a new era of code generation advancements. However, selecting the best solutions from among all possible CodeLLM solutions remains a challenge. Previous methods frequently overlooked the intricate functional similarities and interactions between clusters, resulting in suboptimal results. In this work, we introduce SRank, a novel reranking strategy for selecting the best solution from code generation that focuses on modeling inter-cluster relationship. By quantifying the functional overlap between clusters, our approach provides a better ranking strategy of code solutions. Empirical results show that our method achieves a remarkable results on pass@1 score. For instance, on the Human-Eval benchmark, we achieve 69.66\% in pass@1 with Codex002, 75.31\% for WizardCoder, 53.99\% for StarCoder and 60.55\% for CodeGen, which surpass the state-of-the-arts solution ranking methods, such as CodeT and Coder-Reviewer on the same CodeLLM with significant margin (approx 6.1% improvement on average). Comparing to the random sampling method, we can achieve an average improvement of approx 23.07% on Human-Eval and 17.64\% on MBPP. Even in scenarios with limited test inputs, our approach demonstrates robustness and superiority, marking a new state-of-the-arts in code generation reranking.

The static synaptic connectivity of neuronal circuits stands in direct contrast to the dynamics of their function. As in changing community interactions, different neurons can participate actively in various combinations to effect behaviors at different times. We introduce an unsupervised approach to learn the dynamic affinities between neurons in live, behaving animals, and to reveal which communities form among neurons at different times. The inference occurs in two major steps. First, pairwise non-linear affinities between neuronal traces from brain-wide calcium activity are organized by non-negative tensor factorization (NTF). Each factor specifies which groups of neurons are most likely interacting for an inferred interval in time, and for which animals. Finally, a generative model that allows for weighted community detection is applied to the functional motifs produced by NTF to reveal a dynamic functional connectome. Since time codes the different experimental variables (e.g., application of chemical stimuli), this provides an atlas of neural motifs active during separate stages of an experiment (e.g., stimulus application or spontaneous behaviors). Results from our analysis are experimentally validated, confirming that our method is able to robustly predict causal interactions between neurons to generate behavior. Code is available at https://github.com/dyballa/dynamic-connectomes.

Tucker decomposition is a powerful tensor model to handle multi-aspect data. It demonstrates the low-rank property by decomposing the grid-structured data as interactions between a core tensor and a set of object representations (factors). A fundamental assumption of such decomposition is that there are finite objects in each aspect or mode, corresponding to discrete indexes of data entries. However, real-world data is often not naturally posed in this setting. For example, geographic data is represented as continuous indexes of latitude and longitude coordinates, and cannot fit tensor models directly. To generalize Tucker decomposition to such scenarios, we propose Functional Bayesian Tucker Decomposition (FunBaT). We treat the continuous-indexed data as the interaction between the Tucker core and a group of latent functions. We use Gaussian processes (GP) as functional priors to model the latent functions. Then, we convert each GP into a state-space prior by constructing an equivalent stochastic differential equation (SDE) to reduce computational cost. An efficient inference algorithm is developed for scalable posterior approximation based on advanced message-passing techniques. The advantage of our method is shown in both synthetic data and several real-world applications. We release the code of FunBaT at https://github.com/xuangu-fang/Functional-Bayesian-Tucker-Decomposition.

Modeling the energy and forces of atomic systems is a fundamental problem in computational chemistry with the potential to help address many of the world's most pressing problems, including those related to energy scarcity and climate change. These calculations are traditionally performed using Density Functional Theory, which is computationally very expensive. Machine learning has the potential to dramatically improve the efficiency of these calculations from days or hours to seconds. We propose the Spherical Channel Network (SCN) to model atomic energies and forces. The SCN is a graph neural network where nodes represent atoms and edges their neighboring atoms. The atom embeddings are a set of spherical functions, called spherical channels, represented using spherical harmonics. We demonstrate, that by rotating the embeddings based on the 3D edge orientation, more information may be utilized while maintaining the rotational equivariance of the messages. While equivariance is a desirable property, we find that by relaxing this constraint in both message passing and aggregation, improved accuracy may be achieved. We demonstrate state-of-the-art results on the large-scale Open Catalyst dataset in both energy and force prediction for numerous tasks and metrics.

Prior studies on the emergence in large models have primarily focused on how the functional capabilities of large language models (LLMs) scale with model size. Our research, however, transcends this traditional paradigm, aiming to deepen our understanding of the emergence within LLMs by placing a special emphasis not just on the model size but more significantly on the complex behavior of neuron interactions during the training process. By introducing the concepts of "self-organization" and "multifractal analysis," we explore how neuron interactions dynamically evolve during training, leading to "emergence," mirroring the phenomenon in natural systems where simple micro-level interactions give rise to complex macro-level behaviors. To quantitatively analyze the continuously evolving interactions among neurons in large models during training, we propose the Neuron-based Multifractal Analysis (NeuroMFA). Utilizing NeuroMFA, we conduct a comprehensive examination of the emergent behavior in LLMs through the lens of both model size and training process, paving new avenues for research into the emergence in large models.

Early diagnosis of mild cognitive impairment (MCI) and subjective cognitive decline (SCD) utilizing multi-modal magnetic resonance imaging (MRI) is a pivotal area of research. While various regional and connectivity features from functional MRI (fMRI) and diffusion tensor imaging (DTI) have been employed to develop diagnosis models, most studies integrate these features without adequately addressing their alignment and interactions. This limits the potential to fully exploit the synergistic contributions of combined features and modalities. To solve this gap, our study introduces a novel Hierarchical Alignments and Hierarchical Interactions (HA-HI) method for MCI and SCD classification, leveraging the combined strengths of fMRI and DTI. HA-HI efficiently learns significant MCI- or SCD- related regional and connectivity features by aligning various feature types and hierarchically maximizing their interactions. Furthermore, to enhance the interpretability of our approach, we have developed the Synergistic Activation Map (SAM) technique, revealing the critical brain regions and connections that are indicative of MCI/SCD. Comprehensive evaluations on the ADNI dataset and our self-collected data demonstrate that HA-HI outperforms other existing methods in diagnosing MCI and SCD, making it a potentially vital and interpretable tool for early detection. The implementation of this method is publicly accessible at https://github.com/ICI-BCI/Dual-MRI-HA-HI.git.

How human interact with objects depends on the functional roles of the target objects, which introduces the problem of affordance-aware hand-object interaction. It requires a large number of human demonstrations for the learning and understanding of plausible and appropriate hand-object interactions. In this work, we present AffordPose, a large-scale dataset of hand-object interactions with affordance-driven hand pose. We first annotate the specific part-level affordance labels for each object, e.g. twist, pull, handle-grasp, etc, instead of the general intents such as use or handover, to indicate the purpose and guide the localization of the hand-object interactions. The fine-grained hand-object interactions reveal the influence of hand-centered affordances on the detailed arrangement of the hand poses, yet also exhibit a certain degree of diversity. We collect a total of 26.7K hand-object interactions, each including the 3D object shape, the part-level affordance label, and the manually adjusted hand poses. The comprehensive data analysis shows the common characteristics and diversity of hand-object interactions per affordance via the parameter statistics and contacting computation. We also conduct experiments on the tasks of hand-object affordance understanding and affordance-oriented hand-object interaction generation, to validate the effectiveness of our dataset in learning the fine-grained hand-object interactions. Project page: https://github.com/GentlesJan/AffordPose.

The intimate entanglement between objects affordances and human poses is of large interest, among others, for behavioural sciences, cognitive psychology, and Computer Vision communities. In recent years, the latter has developed several object-centric approaches: starting from items, learning pipelines synthesizing human poses and dynamics in a realistic way, satisfying both geometrical and functional expectations. However, the inverse perspective is significantly less explored: Can we infer 3D objects and their poses from human interactions alone? Our investigation follows this direction, showing that a generic 3D human point cloud is enough to pop up an unobserved object, even when the user is just imitating a functionality (e.g., looking through a binocular) without involving a tangible counterpart. We validate our method qualitatively and quantitatively, with synthetic data and sequences acquired for the task, showing applicability for XR/VR. The code is available at https://github.com/ptrvilya/object-popup.

Large language models (LLMs) have demonstrated notable potential in conducting complex tasks and are increasingly utilized in various financial applications. However, high-quality sequential financial investment decision-making remains challenging. These tasks require multiple interactions with a volatile environment for every decision, demanding sufficient intelligence to maximize returns and manage risks. Although LLMs have been used to develop agent systems that surpass human teams and yield impressive investment returns, opportunities to enhance multi-sourced information synthesis and optimize decision-making outcomes through timely experience refinement remain unexplored. Here, we introduce the FinCon, an LLM-based multi-agent framework with CONceptual verbal reinforcement tailored for diverse FINancial tasks. Inspired by effective real-world investment firm organizational structures, FinCon utilizes a manager-analyst communication hierarchy. This structure allows for synchronized cross-functional agent collaboration towards unified goals through natural language interactions and equips each agent with greater memory capacity than humans. Additionally, a risk-control component in FinCon enhances decision quality by episodically initiating a self-critiquing mechanism to update systematic investment beliefs. The conceptualized beliefs serve as verbal reinforcement for the future agent's behavior and can be selectively propagated to the appropriate node that requires knowledge updates. This feature significantly improves performance while reducing unnecessary peer-to-peer communication costs. Moreover, FinCon demonstrates strong generalization capabilities in various financial tasks, including single stock trading and portfolio management.

