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Oct 29

KETJU -- resolving small-scale supermassive black hole dynamics in GADGET-4

We present the new public version of the KETJU supermassive black hole (SMBH) dynamics module, as implemented into GADGET-4. KETJU adds a small region around each SMBH where the dynamics of the SMBHs and stellar particles are integrated using an algorithmically regularised integrator instead of the leapfrog integrator with gravitational softening used by GADGET-4. This enables modelling SMBHs as point particles even during close interactions with stellar particles or other SMBHs, effectively removing the spatial resolution limitation caused by gravitational softening. KETJU also includes post-Newtonian corrections, which allows following the dynamics of SMBH binaries to sub-parsec scales and down to tens of Schwarzschild radii. Systems with multiple SMBHs are also supported, with the code also including the leading non-linear cross terms that appear in the post-Newtonian equations for such systems. We present tests of the code showing that it correctly captures, at sufficient mass resolution, the sinking driven by dynamical friction and binary hardening driven by stellar scattering. We also present an example application demonstrating how the code can be applied to study the dynamics of SMBHs in mergers of multiple galaxies and the effect they have on the properties of the surrounding galaxy. We expect that the presented KETJU SMBH dynamics module can also be straightforwardly incorporated into other codes similar to GADGET-4, which would allow coupling small-scale SMBH dynamics to the rich variety of galactic physics models that exist in the literature.

  • 8 authors
·
Jun 8, 2023

Monocular 3D Multi-Person Pose Estimation by Integrating Top-Down and Bottom-Up Networks

In monocular video 3D multi-person pose estimation, inter-person occlusion and close interactions can cause human detection to be erroneous and human-joints grouping to be unreliable. Existing top-down methods rely on human detection and thus suffer from these problems. Existing bottom-up methods do not use human detection, but they process all persons at once at the same scale, causing them to be sensitive to multiple-persons scale variations. To address these challenges, we propose the integration of top-down and bottom-up approaches to exploit their strengths. Our top-down network estimates human joints from all persons instead of one in an image patch, making it robust to possible erroneous bounding boxes. Our bottom-up network incorporates human-detection based normalized heatmaps, allowing the network to be more robust in handling scale variations. Finally, the estimated 3D poses from the top-down and bottom-up networks are fed into our integration network for final 3D poses. Besides the integration of top-down and bottom-up networks, unlike existing pose discriminators that are designed solely for single person, and consequently cannot assess natural inter-person interactions, we propose a two-person pose discriminator that enforces natural two-person interactions. Lastly, we also apply a semi-supervised method to overcome the 3D ground-truth data scarcity. Our quantitative and qualitative evaluations show the effectiveness of our method compared to the state-of-the-art baselines.

  • 4 authors
·
Apr 5, 2021

Enhanced Multi-Object Tracking Using Pose-based Virtual Markers in 3x3 Basketball

Multi-object tracking (MOT) is crucial for various multi-agent analyses such as evaluating team sports tactics and player movements and performance. While pedestrian tracking has advanced with Tracking-by-Detection MOT, team sports like basketball pose unique challenges. These challenges include players' unpredictable movements, frequent close interactions, and visual similarities that complicate pose labeling and lead to significant occlusions, frequent ID switches, and high manual annotation costs. To address these challenges, we propose a novel pose-based virtual marker (VM) MOT method for team sports, named Sports-vmTracking. This method builds on the vmTracking approach developed for multi-animal tracking with active learning. First, we constructed a 3x3 basketball pose dataset for VMs and applied active learning to enhance model performance in generating VMs. Then, we overlaid the VMs on video to identify players, extract their poses with unique IDs, and convert these into bounding boxes for comparison with automated MOT methods. Using our 3x3 basketball dataset, we demonstrated that our VM configuration has been highly effective, and reduced the need for manual corrections and labeling during pose model training while maintaining high accuracy. Our approach achieved an average HOTA score of 72.3%, over 10 points higher than other state-of-the-art methods without VM, and resulted in 0 ID switches. Beyond improving performance in handling occlusions and minimizing ID switches, our framework could substantially increase the time and cost efficiency compared to traditional manual annotation.