Parameterized tight-binding models fit to first principles calculations can provide an efficient and accurate quantum mechanical method for predicting properties of molecules and solids. However, well-tested parameter sets are generally only available for a limited number of atom combinations, making routine use of this method difficult. Furthermore, most previous models consider only simple two-body interactions, which limits accuracy. To tackle these challenges, we develop a density functional theory database of nearly one million materials, which we use to fit a universal set of tight-binding parameters for 65 elements and their binary combinations. We include both two-body and three-body effective interaction terms in our model, plus self-consistent charge transfer, enabling our model to work for metallic, covalent, and ionic bonds with the same parameter set. To ensure predictive power, we adopt a learning framework where we repeatedly test the model on new low energy crystal structures and then add them to the fitting dataset, iterating until predictions improve. We distribute the materials database and tools developed in this work publicly.

Large language models (LLMs) have demonstrated exceptional performance in planning the use of various functional tools, such as calculators and retrievers, particularly in question-answering tasks. In this paper, we expand the definition of these tools, centering on conceptual tools within the context of dialogue systems. A conceptual tool specifies a cognitive concept that aids systematic or investigative thought. These conceptual tools play important roles in practice, such as multiple psychological or tutoring strategies being dynamically applied in a single turn to compose helpful responses. To further enhance the reasoning and planning capability of LLMs with these conceptual tools, we introduce a multi-persona collaboration framework: Think-Plan-Execute (TPE). This framework decouples the response generation process into three distinct roles: Thinker, Planner, and Executor. Specifically, the Thinker analyzes the internal status exhibited in the dialogue context, such as user emotions and preferences, to formulate a global guideline. The Planner then generates executable plans to call different conceptual tools (e.g., sources or strategies), while the Executor compiles all intermediate results into a coherent response. This structured approach not only enhances the explainability and controllability of responses but also reduces token redundancy. We demonstrate the effectiveness of TPE across various dialogue response generation tasks, including multi-source (FoCus) and multi-strategy interactions (CIMA and PsyQA). This reveals its potential to handle real-world dialogue interactions that require more complicated tool learning beyond just functional tools. The full code and data will be released for reproduction.

Large Language Models (LLMs) have shown strong potential for tabular data generation by modeling textualized feature-value pairs. However, tabular data inherently exhibits sparse feature-level dependencies, where many feature interactions are structurally insignificant. This creates a fundamental mismatch as LLMs' self-attention mechanism inevitably distributes focus across all pairs, diluting attention on critical relationships, particularly in datasets with complex dependencies or semantically ambiguous features. To address this limitation, we propose GraDe (Graph-Guided Dependency Learning), a novel method that explicitly integrates sparse dependency graphs into LLMs' attention mechanism. GraDe employs a lightweight dynamic graph learning module guided by externally extracted functional dependencies, prioritizing key feature interactions while suppressing irrelevant ones. Our experiments across diverse real-world datasets demonstrate that GraDe outperforms existing LLM-based approaches by up to 12% on complex datasets while achieving competitive results with state-of-the-art approaches in synthetic data quality. Our method is minimally intrusive yet effective, offering a practical solution for structure-aware tabular data modeling with LLMs.

Large Language Models (LLMs) and code agents in software development are rapidly evolving from generating isolated code snippets to producing full-fledged software applications with graphical interfaces, interactive logic, and dynamic behaviors. However, current benchmarks fall short in evaluating such production-ready software, as they often rely on static checks or binary pass/fail scripts, failing to capture the interactive behaviors and runtime dynamics that define real-world usability - qualities that only emerge when an application is actively used. This is the blind spot of current evaluation: you don't know if an app works until you click through it, interact with it, and observe how it responds. To bridge this gap, we introduce RealDevWorld, a novel evaluation framework for automated end-to-end assessment of LLMs' ability to generate production-ready repositories from scratch. It features two key components: (1) RealDevBench, a diverse collection of 194 open-ended software engineering tasks across multiple domains, incorporating multimodal elements to reflect real-world complexity; and (2) AppEvalPilot, a new agent-as-a-judge evaluation system that simulates realistic, GUI-based user interactions to automatically and holistically assess software functional correctness, visual fidelity, and runtime behavior. The framework delivers fine-grained, task-specific diagnostic feedback, supporting nuanced evaluation beyond simple success/failure judgments. Empirical results show that RealDevWorld delivers effective, automatic, and human-aligned evaluations, achieving an accuracy of 0.92 and a correlation of 0.85 with expert human assessments, while significantly reducing the reliance on manual review. This enables scalable, human-aligned assessment of production-level software generated by LLMs. Our code is available on GitHub.

Interactions among features are central to understanding the behavior of machine learning models. Recent research has made significant strides in detecting and quantifying feature interactions in single predictive models. However, we argue that the feature interactions extracted from a single pre-specified model may not be trustworthy since: a well-trained predictive model may not preserve the true feature interactions and there exist multiple well-performing predictive models that differ in feature interaction strengths. Thus, we recommend exploring feature interaction strengths in a model class of approximately equally accurate predictive models. In this work, we introduce the feature interaction score (FIS) in the context of a Rashomon set, representing a collection of models that achieve similar accuracy on a given task. We propose a general and practical algorithm to calculate the FIS in the model class. We demonstrate the properties of the FIS via synthetic data and draw connections to other areas of statistics. Additionally, we introduce a Halo plot for visualizing the feature interaction variance in high-dimensional space and a swarm plot for analyzing FIS in a Rashomon set. Experiments with recidivism prediction and image classification illustrate how feature interactions can vary dramatically in importance for similarly accurate predictive models. Our results suggest that the proposed FIS can provide valuable insights into the nature of feature interactions in machine learning models.

It is desirable for statistical models to detect signals of interest independently of their position. If the data is generated by some smooth process, this additional structure should be taken into account. We introduce a new class of neural networks that are shift invariant and preserve smoothness of the data: functional neural networks (FNNs). For this, we use methods from functional data analysis (FDA) to extend multi-layer perceptrons and convolutional neural networks to functional data. We propose different model architectures, show that the models outperform a benchmark model from FDA in terms of accuracy and successfully use FNNs to classify electroencephalography (EEG) data.

Reconstructing images seen by people from their fMRI brain recordings provides a non-invasive window into the human brain. Despite recent progress enabled by diffusion models, current methods often lack faithfulness to the actual seen images. We present "Brain-IT", a brain-inspired approach that addresses this challenge through a Brain Interaction Transformer (BIT), allowing effective interactions between clusters of functionally-similar brain-voxels. These functional-clusters are shared by all subjects, serving as building blocks for integrating information both within and across brains. All model components are shared by all clusters & subjects, allowing efficient training with a limited amount of data. To guide the image reconstruction, BIT predicts two complementary localized patch-level image features: (i)high-level semantic features which steer the diffusion model toward the correct semantic content of the image; and (ii)low-level structural features which help to initialize the diffusion process with the correct coarse layout of the image. BIT's design enables direct flow of information from brain-voxel clusters to localized image features. Through these principles, our method achieves image reconstructions from fMRI that faithfully reconstruct the seen images, and surpass current SotA approaches both visually and by standard objective metrics. Moreover, with only 1-hour of fMRI data from a new subject, we achieve results comparable to current methods trained on full 40-hour recordings.

Hamiltonian matrix prediction is pivotal in computational chemistry, serving as the foundation for determining a wide range of molecular properties. While SE(3) equivariant graph neural networks have achieved remarkable success in this domain, their substantial computational cost--driven by high-order tensor product (TP) operations--restricts their scalability to large molecular systems with extensive basis sets. To address this challenge, we introduce SPHNet, an efficient and scalable equivariant network, that incorporates adaptive SParsity into Hamiltonian prediction. SPHNet employs two innovative sparse gates to selectively constrain non-critical interaction combinations, significantly reducing tensor product computations while maintaining accuracy. To optimize the sparse representation, we develop a Three-phase Sparsity Scheduler, ensuring stable convergence and achieving high performance at sparsity rates of up to 70%. Extensive evaluations on QH9 and PubchemQH datasets demonstrate that SPHNet achieves state-of-the-art accuracy while providing up to a 7x speedup over existing models. Beyond Hamiltonian prediction, the proposed sparsification techniques also hold significant potential for improving the efficiency and scalability of other SE(3) equivariant networks, further broadening their applicability and impact. Our code can be found at https://github.com/microsoft/SPHNet.

Despite its fruitful applications in remote sensing, image super-resolution is troublesome to train and deploy as it handles different resolution magnifications with separate models. Accordingly, we propose a highly-applicable super-resolution framework called FunSR, which settles different magnifications with a unified model by exploiting context interaction within implicit function space. FunSR composes a functional representor, a functional interactor, and a functional parser. Specifically, the representor transforms the low-resolution image from Euclidean space to multi-scale pixel-wise function maps; the interactor enables pixel-wise function expression with global dependencies; and the parser, which is parameterized by the interactor's output, converts the discrete coordinates with additional attributes to RGB values. Extensive experimental results demonstrate that FunSR reports state-of-the-art performance on both fixed-magnification and continuous-magnification settings, meanwhile, it provides many friendly applications thanks to its unified nature.

Functional data play a pivotal role across science and engineering, yet their infinite-dimensional nature makes representation learning challenging. Conventional statistical models depend on pre-chosen basis expansions or kernels, limiting the flexibility of data-driven discovery, while many deep-learning pipelines treat functions as fixed-grid vectors, ignoring inherent continuity. In this paper, we introduce Functional Attention with a Mixture-of-Experts (FAME), an end-to-end, fully data-driven framework for function-on-function regression. FAME forms continuous attention by coupling a bidirectional neural controlled differential equation with MoE-driven vector fields to capture intra-functional continuity, and further fuses change to inter-functional dependencies via multi-head cross attention. Extensive experiments on synthetic and real-world functional-regression benchmarks show that FAME achieves state-of-the-art accuracy, strong robustness to arbitrarily sampled discrete observations of functions.

Multitask Gaussian process (MTGP) is powerful for joint learning of multiple tasks with complicated correlation patterns. However, due to the assembling of additive independent latent functions, all current MTGPs including the salient linear model of coregionalization (LMC) and convolution frameworks cannot effectively represent and learn the hierarchical latent interactions between its latent functions. In this paper, we further investigate the interactions in LMC of MTGP and then propose a novel kernel representation of the hierarchical interactions, which ameliorates both the expressiveness and the interpretability of MTGP. Specifically, we express the interaction as a product of function interaction and coefficient interaction. The function interaction is modeled by using cross convolution of latent functions. The coefficient interaction between the LMCs is described as a cross coregionalization term. We validate that considering the interactions can promote knowledge transferring in MTGP and compare our approach with some state-of-the-art MTGPs on both synthetic- and real-world datasets.

The development of general robotic systems capable of manipulating in unstructured environments is a significant challenge. While Vision-Language Models(VLM) excel in high-level commonsense reasoning, they lack the fine-grained 3D spatial understanding required for precise manipulation tasks. Fine-tuning VLM on robotic datasets to create Vision-Language-Action Models(VLA) is a potential solution, but it is hindered by high data collection costs and generalization issues. To address these challenges, we propose a novel object-centric representation that bridges the gap between VLM's high-level reasoning and the low-level precision required for manipulation. Our key insight is that an object's canonical space, defined by its functional affordances, provides a structured and semantically meaningful way to describe interaction primitives, such as points and directions. These primitives act as a bridge, translating VLM's commonsense reasoning into actionable 3D spatial constraints. In this context, we introduce a dual closed-loop, open-vocabulary robotic manipulation system: one loop for high-level planning through primitive resampling, interaction rendering and VLM checking, and another for low-level execution via 6D pose tracking. This design ensures robust, real-time control without requiring VLM fine-tuning. Extensive experiments demonstrate strong zero-shot generalization across diverse robotic manipulation tasks, highlighting the potential of this approach for automating large-scale simulation data generation.

Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability to reconstruct biologically meaningful PPI networks, which is crucial for biology research. To address this gap, we introduce PRING, the first comprehensive benchmark that evaluates protein-protein interaction prediction from a graph-level perspective. PRING curates a high-quality, multi-species PPI network dataset comprising 21,484 proteins and 186,818 interactions, with well-designed strategies to address both data redundancy and leakage. Building on this golden-standard dataset, we establish two complementary evaluation paradigms: (1) topology-oriented tasks, which assess intra and cross-species PPI network construction, and (2) function-oriented tasks, including protein complex pathway prediction, GO module analysis, and essential protein justification. These evaluations not only reflect the model's capability to understand the network topology but also facilitate protein function annotation, biological module detection, and even disease mechanism analysis. Extensive experiments on four representative model categories, consisting of sequence similarity-based, naive sequence-based, protein language model-based, and structure-based approaches, demonstrate that current PPI models have potential limitations in recovering both structural and functional properties of PPI networks, highlighting the gap in supporting real-world biological applications. We believe PRING provides a reliable platform to guide the development of more effective PPI prediction models for the community. The dataset and source code of PRING are available at https://github.com/SophieSarceau/PRING.

The webpage-to-code task requires models to understand visual representations of webpages and generate corresponding code. However, existing benchmarks primarily focus on static screenshot-to-code tasks, thereby overlooking the dynamic interactions fundamental to real-world web applications. To address this limitation, this paper introduces IWR-Bench, a novel benchmark for evaluating the capabilities of Large Vision-Language Models (LVLMs) in interactive webpage reconstruction from video. IWR-Bench comprises 113 meticulously curated tasks from 100 real-world websites, with 1,001 actions and featuring diverse interaction complexities (e.g., web games), visual styles, and domains. Aligning with standard web development practices, each task includes not only user interaction videos but also all crawled static assets (e.g., images, videos). This benchmark evaluates models on two fundamental challenges: comprehensive multi-modal reasoning to infer interaction logic from video and assets, and advanced code generation to translate this logic into functional code. An agent-as-a-judge framework with a comprehensive metric system automatically assesses the functional correctness and visual fidelity of generated webpages. Extensive experiments on 28 LVLMs reveal a significant challenge: the best model achieves an overall score of only 36.35%, as functional correctness (24.39% IFS) lags significantly behind visual fidelity (64.25% VFS). These results highlight critical limitations in current models' ability to reason about temporal dynamics and synthesize event-driven logic, establishing IWR-Bench as a challenging frontier for vision-language research. The benchmark and evaluation code will be made publicly available. Code is available at https://github.com/L-O-I/IWR-Bench.

The concept of 3D scene graphs is increasingly recognized as a powerful semantic and hierarchical representation of the environment. Current approaches often address this at a coarse, object-level resolution. In contrast, our goal is to develop a representation that enables robots to directly interact with their environment by identifying both the location of functional interactive elements and how these can be used. To achieve this, we focus on detecting and storing objects at a finer resolution, focusing on affordance-relevant parts. The primary challenge lies in the scarcity of data that extends beyond instance-level detection and the inherent difficulty of capturing detailed object features using robotic sensors. We leverage currently available 3D resources to generate 2D data and train a detector, which is then used to augment the standard 3D scene graph generation pipeline. Through our experiments, we demonstrate that our approach achieves functional element segmentation comparable to state-of-the-art 3D models and that our augmentation enables task-driven affordance grounding with higher accuracy than the current solutions. See our project page at https://fungraph.github.io.

The increasing deployment of autonomous AI agents on the web is hampered by a fundamental misalignment: agents must infer affordances from human-oriented user interfaces, leading to brittle, inefficient, and insecure interactions. To address this, we introduce VOIX, a web-native framework that enables websites to expose reliable, auditable, and privacy-preserving capabilities for AI agents through simple, declarative HTML elements. VOIX introduces <tool> and <context> tags, allowing developers to explicitly define available actions and relevant state, thereby creating a clear, machine-readable contract for agent behavior. This approach shifts control to the website developer while preserving user privacy by disconnecting the conversational interactions from the website. We evaluated the framework's practicality, learnability, and expressiveness in a three-day hackathon study with 16 developers. The results demonstrate that participants, regardless of prior experience, were able to rapidly build diverse and functional agent-enabled web applications. Ultimately, this work provides a foundational mechanism for realizing the Agentic Web, enabling a future of seamless and secure human-AI collaboration on the web.

We propose a new class of generative diffusion models, called functional diffusion. In contrast to previous work, functional diffusion works on samples that are represented by functions with a continuous domain. Functional diffusion can be seen as an extension of classical diffusion models to an infinite-dimensional domain. Functional diffusion is very versatile as images, videos, audio, 3D shapes, deformations, \etc, can be handled by the same framework with minimal changes. In addition, functional diffusion is especially suited for irregular data or data defined in non-standard domains. In our work, we derive the necessary foundations for functional diffusion and propose a first implementation based on the transformer architecture. We show generative results on complicated signed distance functions and deformation functions defined on 3D surfaces.

Functional grasping is essential for humans to perform specific tasks, such as grasping scissors by the finger holes to cut materials or by the blade to safely hand them over. Enabling dexterous robot hands with functional grasping capabilities is crucial for their deployment to accomplish diverse real-world tasks. Recent research in dexterous grasping, however, often focuses on power grasps while overlooking task- and object-specific functional grasping poses. In this paper, we introduce FunGrasp, a system that enables functional dexterous grasping across various robot hands and performs one-shot transfer to unseen objects. Given a single RGBD image of functional human grasping, our system estimates the hand pose and transfers it to different robotic hands via a human-to-robot (H2R) grasp retargeting module. Guided by the retargeted grasping poses, a policy is trained through reinforcement learning in simulation for dynamic grasping control. To achieve robust sim-to-real transfer, we employ several techniques including privileged learning, system identification, domain randomization, and gravity compensation. In our experiments, we demonstrate that our system enables diverse functional grasping of unseen objects using single RGBD images, and can be successfully deployed across various dexterous robot hands. The significance of the components is validated through comprehensive ablation studies. Project page: https://hly-123.github.io/FunGrasp/ .