  • 7 authors
·
Dec 8, 2024

MoReact: Generating Reactive Motion from Textual Descriptions

Modeling and generating human reactions poses a significant challenge with broad applications for computer vision and human-computer interaction. Existing methods either treat multiple individuals as a single entity, directly generating interactions, or rely solely on one person's motion to generate the other's reaction, failing to integrate the rich semantic information that underpins human interactions. Yet, these methods often fall short in adaptive responsiveness, i.e., the ability to accurately respond to diverse and dynamic interaction scenarios. Recognizing this gap, our work introduces an approach tailored to address the limitations of existing models by focusing on text-driven human reaction generation. Our model specifically generates realistic motion sequences for individuals that responding to the other's actions based on a descriptive text of the interaction scenario. The goal is to produce motion sequences that not only complement the opponent's movements but also semantically fit the described interactions. To achieve this, we present MoReact, a diffusion-based method designed to disentangle the generation of global trajectories and local motions sequentially. This approach stems from the observation that generating global trajectories first is crucial for guiding local motion, ensuring better alignment with given action and text. Furthermore, we introduce a novel interaction loss to enhance the realism of generated close interactions. Our experiments, utilizing data adapted from a two-person motion dataset, demonstrate the efficacy of our approach for this novel task, which is capable of producing realistic, diverse, and controllable reactions that not only closely match the movements of the counterpart but also adhere to the textual guidance. Please find our webpage at https://xiyan-xu.github.io/MoReactWebPage.

  • 4 authors
·
Sep 28, 2025

MAMMA: Markerless & Automatic Multi-Person Motion Action Capture

We present MAMMA, a markerless motion-capture pipeline that accurately recovers SMPL-X parameters from multi-view video of two-person interaction sequences. Traditional motion-capture systems rely on physical markers. Although they offer high accuracy, their requirements of specialized hardware, manual marker placement, and extensive post-processing make them costly and time-consuming. Recent learning-based methods attempt to overcome these limitations, but most are designed for single-person capture, rely on sparse keypoints, or struggle with occlusions and physical interactions. In this work, we introduce a method that predicts dense 2D contact-aware surface landmarks conditioned on segmentation masks, enabling person-specific correspondence estimation even under heavy occlusion. We employ a novel architecture that exploits learnable queries for each landmark. We demonstrate that our approach can handle complex person--person interaction and offers greater accuracy than existing methods. To train our network, we construct a large, synthetic multi-view dataset combining human motions from diverse sources, including extreme poses, hand motions, and close interactions. Our dataset yields high-variability synthetic sequences with rich body contact and occlusion, and includes SMPL-X ground-truth annotations with dense 2D landmarks. The result is a system capable of capturing human motion without the need for markers. Our approach offers competitive reconstruction quality compared to commercial marker-based motion-capture solutions, without the extensive manual cleanup. Finally, we address the absence of common benchmarks for dense-landmark prediction and markerless motion capture by introducing two evaluation settings built from real multi-view sequences. Our dataset is available in https://mamma.is.tue.mpg.de for research purposes.

  • 10 authors
·
Apr 6

Harmony4D: A Video Dataset for In-The-Wild Close Human Interactions

Understanding how humans interact with each other is key to building realistic multi-human virtual reality systems. This area remains relatively unexplored due to the lack of large-scale datasets. Recent datasets focusing on this issue mainly consist of activities captured entirely in controlled indoor environments with choreographed actions, significantly affecting their diversity. To address this, we introduce Harmony4D, a multi-view video dataset for human-human interaction featuring in-the-wild activities such as wrestling, dancing, MMA, and more. We use a flexible multi-view capture system to record these dynamic activities and provide annotations for human detection, tracking, 2D/3D pose estimation, and mesh recovery for closely interacting subjects. We propose a novel markerless algorithm to track 3D human poses in severe occlusion and close interaction to obtain our annotations with minimal manual intervention. Harmony4D consists of 1.66 million images and 3.32 million human instances from more than 20 synchronized cameras with 208 video sequences spanning diverse environments and 24 unique subjects. We rigorously evaluate existing state-of-the-art methods for mesh recovery and highlight their significant limitations in modeling close interaction scenarios. Additionally, we fine-tune a pre-trained HMR2.0 model on Harmony4D and demonstrate an improved performance of 54.8% PVE in scenes with severe occlusion and contact. Code and data are available at https://jyuntins.github.io/harmony4d/.