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

Model merging is an efficient post-training strategy for integrating knowledge from multiple finetuned checkpoints of a shared foundation model. Existing methods operate in the parameter space, combining task vectors to mitigate conflicts, but remain constrained by parameter inconsistencies. We propose Functional Dual Anchors (FDAs), a framework that instead models the input-representation space. FDAs are synthetic inputs whose induced gradients align with task vectors, capturing task-specific functional shifts relative to the pretrained model. This perspective bridges joint multi-task training and post-hoc merging, offering both robustness and flexibility. We further introduce a principled initialization scheme and show that FDAs are complementary to parameter-space model merging. Comprehensive experiments demonstrate the effectiveness of FDAs in model merging.

We introduce the task of predicting functional 3D scene graphs for real-world indoor environments from posed RGB-D images. Unlike traditional 3D scene graphs that focus on spatial relationships of objects, functional 3D scene graphs capture objects, interactive elements, and their functional relationships. Due to the lack of training data, we leverage foundation models, including visual language models (VLMs) and large language models (LLMs), to encode functional knowledge. We evaluate our approach on an extended SceneFun3D dataset and a newly collected dataset, FunGraph3D, both annotated with functional 3D scene graphs. Our method significantly outperforms adapted baselines, including Open3DSG and ConceptGraph, demonstrating its effectiveness in modeling complex scene functionalities. We also demonstrate downstream applications such as 3D question answering and robotic manipulation using functional 3D scene graphs. See our project page at https://openfungraph.github.io

A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Network analysis has revealed keystone species that regulate ecosystems and master regulators that regulate cellular genetic networks. Yet these studies have focused on pairwise biological interactions, which can be affected by the context of genetic background and other species present generating higher-order interactions. The important regulators of higher-order interactions are unstudied. To address this, we applied a new high-dimensional geometry approach that quantifies epistasis in a fitness landscape to ask how individual genes and species influence the interactions in the rest of the biological network. We then generated and also reanalyzed 5-dimensional datasets (two genetic, two microbiome). We identified key genes (e.g. the rbs locus and pykF) and species (e.g. Lactobacilli) that control the interactions of many other genes and species. These higher-order master regulators can induce or suppress evolutionary and ecological diversification by controlling the topography of the fitness landscape. Thus, we provide mathematical intuition and justification for exploration of biological networks in higher dimensions.

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids. We show that it captures inter-chain coevolution, while it was trained on single-chain data, which means that it can be used out-of-distribution. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer, without significantly deteriorating any of those we tested. It also achieves competitive performance with using orthology-based pairing.

We describe the accurate prediction of ligand-protein interaction (LPI) affinities, also known as drug-target interactions (DTI), with instruction fine-tuned pretrained generative small language models (SLMs). We achieved accurate predictions for a range of affinity values associated with ligand-protein interactions on out-of-sample data in a zero-shot setting. Only the SMILES string of the ligand and the amino acid sequence of the protein were used as the model inputs. Our results demonstrate a clear improvement over machine learning (ML) and free-energy perturbation (FEP+) based methods in accurately predicting a range of ligand-protein interaction affinities, which can be leveraged to further accelerate drug discovery campaigns against challenging therapeutic targets.

Accurate prediction of drug-target interactions is critical for advancing drug discovery. By reducing time and cost, machine learning and deep learning can accelerate this discovery process. Our approach utilises the powerful Barlow Twins architecture for feature-extraction while considering the structure of the target protein, achieving state-of-the-art predictive performance against multiple established benchmarks. The use of gradient boosting machine as the underlying predictor ensures fast and efficient predictions without the need for large computational resources. In addition, we further benchmarked new baselines against existing methods. Together, these innovations improve the efficiency and effectiveness of drug-target interaction predictions, providing robust tools for accelerating drug development and deepening the understanding of molecular interactions.

We introduce Lemur and Lemur-Chat, openly accessible language models optimized for both natural language and coding capabilities to serve as the backbone of versatile language agents. The evolution from language chat models to functional language agents demands that models not only master human interaction, reasoning, and planning but also ensure grounding in the relevant environments. This calls for a harmonious blend of language and coding capabilities in the models. Lemur and Lemur-Chat are proposed to address this necessity, demonstrating balanced proficiencies in both domains, unlike existing open-source models that tend to specialize in either. Through meticulous pre-training using a code-intensive corpus and instruction fine-tuning on text and code data, our models achieve state-of-the-art averaged performance across diverse text and coding benchmarks among open-source models. Comprehensive experiments demonstrate Lemur's superiority over existing open-source models and its proficiency across various agent tasks involving human communication, tool usage, and interaction under fully- and partially- observable environments. The harmonization between natural and programming languages enables Lemur-Chat to significantly narrow the gap with proprietary models on agent abilities, providing key insights into developing advanced open-source agents adept at reasoning, planning, and operating seamlessly across environments. https://github.com/OpenLemur/Lemur

Reasoning over visual relationships-spatial, functional, interactional, social, etc.-is considered to be a fundamental component of human cognition. Yet, despite the major advances in visual comprehension in multimodal language models (MLMs), precise reasoning over relationships and their generations remains a challenge. We introduce ROBIN: an MLM instruction-tuned with densely annotated relationships capable of constructing high-quality dense scene graphs at scale. To train ROBIN, we curate SVG, a synthetic scene graph dataset by completing the missing relations of selected objects in existing scene graphs using a teacher MLM and a carefully designed filtering process to ensure high-quality. To generate more accurate and rich scene graphs at scale for any image, we introduce SG-EDIT: a self-distillation framework where GPT-4o further refines ROBIN's predicted scene graphs by removing unlikely relations and/or suggesting relevant ones. In total, our dataset contains 146K images and 5.6M relationships for 2.6M objects. Results show that our ROBIN-3B model, despite being trained on less than 3 million instances, outperforms similar-size models trained on over 300 million instances on relationship understanding benchmarks, and even surpasses larger models up to 13B parameters. Notably, it achieves state-of-the-art performance in referring expression comprehension with a score of 88.9, surpassing the previous best of 87.4. Our results suggest that training on the refined scene graph data is crucial to maintaining high performance across diverse visual reasoning task.

Large Language Models (LLMs) are increasingly capable of generating complete applications from natural language instructions, creating new opportunities in science and education. In these domains, interactive scientific demonstrations are particularly valuable for explaining concepts, supporting new teaching methods, and presenting research findings. Generating such demonstrations requires models to combine accurate scientific knowledge with the ability to implement interactive front-end code that behaves correctly and responds to user actions. This capability goes beyond the scope of existing benchmarks, which typically evaluate either knowledge question answering without grounding in code or static web code generation without scientific interactivity. To evaluate this integrated ability, we design a hybrid framework that combines programmatic functional testing to rigorously verify interaction logic with visually-grounded qualitative testing to assess rendered outputs against reference snapshots. Building on this framework, we present InteractScience, a benchmark consisting of a substantial set of carefully designed questions across five scientific domains, each paired with unit tests, reference snapshots, and checklists. We evaluate 30 leading open- and closed-source LLMs and report results that highlight ongoing weaknesses in integrating domain knowledge with interactive front-end coding. Our work positions InteractScience as the first benchmark to automatically measure this combined capability with realistic interactive operations, providing a foundation for advancing reliable and educationally useful scientific demonstration code generation. All code and data are publicly available at https://github.com/open-compass/InteractScience.

Despite their widespread success, the application of deep neural networks to functional data remains scarce today. The infinite dimensionality of functional data means standard learning algorithms can be applied only after appropriate dimension reduction, typically achieved via basis expansions. Currently, these bases are chosen a priori without the information for the task at hand and thus may not be effective for the designated task. We instead propose to adaptively learn these bases in an end-to-end fashion. We introduce neural networks that employ a new Basis Layer whose hidden units are each basis functions themselves implemented as a micro neural network. Our architecture learns to apply parsimonious dimension reduction to functional inputs that focuses only on information relevant to the target rather than irrelevant variation in the input function. Across numerous classification/regression tasks with functional data, our method empirically outperforms other types of neural networks, and we prove that our approach is statistically consistent with low generalization error. Code is available at: https://github.com/jwyyy/AdaFNN.

Tables are prevalent in real-world databases, requiring significant time and effort for humans to analyze and manipulate. The advancements in large language models (LLMs) have made it possible to interact with tables using natural language input, bringing this capability closer to reality. In this paper, we present TableGPT, a unified fine-tuned framework that enables LLMs to understand and operate on tables using external functional commands. It introduces the capability to seamlessly interact with tables, enabling a wide range of functionalities such as question answering, data manipulation (e.g., insert, delete, query, and modify operations), data visualization, analysis report generation, and automated prediction. TableGPT aims to provide convenience and accessibility to users by empowering them to effortlessly leverage tabular data. At the core of TableGPT lies the novel concept of global tabular representations, which empowers LLMs to gain a comprehensive understanding of the entire table beyond meta-information. By jointly training LLMs on both table and text modalities, TableGPT achieves a deep understanding of tabular data and the ability to perform complex operations on tables through chain-of-command instructions. Importantly, TableGPT offers the advantage of being a self-contained system rather than relying on external API interfaces. Moreover, it supports efficient data process flow, query rejection (when appropriate) and private deployment, enabling faster domain data fine-tuning and ensuring data privacy, which enhances the framework's adaptability to specific use cases.

Recent advancements in LLM-based agents have led to significant progress in automatic software engineering, particularly in software maintenance and evolution. Despite these encouraging advances, current research faces two major challenges. First, SOTA performance primarily depends on closed-source models, which significantly limits the technology's accessibility, and potential for customization in diverse SE tasks. Second, these models are predominantly trained on static code data, lacking a deep understanding of the dynamic interactions, iterative problem-solving processes, and evolutionary characteristics inherent in software development. To address these challenges, our study adopts a software engineering perspective. We recognize that real-world software maintenance and evolution processes encompass not only static code data but also developers' thought processes, utilization of external tools, and the interaction between different functional personnel. Consequently, we introduce the Lingma SWE-GPT series, comprising Lingma SWE-GPT 7B and 72B. By learning from and simulating real-world code submission activities, Lingma SWE-GPT systematically incorporates the dynamic interactions and iterative problem-solving inherent in software development process, thereby achieving a more comprehensive understanding of software improvement processes. We conducted experimental evaluations using SWE-bench Verified benchmark. The results demonstrate that Lingma SWE-GPT 72B successfully resolves 30.20% of the GitHub issues, marking a significant improvement in automatic issue resolution (22.76% relative improvement compared to Llama 3.1 405B), approaching the performance of closed-source models (31.80\% issues of GPT-4o resolved). Notably, Lingma SWE-GPT 7B resolves 18.20% of the issues, highlighting the potential for applying smaller models to ASE tasks.

Spoken dialogue models currently lack the ability for fine-grained speech style control, a critical capability for human-like interaction that is often overlooked in favor of purely functional capabilities like reasoning and question answering. To address this limitation, we introduce UltraVoice, the first large-scale speech dialogue dataset engineered for multiple fine-grained speech style control. Encompassing over 830 hours of speech dialogues, UltraVoice provides instructions across six key speech stylistic dimensions: emotion, speed, volume, accent, language, and composite styles. Fine-tuning leading models such as SLAM-Omni and VocalNet on UltraVoice significantly enhances their fine-grained speech stylistic controllability without degrading core conversational abilities. Specifically, our fine-tuned models achieve improvements of 29.12-42.33% in Mean Opinion Score (MOS) and 14.61-40.09 percentage points in Instruction Following Rate (IFR) on multi-dimensional control tasks designed in the UltraVoice. Moreover, on the URO-Bench benchmark, our fine-tuned models demonstrate substantial gains in core understanding, reasoning, and conversational abilities, with average improvements of +10.84% on the Basic setting and +7.87% on the Pro setting. Furthermore, the dataset's utility extends to training controllable Text-to-Speech (TTS) models, underscoring its high quality and broad applicability for expressive speech synthesis. The complete dataset and model checkpoints are available at: https://github.com/bigai-nlco/UltraVoice.

Robotic manipulation and navigation are fundamental capabilities of embodied intelligence, enabling effective robot interactions with the physical world. Achieving these capabilities requires a cohesive understanding of the environment, including object recognition to localize target objects, object affordances to identify potential interaction areas and spatial affordances to discern optimal areas for both object placement and robot movement. While Vision-Language Models (VLMs) excel at high-level task planning and scene understanding, they often struggle to infer actionable positions for physical interaction, such as functional grasping points and permissible placement regions. This limitation stems from the lack of fine-grained annotations for object and spatial affordances in their training datasets. To tackle this challenge, we introduce RoboAfford++, a generative AI-enhanced dataset for multimodal affordance learning for both robotic manipulation and navigation. Our dataset comprises 869,987 images paired with 2.0 million question answering (QA) annotations, covering three critical tasks: object affordance recognition to identify target objects based on attributes and spatial relationships, object affordance prediction to pinpoint functional parts for manipulation, and spatial affordance localization to identify free space for object placement and robot navigation. Complementing this dataset, we propose RoboAfford-Eval, a comprehensive benchmark for assessing affordance-aware prediction in real-world scenarios, featuring 338 meticulously annotated samples across the same three tasks. Extensive experimental results reveal the deficiencies of existing VLMs in affordance learning, while fine-tuning on the RoboAfford++ dataset significantly enhances their ability to reason about object and spatial affordances, validating the dataset's effectiveness.

Large language models (LLMs) are increasingly seen as assistants, copilots, and consultants, capable of supporting a wide range of tasks through natural conversation. However, most systems remain constrained by a linear request-response format that often makes interactions inefficient in multi-turn, information-dense, and exploratory tasks. To address these limitations, we propose Generative Interfaces for Language Models, a paradigm in which LLMs respond to user queries by proactively generating user interfaces (UIs) that enable more adaptive and interactive engagement. Our framework leverages structured interface-specific representations and iterative refinements to translate user queries into task-specific UIs. For systematic evaluation, we introduce a multidimensional assessment framework that compares generative interfaces with traditional chat-based ones across diverse tasks, interaction patterns, and query types, capturing functional, interactive, and emotional aspects of user experience. Results show that generative interfaces consistently outperform conversational ones, with humans preferring them in over 70% of cases. These findings clarify when and why users favor generative interfaces, paving the way for future advancements in human-AI interaction.

Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on individual proteins with short context lengths. Such protein LMs cannot extrapolate to longer proteins and protein complexes well. They also fail to account for the underlying biological mechanisms carried out by biomolecular interactions and dynamics i.e., proteins often interact with other proteins, molecules, and pathways in complex biological systems. In this work, we propose LC-PLM based on an alternative protein LM architecture, BiMamba-S, built off selective structured state-space models, to learn high-quality universal protein representations at the amino acid token level using masked language modeling. We also introduce its graph-contextual variant, LC-PLM-G, which contextualizes protein-protein interaction (PPI) graphs for a second stage of training. LC-PLM demonstrates favorable neural scaling laws, better length extrapolation capability, and a 7% to 34% improvement on protein downstream tasks than Transformer-based ESM-2. LC-PLM-G further trained within the context of PPI graphs shows promising results on protein structure and function prediction tasks. Our study demonstrates the benefit of increasing the context size with computationally efficient LM architecture (e.g. structured state space models) in learning universal protein representations and incorporating molecular interaction context contained in biological graphs.

Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated remarkable success in predicting protein structure and function, their application to sequence-based PPI binding affinity prediction remains relatively underexplored. This gap is often attributed to the scarcity of high-quality, rigorously refined datasets and the reliance on simple strategies for concatenating protein representations. In this work, we address these limitations. First, we introduce a meticulously curated version of the PPB-Affinity dataset of a total of 8,207 unique protein-protein interaction entries, by resolving annotation inconsistencies and duplicate entries for multi-chain protein interactions. This dataset incorporates a stringent, less than or equal to 30%, sequence identity threshold to ensure robust splitting into training, validation, and test sets, minimizing data leakage. Second, we propose and systematically evaluate four architectures for adapting PLMs to PPI binding affinity prediction: embeddings concatenation (EC), sequences concatenation (SC), hierarchical pooling (HP), and pooled attention addition (PAD). These architectures were assessed using two training methods: full fine-tuning and a lightweight approach employing ConvBERT heads over frozen PLM features. Our comprehensive experiments across multiple leading PLMs (ProtT5, ESM2, Ankh, Ankh2, and ESM3) demonstrated that the HP and PAD architectures consistently outperform conventional concatenation methods, achieving up to 12% increase in terms of Spearman correlation. These results highlight the necessity of sophisticated architectural designs to fully exploit the capabilities of PLMs for nuanced PPI binding affinity prediction.