  • 5 authors
·
Oct 26, 2024

Dual networks based 3D Multi-Person Pose Estimation from Monocular Video

Monocular 3D human pose estimation has made progress in recent years. Most of the methods focus on single persons, which estimate the poses in the person-centric coordinates, i.e., the coordinates based on the center of the target person. Hence, these methods are inapplicable for multi-person 3D pose estimation, where the absolute coordinates (e.g., the camera coordinates) are required. Moreover, multi-person pose estimation is more challenging than single pose estimation, due to inter-person occlusion and close human interactions. Existing top-down multi-person methods rely on human detection (i.e., top-down approach), and thus suffer from the detection errors and cannot produce reliable pose estimation in multi-person scenes. Meanwhile, existing bottom-up methods that do not use human detection are not affected by detection errors, but since they process all persons in a scene at once, they are prone to errors, particularly for persons in small scales. To address all these challenges, we propose the integration of top-down and bottom-up approaches to exploit their strengths. Our top-down network estimates human joints from all persons instead of one in an image patch, making it robust to possible erroneous bounding boxes. Our bottom-up network incorporates human-detection based normalized heatmaps, allowing the network to be more robust in handling scale variations. Finally, the estimated 3D poses from the top-down and bottom-up networks are fed into our integration network for final 3D poses. To address the common gaps between training and testing data, we do optimization during the test time, by refining the estimated 3D human poses using high-order temporal constraint, re-projection loss, and bone length regularizations. Our evaluations demonstrate the effectiveness of the proposed method. Code and models are available: https://github.com/3dpose/3D-Multi-Person-Pose.

  • 3 authors
·
May 2, 2022

Multimodal Active Measurement for Human Mesh Recovery in Close Proximity

For physical human-robot interactions (pHRI), a robot needs to estimate the accurate body pose of a target person. However, in these pHRI scenarios, the robot cannot fully observe the target person's body with equipped cameras because the target person must be close to the robot for physical interaction. This close distance leads to severe truncation and occlusions and thus results in poor accuracy of human pose estimation. For better accuracy in this challenging environment, we propose an active measurement and sensor fusion framework of the equipped cameras with touch and ranging sensors such as 2D LiDAR. Touch and ranging sensor measurements are sparse but reliable and informative cues for localizing human body parts. In our active measurement process, camera viewpoints and sensor placements are dynamically optimized to measure body parts with higher estimation uncertainty, which is closely related to truncation or occlusion. In our sensor fusion process, assuming that the measurements of touch and ranging sensors are more reliable than the camera-based estimations, we fuse the sensor measurements to the camera-based estimated pose by aligning the estimated pose towards the measured points. Our proposed method outperformed previous methods on the standard occlusion benchmark with simulated active measurement. Furthermore, our method reliably estimated human poses using a real robot, even with practical constraints such as occlusion by blankets.

  • 4 authors
·
Oct 12, 2023

Effects of Dark Matter Self Interactions on Sagittarius and Its Stream

This work explores how assumptions regarding the particle-physics nature of dark matter can alter the evolution of the Sagittarius (Sgr) dwarf spheroidal galaxy and its expansive stellar stream. We run a large suite of N-body simulations to model the infall of a Sgr-like dwarf, exploring how the presence of dark matter self interactions impacts its evolution. For a scattering cross section of sigma/m_chi = 30 cm^2/g (at orbital velocity scales), these interactions result in significantly less stellar mass and little to no dark matter bound to the progenitor at the present day. To isolate the cause of this mass loss, we introduce a novel technique for controlling which pairs of dark matter simulation particles can interact. This enables us to identify ram-pressure evaporation - the scattering of satellite and host dark matter particles - as the primary source of the enhanced mass loss. The rapid disintegration of the Sgr progenitor when self interactions are allowed alters some key properties of the resulting stellar stream, most dramatically suppressing the presence of a "spur" on the apocenter of the trailing stream arm that correlates with the mass of the satellite at last pericenter. We demonstrate how the effects on the Sgr system scale with the particular choice of self-interaction cross section, which affects the degree of ram-pressure evaporation. These findings generalize beyond the Sgr system, underscoring that dwarf stellar streams and dwarf galaxies with close passages may serve as sensitive probes for dark matter self interactions.

  • 4 authors
·
Mar 19, 2025

DivOPD: Spread Wide, Look Close for Asynchronous On-Policy Distillation of Multi-turn Agents