In this paper, we propose a real-world benchmark for studying robotic learning in the context of functional manipulation: a robot needs to accomplish complex long-horizon behaviors by composing individual manipulation skills in functionally relevant ways. The core design principles of our Functional Manipulation Benchmark (FMB) emphasize a harmonious balance between complexity and accessibility. Tasks are deliberately scoped to be narrow, ensuring that models and datasets of manageable scale can be utilized effectively to track progress. Simultaneously, they are diverse enough to pose a significant generalization challenge. Furthermore, the benchmark is designed to be easily replicable, encompassing all essential hardware and software components. To achieve this goal, FMB consists of a variety of 3D-printed objects designed for easy and accurate replication by other researchers. The objects are procedurally generated, providing a principled framework to study generalization in a controlled fashion. We focus on fundamental manipulation skills, including grasping, repositioning, and a range of assembly behaviors. The FMB can be used to evaluate methods for acquiring individual skills, as well as methods for combining and ordering such skills to solve complex, multi-stage manipulation tasks. We also offer an imitation learning framework that includes a suite of policies trained to solve the proposed tasks. This enables researchers to utilize our tasks as a versatile toolkit for examining various parts of the pipeline. For example, researchers could propose a better design for a grasping controller and evaluate it in combination with our baseline reorientation and assembly policies as part of a pipeline for solving multi-stage tasks. Our dataset, object CAD files, code, and evaluation videos can be found on our project website: https://functional-manipulation-benchmark.github.io

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

We introduce Functional Diffusion Processes (FDPs), which generalize score-based diffusion models to infinite-dimensional function spaces. FDPs require a new mathematical framework to describe the forward and backward dynamics, and several extensions to derive practical training objectives. These include infinite-dimensional versions of Girsanov theorem, in order to be able to compute an ELBO, and of the sampling theorem, in order to guarantee that functional evaluations in a countable set of points are equivalent to infinite-dimensional functions. We use FDPs to build a new breed of generative models in function spaces, which do not require specialized network architectures, and that can work with any kind of continuous data. Our results on real data show that FDPs achieve high-quality image generation, using a simple MLP architecture with orders of magnitude fewer parameters than existing diffusion models.

Recent sequential recommendation models rely increasingly on consecutive short-term user-item interaction sequences to model user interests. These approaches have, however, raised concerns about both short- and long-term interests. (1) {\it short-term}: interaction sequences may not result from a monolithic interest, but rather from several intertwined interests, even within a short period of time, resulting in their failures to model skip behaviors; (2) {\it long-term}: interaction sequences are primarily observed sparsely at discrete intervals, other than consecutively over the long run. This renders difficulty in inferring long-term interests, since only discrete interest representations can be derived, without taking into account interest dynamics across sequences. In this study, we address these concerns by learning (1) multi-scale representations of short-term interests; and (2) dynamics-aware representations of long-term interests. To this end, we present an Interest Dynamics modeling framework using generative Neural Processes, coined IDNP, to model user interests from a functional perspective. IDNP learns a global interest function family to define each user's long-term interest as a function instantiation, manifesting interest dynamics through function continuity. Specifically, IDNP first encodes each user's short-term interactions into multi-scale representations, which are then summarized as user context. By combining latent global interest with user context, IDNP then reconstructs long-term user interest functions and predicts interactions at upcoming query timestep. Moreover, IDNP can model such interest functions even when interaction sequences are limited and non-consecutive. Extensive experiments on four real-world datasets demonstrate that our model outperforms state-of-the-arts on various evaluation metrics.

RNA is a vital biomolecule with numerous roles and functions within cells, and interest in targeting it for therapeutic purposes has grown significantly in recent years. However, fully understanding and predicting RNA behavior, particularly for applications in drug discovery, remains a challenge due to the complexity of RNA structures and interactions. While foundational models in biology have demonstrated success in modeling several biomolecules, especially proteins, achieving similar breakthroughs for RNA has proven more difficult. Current RNA models have yet to match the performance observed in the protein domain, leaving an important gap in computational biology. In this work, we present ChaRNABERT, a suite of sample and parameter-efficient RNA foundational models, that through a learnable tokenization process, are able to reach state-of-the-art performance on several tasks in established benchmarks. We extend its testing in relevant downstream tasks such as RNA-protein and aptamer-protein interaction prediction. Weights and inference code for ChaRNABERT-8M will be provided for academic research use. The other models will be available upon request.

Mechanistic interpretability aims to understand the behavior of neural networks by reverse-engineering their internal computations. However, current methods struggle to find clear interpretations of neural network activations because a decomposition of activations into computational features is missing. Individual neurons or model components do not cleanly correspond to distinct features or functions. We present a novel interpretability method that aims to overcome this limitation by transforming the activations of the network into a new basis - the Local Interaction Basis (LIB). LIB aims to identify computational features by removing irrelevant activations and interactions. Our method drops irrelevant activation directions and aligns the basis with the singular vectors of the Jacobian matrix between adjacent layers. It also scales features based on their importance for downstream computation, producing an interaction graph that shows all computationally-relevant features and interactions in a model. We evaluate the effectiveness of LIB on modular addition and CIFAR-10 models, finding that it identifies more computationally-relevant features that interact more sparsely, compared to principal component analysis. However, LIB does not yield substantial improvements in interpretability or interaction sparsity when applied to language models. We conclude that LIB is a promising theory-driven approach for analyzing neural networks, but in its current form is not applicable to large language models.

Biomolecular interactions underpin almost all biological processes, and their rational design is central to programming new biological functions. Generative AI models have emerged as powerful tools for molecular design, yet most remain specialized for individual molecular types and lack fine-grained control over interaction details. Here we present ODesign, an all-atom generative world model for all-to-all biomolecular interaction design. ODesign allows scientists to specify epitopes on arbitrary targets and generate diverse classes of binding partners with fine-grained control. Across entity-, token-, and atom-level benchmarks in the protein modality, ODesign demonstrates superior controllability and performance to modality-specific baselines. Extending beyond proteins, it generalizes to nucleic acid and small-molecule design, enabling interaction types such as protein-binding RNA/DNA and RNA/DNA-binding ligands that were previously inaccessible. By unifying multimodal biomolecular interactions within a single generative framework, ODesign moves toward a general-purpose molecular world model capable of programmable design. ODesign is available at https://odesign.lglab.ac.cn ,

Deep sparse networks are widely investigated as a neural network architecture for prediction tasks with high-dimensional sparse features, with which feature interaction selection is a critical component. While previous methods primarily focus on how to search feature interaction in a coarse-grained space, less attention has been given to a finer granularity. In this work, we introduce a hybrid-grained feature interaction selection approach that targets both feature field and feature value for deep sparse networks. To explore such expansive space, we propose a decomposed space which is calculated on the fly. We then develop a selection algorithm called OptFeature, which efficiently selects the feature interaction from both the feature field and the feature value simultaneously. Results from experiments on three large real-world benchmark datasets demonstrate that OptFeature performs well in terms of accuracy and efficiency. Additional studies support the feasibility of our method.

Click-through prediction (CTR) models transform features into latent vectors and enumerate possible feature interactions to improve performance based on the input feature set. Therefore, when selecting an optimal feature set, we should consider the influence of both feature and its interaction. However, most previous works focus on either feature field selection or only select feature interaction based on the fixed feature set to produce the feature set. The former restricts search space to the feature field, which is too coarse to determine subtle features. They also do not filter useless feature interactions, leading to higher computation costs and degraded model performance. The latter identifies useful feature interaction from all available features, resulting in many redundant features in the feature set. In this paper, we propose a novel method named OptFS to address these problems. To unify the selection of feature and its interaction, we decompose the selection of each feature interaction into the selection of two correlated features. Such a decomposition makes the model end-to-end trainable given various feature interaction operations. By adopting feature-level search space, we set a learnable gate to determine whether each feature should be within the feature set. Because of the large-scale search space, we develop a learning-by-continuation training scheme to learn such gates. Hence, OptFS generates the feature set only containing features which improve the final prediction results. Experimentally, we evaluate OptFS on three public datasets, demonstrating OptFS can optimize feature sets which enhance the model performance and further reduce both the storage and computational cost.

In the early 2000s, renowned chef Heston Blumenthal formulated his "food pairing" hypothesis, positing that if foods share many flavor compounds, then they tend to taste good when eaten together. In 2011, Ahn et al. conducted a study using a dataset of recipes, ingredients, and flavor compounds, finding that, in Western cuisine, ingredients in recipes often share more flavor compounds than expected by chance, indicating a natural tendency towards food pairing. Building upon Ahn's research, our work applies state-of-the-art collaborative filtering techniques to the dataset, providing a tool that can recommend new foods to add in recipes, retrieve missing ingredients and advise against certain combinations. We create our recommender in two ways, by taking into account ingredients appearances in recipes or shared flavor compounds between foods. While our analysis confirms the existence of food pairing, the recipe-based recommender performs significantly better than the flavor-based one, leading to the conclusion that food pairing is just one of the principles to take into account when creating recipes. Furthermore, and more interestingly, we find that food pairing in data is mostly due to trivial couplings of very similar ingredients, leading to a reconsideration of its current role in recipes, from being an already existing feature to a key to open up new scenarios in gastronomy. Our flavor-based recommender can thus leverage this novel concept and provide a new tool to lead culinary innovation.

Deep functional maps have recently emerged as a powerful tool for solving non-rigid shape correspondence tasks. Methods that use this approach combine the power and flexibility of the functional map framework, with data-driven learning for improved accuracy and generality. However, most existing methods in this area restrict the learning aspect only to the feature functions and still rely on axiomatic modeling for formulating the training loss or for functional map regularization inside the networks. This limits both the accuracy and the applicability of the resulting approaches only to scenarios where assumptions of the axiomatic models hold. In this work, we show, for the first time, that both in-network regularization and functional map training can be replaced with data-driven methods. For this, we first train a generative model of functional maps in the spectral domain using score-based generative modeling, built from a large collection of high-quality maps. We then exploit the resulting model to promote the structural properties of ground truth functional maps on new shape collections. Remarkably, we demonstrate that the learned models are category-agnostic, and can fully replace commonly used strategies such as enforcing Laplacian commutativity or orthogonality of functional maps. Our key technical contribution is a novel distillation strategy from diffusion models in the spectral domain. Experiments demonstrate that our learned regularization leads to better results than axiomatic approaches for zero-shot non-rigid shape matching. Our code is available at: https://github.com/daidedou/diffumatch/

Drug-target interaction (DTI) prediction is crucial for identifying new therapeutics and detecting mechanisms of action. While structure-based methods accurately model physical interactions between a drug and its protein target, cell-based assays such as Cell Painting can better capture complex DTI interactions. This paper introduces MOTIVE, a Morphological cOmpound Target Interaction Graph dataset that comprises Cell Painting features for 11,000 genes and 3,600 compounds along with their relationships extracted from seven publicly available databases. We provide random, cold-source (new drugs), and cold-target (new genes) data splits to enable rigorous evaluation under realistic use cases. Our benchmark results show that graph neural networks that use Cell Painting features consistently outperform those that learn from graph structure alone, feature-based models, and topological heuristics. MOTIVE accelerates both graph ML research and drug discovery by promoting the development of more reliable DTI prediction models. MOTIVE resources are available at https://github.com/carpenter-singh-lab/motive.

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose FABind, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. FABind incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed FABind demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at https://github.com/QizhiPei/FABind

The structure-function relationship is at the heart of biology and major protein deformations are correlated to specific functions. In the case of heme proteins, doming is associated with the respiratory function in hemoglobin and myoglobin, while ruffling has been correlated with electron transfer processes, such as in the case of Cytochrome c (Cyt c). The latter has indeed evolved to become an important electron transfer protein in humans. In its ferrous form, it undergoes ligand release and doming upon photoexcitation, but its ferric form does not release the distal ligand, while the return to the ground state has been attributed to thermal relaxation. Here, by combining femtosecond Fe K-edge X-ray absorption near-edge structure (XANES) studies and femtosecond Fe Kalpha and Kbeta X-ray emission spectroscopy (XES), we demonstrate that the photocycle of ferric Cyt c is entirely due to a cascade among excited spin states of the Iron ion, causing the ferric heme to undergo doming, which we identify for the first time. We also argue that this pattern is common to all ferric haems, raising the question of the biological relevance of doming in such proteins.

This report introduces FunAudioLLM, a model family designed to enhance natural voice interactions between humans and large language models (LLMs). At its core are two innovative models: SenseVoice, which handles multilingual speech recognition, emotion recognition, and audio event detection; and CosyVoice, which facilitates natural speech generation with control over multiple languages, timbre, speaking style, and speaker identity. SenseVoice-Small delivers exceptionally low-latency ASR for 5 languages, and SenseVoice-Large supports high-precision ASR for over 50 languages, while CosyVoice excels in multi-lingual voice generation, zero-shot in-context learning, cross-lingual voice cloning, and instruction-following capabilities. The models related to SenseVoice and CosyVoice have been open-sourced on Modelscope and Huggingface, along with the corresponding training, inference, and fine-tuning codes released on GitHub. By integrating these models with LLMs, FunAudioLLM enables applications such as speech-to-speech translation, emotional voice chat, interactive podcasts, and expressive audiobook narration, thereby pushing the boundaries of voice interaction technology. Demos are available at https://fun-audio-llm.github.io, and the code can be accessed at https://github.com/FunAudioLLM.

Click-through rate prediction is one of the core tasks in commercial recommender systems. It aims to predict the probability of a user clicking a particular item given user and item features. As feature interactions bring in non-linearity, they are widely adopted to improve the performance of CTR prediction models. Therefore, effectively modelling feature interactions has attracted much attention in both the research and industry field. The current approaches can generally be categorized into three classes: (1) na\"ive methods, which do not model feature interactions and only use original features; (2) memorized methods, which memorize feature interactions by explicitly viewing them as new features and assigning trainable embeddings; (3) factorized methods, which learn latent vectors for original features and implicitly model feature interactions through factorization functions. Studies have shown that modelling feature interactions by one of these methods alone are suboptimal due to the unique characteristics of different feature interactions. To address this issue, we first propose a general framework called OptInter which finds the most suitable modelling method for each feature interaction. Different state-of-the-art deep CTR models can be viewed as instances of OptInter. To realize the functionality of OptInter, we also introduce a learning algorithm that automatically searches for the optimal modelling method. We conduct extensive experiments on four large datasets. Our experiments show that OptInter improves the best performed state-of-the-art baseline deep CTR models by up to 2.21%. Compared to the memorized method, which also outperforms baselines, we reduce up to 91% parameters. In addition, we conduct several ablation studies to investigate the influence of different components of OptInter. Finally, we provide interpretable discussions on the results of OptInter.

This article presents Individual Conditional Expectation (ICE) plots, a tool for visualizing the model estimated by any supervised learning algorithm. Classical partial dependence plots (PDPs) help visualize the average partial relationship between the predicted response and one or more features. In the presence of substantial interaction effects, the partial response relationship can be heterogeneous. Thus, an average curve, such as the PDP, can obfuscate the complexity of the modeled relationship. Accordingly, ICE plots refine the partial dependence plot by graphing the functional relationship between the predicted response and the feature for individual observations. Specifically, ICE plots highlight the variation in the fitted values across the range of a covariate, suggesting where and to what extent heterogeneities might exist. In addition to providing a plotting suite for exploratory analysis, we include a visual test for additive structure in the data generating model. Through simulated examples and real data sets, we demonstrate how ICE plots can shed light on estimated models in ways PDPs cannot. Procedures outlined are available in the R package ICEbox.

We introduce Functional Group-Aware Representations for Small Molecules (FARM), a novel foundation model designed to bridge the gap between SMILES, natural language, and molecular graphs. The key innovation of FARM lies in its functional group-aware tokenization, which incorporates functional group information directly into the representations. This strategic reduction in tokenization granularity in a way that is intentionally interfaced with key drivers of functional properties (i.e., functional groups) enhances the model's understanding of chemical language, expands the chemical lexicon, more effectively bridging SMILES and natural language, and ultimately advances the model's capacity to predict molecular properties. FARM also represents molecules from two perspectives: by using masked language modeling to capture atom-level features and by employing graph neural networks to encode the whole molecule topology. By leveraging contrastive learning, FARM aligns these two views of representations into a unified molecular embedding. We rigorously evaluate FARM on the MoleculeNet dataset, where it achieves state-of-the-art performance on 10 out of 12 tasks. These results highlight FARM's potential to improve molecular representation learning, with promising applications in drug discovery and pharmaceutical research.

Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream tasks. However, there is limited empirical work that examines the structure of these interactions. This paper analyzes 1.86 million models on Hugging Face, a leading peer production platform for model development. Our study of model family trees -- networks that connect fine-tuned models to their base or parent -- reveals sprawling fine-tuning lineages that vary widely in size and structure. Using an evolutionary biology lens to study ML models, we use model metadata and model cards to measure the genetic similarity and mutation of traits over model families. We find that models tend to exhibit a family resemblance, meaning their genetic markers and traits exhibit more overlap when they belong to the same model family. However, these similarities depart in certain ways from standard models of asexual reproduction, because mutations are fast and directed, such that two `sibling' models tend to exhibit more similarity than parent/child pairs. Further analysis of the directional drifts of these mutations reveals qualitative insights about the open machine learning ecosystem: Licenses counter-intuitively drift from restrictive, commercial licenses towards permissive or copyleft licenses, often in violation of upstream license's terms; models evolve from multi-lingual compatibility towards english-only compatibility; and model cards reduce in length and standardize by turning, more often, to templates and automatically generated text. Overall, this work takes a step toward an empirically grounded understanding of model fine-tuning and suggests that ecological models and methods can yield novel scientific insights.

Language is an intricately structured system, and a key goal of NLP interpretability is to provide methodological insights for understanding how language models represent this structure internally. In this paper, we use Shapley Taylor interaction indices (STII) in order to examine how language and speech models internally relate and structure their inputs. Pairwise Shapley interactions measure how much two inputs work together to influence model outputs beyond if we linearly added their independent influences, providing a view into how models encode structural interactions between inputs. We relate the interaction patterns in models to three underlying linguistic structures: syntactic structure, non-compositional semantics, and phonetic coarticulation. We find that autoregressive text models encode interactions that correlate with the syntactic proximity of inputs, and that both autoregressive and masked models encode nonlinear interactions in idiomatic phrases with non-compositional semantics. Our speech results show that inputs are more entangled for pairs where a neighboring consonant is likely to influence a vowel or approximant, showing that models encode the phonetic interaction needed for extracting discrete phonemic representations.