On-policy distillation (OPD) trains student agents through teacher supervision on their own interactions with an environment. However, in asynchronous multi-turn training, arrival-order batching can allow a few early or long rollouts to dominate learner updates while other valid rollouts become stale before being used, wasting already-generated experience. To address this problem, we introduce DivOPD, a simple learner-side batch-selection method that spreads a fixed turn budget across more rollouts and, within each rollout, prioritizes turns with larger cumulative teacher-student disagreement. Turns without usable teacher feedback are excluded. The per-turn loss and optimizer remain fixed; selection only changes which student-visited turns receive training weight. For no-progress rollouts, an optional extension briefly hands control to the teacher before returning it to the student. Across six teacher-student settings on the simulated ALFWorld, ScienceWorld, and WebShop benchmarks, with 1.5B-7B students, DivOPD raises cross-setting mean peak success rate from 77.4 to 84.4 and mean success over the last five evaluations from 71.5 to 78.6. It reaches all reported setting-specific targets with geometric-mean speedups of 1.84x in training tokens and 1.87x in learner GPU time relative to vanilla OPD. Teacher intervention further raises this last-five mean to 82.4 while retaining about 1.7x learner-GPU speedup over vanilla OPD. Code will be released at https://github.com/HanyangWang0418-oss/DivOPD.

  • 10 authors
·
Sep 27

MoSE3: Learning World-Space SE(3) at Every Pixel

Dense 3D point tracking has been a prominent paradigm for modeling motion in dynamic scenes, but a point track is just a 3-DoF translation curve per pixel: it captures where pixels go, not the rotation of the underlying part, nor which pixels move together as one body. We propose MoSE3, the first feed-forward model that predicts dense SE(3) motion from monocular RGB video, producing full 6-DoF rigid transforms at every pixel in world space. Per-pixel SE(3) motion offers a richer view of how a scene moves: rotation, translation, and grouping all at once. Directly predicting SE(3) is challenging: rotations lie on a curved manifold that is ill-suited to Euclidean regression, and annotations for SE(3) are particularly difficult to acquire. To address these challenges, MoSE3 predicts per-pixel SE(3) through two jointly learned intermediates, 3D point tracks and rigidity embeddings, and recovers SE(3) by differentiably fitting transforms within each soft rigid cluster, enabling end-to-end prediction and supervision. To close the data gap, we introduce Art-Kubric, a large-scale synthetic dataset with dense SE(3) and rigidity labels for articulated objects with rich physical interactions. MoSE3 achieves state-of-the-art SE(3) estimation at pixel, part, and object levels on both rigid and articulated benchmarks, and state-of-the-art average 3D point tracking accuracy across three datasets, while showing strong generalization to real-world videos despite being trained solely on synthetic motion data.

  • 6 authors
·
Oct 1

Attraction from repulsion in an interacting Chern band: chiral superconductivity, generalized Hall crystals, and competing fractional Chern insulators

Experiments realizing strong interactions in partially filled Chern bands have observed fractional Chern insulators (FCIs), superconductors, and topological crystals in close proximity. Yet the microscopic relation between them remains poorly understood. Here, we use tensor network simulations to study repulsively interacting spinless fermions in a tunable topological band of the checkerboard lattice. We characterize the competing phases and identify key features of the experimental phenomenology. FCIs from the Jain sequence transition into chiral p-wave superconductivity both below and above half filling as the band dispersion is enhanced. By contrast, at half filling, a generalized Hall crystal with quantized Hall conductance and a doubled unit cell forms for sufficiently strong coupling. Surprisingly, a weak-coupling approach starting from a metallic parent state captures the nature of both ordered phases at intermediate coupling. We find that fluctuations in the metal generate longer-range attraction, which we analyze within the random-phase approximation. This approach captures the pairing symmetry as well as the radial form factors of the Cooper pairs, and incorporating this attraction into Hartree-Fock selects the observed Hall crystal. Together, these results identify fluctuation-induced attraction from repulsion as a common microscopic ingredient of ordering, while our tensor network computations establish the direct competition of both phases with FCIs.

  • 4 authors
·
Oct 14

Learning Human-Object Interaction for 3D Human Pose Estimation from LiDAR Point Clouds

Understanding humans from LiDAR point clouds is one of the most critical tasks in autonomous driving due to its close relationships with pedestrian safety, yet it remains challenging in the presence of diverse human-object interactions and cluttered backgrounds. Nevertheless, existing methods largely overlook the potential of leveraging human-object interactions to build robust 3D human pose estimation frameworks. There are two major challenges that motivate the incorporation of human-object interaction. First, human-object interactions introduce spatial ambiguity between human and object points, which often leads to erroneous 3D human keypoint predictions in interaction regions. Second, there exists severe class imbalance in the number of points between interacting and non-interacting body parts, with the interaction-frequent regions such as hand and foot being sparsely observed in LiDAR data. To address these challenges, we propose a Human-Object Interaction Learning (HOIL) framework for robust 3D human pose estimation from LiDAR point clouds. To mitigate the spatial ambiguity issue, we present human-object interaction-aware contrastive learning (HOICL) that effectively enhances feature discrimination between human and object points, particularly in interaction regions. To alleviate the class imbalance issue, we introduce contact-aware part-guided pooling (CPPool) that adaptively reallocates representational capacity by compressing overrepresented points while preserving informative points from interacting body parts. In addition, we present an optional contact-based temporal refinement that refines erroneous per-frame keypoint estimates using contact cues over time. As a result, our HOIL effectively leverages human-object interaction to resolve spatial ambiguity and class imbalance in interaction regions. Codes will be released.