Food polysaccharides have emerged as suitable carriers of active substances and as additives to food and nutraceutical formulations, showing potential to stabilize bioactive compounds during the storage of microencapsulate preparations, even in the gastrointestinal tract following the intake of bioactive compounds, thereby improving their bioaccessibility and bioavailability. This review provides a comprehensive overview of the main polysaccharides employed as wall materials, including starch, maltodextrin, alginate, pectin, inulin, chitosan, and gum arabic, and discusses how structural interactions and physicochemical properties can benefit the microencapsulation of polyphenols and pigments. The main findings and principles of the major encapsulation techniques, including spray drying, freeze drying, extrusion, emulsification, and coacervation, related to the production of microparticles, were briefly described. Polysaccharides can entrap hydrophilic and hydrophobic compounds by physical interactions, forming a barrier around the nucleus or binding to the bioactive compound. Intermolecular binding between polysaccharides in the wall matrix, polyphenols, and pigments in the nucleus can confer up to 90% of encapsulation efficiency, governed mainly by hydrogen bonds and electrostatic interactions. The mixture of wall polysaccharides in the microparticles synthesis favors the encapsulation solubility, storage stability, bioaccessibility, and bioactivity of the microencapsulate compounds. Clinical trials on the bioefficacy of polyphenols and pigments loaded in polysaccharide microparticles are scarce and require further evidence to reinforce the use of this technology.

A long standing goal in neuroscience has been to elucidate the functional organization of the brain. Within higher visual cortex, functional accounts have remained relatively coarse, focusing on regions of interest (ROIs) and taking the form of selectivity for broad categories such as faces, places, bodies, food, or words. Because the identification of such ROIs has typically relied on manually assembled stimulus sets consisting of isolated objects in non-ecological contexts, exploring functional organization without robust a priori hypotheses has been challenging. To overcome these limitations, we introduce a data-driven approach in which we synthesize images predicted to activate a given brain region using paired natural images and fMRI recordings, bypassing the need for category-specific stimuli. Our approach -- Brain Diffusion for Visual Exploration ("BrainDiVE") -- builds on recent generative methods by combining large-scale diffusion models with brain-guided image synthesis. Validating our method, we demonstrate the ability to synthesize preferred images with appropriate semantic specificity for well-characterized category-selective ROIs. We then show that BrainDiVE can characterize differences between ROIs selective for the same high-level category. Finally we identify novel functional subdivisions within these ROIs, validated with behavioral data. These results advance our understanding of the fine-grained functional organization of human visual cortex, and provide well-specified constraints for further examination of cortical organization using hypothesis-driven methods.

We introduce a dynamic benchmarking system for conversational agents that evaluates their performance through a single, simulated, and lengthy userleftrightarrowagent interaction. The interaction is a conversation between the user and agent, where multiple tasks are introduced and then undertaken concurrently. We context switch regularly to interleave the tasks, which constructs a realistic testing scenario in which we assess the Long-Term Memory, Continual Learning, and Information Integration capabilities of the agents. Results from both proprietary and open-source Large-Language Models show that LLMs in general perform well on single-task interactions, but they struggle on the same tasks when they are interleaved. Notably, short-context LLMs supplemented with an LTM system perform as well as or better than those with larger contexts. Our benchmark suggests that there are other challenges for LLMs responding to more natural interactions that contemporary benchmarks have heretofore not been able to capture.

Feature interaction has long been a cornerstone of ranking models in large-scale recommender systems due to its proven effectiveness in capturing complex dependencies among features. However, existing feature interaction strategies face two critical challenges in industrial applications: (1) The vast number of categorical and sequential features makes exhaustive interaction computationally prohibitive, often resulting in optimization difficulties. (2) Real-world recommender systems typically involve multiple prediction objectives, yet most current approaches apply feature interaction modules prior to the multi-task learning layers. This late-fusion design overlooks task-specific feature dependencies and inherently limits the capacity of multi-task modeling. To address these limitations, we propose the Information Flow Network (INFNet), a task-aware architecture designed for large-scale recommendation scenarios. INFNet distinguishes features into three token types, categorical tokens, sequence tokens, and task tokens, and introduces a novel dual-flow design comprising heterogeneous and homogeneous alternating information blocks. For heterogeneous information flow, we employ a cross-attention mechanism with proxy that facilitates efficient cross-modal token interaction with balanced computational cost. For homogeneous flow, we design type-specific Proxy Gated Units (PGUs) to enable fine-grained intra-type feature processing. Extensive experiments on multiple offline benchmarks confirm that INFNet achieves state-of-the-art performance. Moreover, INFNet has been successfully deployed in a commercial online advertising system, yielding significant gains of +1.587% in Revenue (REV) and +1.155% in Click-Through Rate (CTR).

Despite the recent successes of vanilla Graph Neural Networks (GNNs) on many tasks, their foundation on pairwise interaction networks inherently limits their capacity to discern latent higher-order interactions in complex systems. To bridge this capability gap, we propose a novel approach exploiting the rich mathematical theory of simplicial complexes (SCs) - a robust tool for modeling higher-order interactions. Current SC-based GNNs are burdened by high complexity and rigidity, and quantifying higher-order interaction strengths remains challenging. Innovatively, we present a higher-order Flower-Petals (FP) model, incorporating FP Laplacians into SCs. Further, we introduce a Higher-order Graph Convolutional Network (HiGCN) grounded in FP Laplacians, capable of discerning intrinsic features across varying topological scales. By employing learnable graph filters, a parameter group within each FP Laplacian domain, we can identify diverse patterns where the filters' weights serve as a quantifiable measure of higher-order interaction strengths. The theoretical underpinnings of HiGCN's advanced expressiveness are rigorously demonstrated. Additionally, our empirical investigations reveal that the proposed model accomplishes state-of-the-art (SOTA) performance on a range of graph tasks and provides a scalable and flexible solution to explore higher-order interactions in graphs.

Biological processes, functions, and properties are intricately linked to the ensemble of protein conformations, rather than being solely determined by a single stable conformation. In this study, we have developed P2DFlow, a generative model based on SE(3) flow matching, to predict the structural ensembles of proteins. We specifically designed a valuable prior for the flow process and enhanced the model's ability to distinguish each intermediate state by incorporating an additional dimension to describe the ensemble data, which can reflect the physical laws governing the distribution of ensembles, so that the prior knowledge can effectively guide the generation process. When trained and evaluated on the MD datasets of ATLAS, P2DFlow outperforms other baseline models on extensive experiments, successfully capturing the observable dynamic fluctuations as evidenced in crystal structure and MD simulations. As a potential proxy agent for protein molecular simulation, the high-quality ensembles generated by P2DFlow could significantly aid in understanding protein functions across various scenarios. Code is available at https://github.com/BLEACH366/P2DFlow

In many machine learning systems that jointly learn from multiple modalities, a core research question is to understand the nature of multimodal interactions: the emergence of new task-relevant information during learning from both modalities that was not present in either alone. We study this challenge of interaction quantification in a semi-supervised setting with only labeled unimodal data and naturally co-occurring multimodal data (e.g., unlabeled images and captions, video and corresponding audio) but when labeling them is time-consuming. Using a precise information-theoretic definition of interactions, our key contributions are the derivations of lower and upper bounds to quantify the amount of multimodal interactions in this semi-supervised setting. We propose two lower bounds based on the amount of shared information between modalities and the disagreement between separately trained unimodal classifiers, and derive an upper bound through connections to approximate algorithms for min-entropy couplings. We validate these estimated bounds and show how they accurately track true interactions. Finally, two semi-supervised multimodal applications are explored based on these theoretical results: (1) analyzing the relationship between multimodal performance and estimated interactions, and (2) self-supervised learning that embraces disagreement between modalities beyond agreement as is typically done.

Prediction of protein-ligand (PL) binding affinity remains the key to drug discovery. Popular approaches in recent years involve graph neural networks (GNNs), which are used to learn the topology and geometry of PL complexes. However, GNNs are computationally heavy and have poor scalability to graph sizes. On the other hand, traditional machine learning (ML) approaches, such as gradient-boosted decision trees (GBDTs), are lightweight yet extremely efficient for tabular data. We propose to use PL interaction features along with PL graph-level features in GBDT. We show that this combination outperforms the existing solutions.

We explore the effects of various plasticity functions on assemblies of neurons. To bridge the gap between experimental and computational theories we make use of a conceptual framework, the Assembly Calculus, which is a formal system for the description of brain function based on assemblies of neurons. The Assembly Calculus includes operations for projecting, associating, and merging assemblies of neurons. Our research is focused on simulating different plasticity functions with Assembly Calculus. Our main contribution is the modification and evaluation of the projection operation. We experiment with Oja's and Spike Time-Dependent Plasticity (STDP) rules and test the effect of various hyper-parameters.