From Clinical Intent to Clinical Model: An Autonomous Coding-Agent Framework for Clinician-driven AI Development

Clinical AI development has traditionally followed a collaborative paradigm that depends on close interaction between clinicians and specialized AI teams. This paradigm imposes a practical challenge: clinicians must repeatedly communicate and refine their requirements with AI developers before those requirements can be translated into executable model development. This iterative process is time-consuming, and even after repeated discussion, misalignment may still exist because the two sides do not fully share each other's expertise. However, autonomous coding agents may change this paradigm, raising the possibility that clinicians could develop clinical AI models independently through natural-language interaction alone. In this study, we present such an autonomous prototype for clinician-driven clinical AI development. We evaluated the system on five clinical tasks spanning dermoscopic lesion classification, melanoma-versus-nevus triage, wrist-fracture detection (including a weakly supervised variant with only 5% bounding-box annotations), and debiased pneumothorax classification on chest radiographs. Across these settings, the system consistently developed models from clinician requests and achieved promising performance. Notably, in a debiased pneumothorax classification task on chest radiographs, where chest drains can act as a major confounder, the system successfully mitigated shortcut learning and nearly halved the model's reliance on chest drains. These findings provide proof of concept that autonomous coding agents may help shift clinical AI development toward a more clinician-driven paradigm, reducing the communication overhead and dependence on specialized AI developers. Although further validation and robustness assessment are needed, this study suggests a promising path toward making clinical AI development more accessible.

  • 6 authors
·
Apr 17

RIFT: Closed-Loop RL Fine-Tuning for Realistic and Controllable Traffic Simulation

Achieving both realism and controllability in interactive closed-loop traffic simulation remains a key challenge in autonomous driving. Data-driven simulation methods reproduce realistic trajectories but suffer from covariate shift in closed-loop deployment, compounded by simplified dynamics models that further reduce reliability. Conversely, physics-based simulation methods enhance reliable and controllable closed-loop interactions but often lack expert demonstrations, compromising realism. To address these challenges, we introduce a dual-stage AV-centered simulation framework that conducts open-loop imitation learning pre-training in a data-driven simulator to capture trajectory-level realism and multimodality, followed by closed-loop reinforcement learning fine-tuning in a physics-based simulator to enhance controllability and mitigate covariate shift. In the fine-tuning stage, we propose RIFT, a simple yet effective closed-loop RL fine-tuning strategy that preserves the trajectory-level multimodality through a GRPO-style group-relative advantage formulation, while enhancing controllability and training stability by replacing KL regularization with the dual-clip mechanism. Extensive experiments demonstrate that RIFT significantly improves the realism and controllability of generated traffic scenarios, providing a robust platform for evaluating autonomous vehicle performance in diverse and interactive scenarios.

  • 4 authors
·
May 6, 2025

RAD-2: Scaling Reinforcement Learning in a Generator-Discriminator Framework

High-level autonomous driving requires motion planners capable of modeling multimodal future uncertainties while remaining robust in closed-loop interactions. Although diffusion-based planners are effective at modeling complex trajectory distributions, they often suffer from stochastic instabilities and the lack of corrective negative feedback when trained purely with imitation learning. To address these issues, we propose RAD-2, a unified generator-discriminator framework for closed-loop planning. Specifically, a diffusion-based generator is used to produce diverse trajectory candidates, while an RL-optimized discriminator reranks these candidates according to their long-term driving quality. This decoupled design avoids directly applying sparse scalar rewards to the full high-dimensional trajectory space, thereby improving optimization stability. To further enhance reinforcement learning, we introduce Temporally Consistent Group Relative Policy Optimization, which exploits temporal coherence to alleviate the credit assignment problem. In addition, we propose On-policy Generator Optimization, which converts closed-loop feedback into structured longitudinal optimization signals and progressively shifts the generator toward high-reward trajectory manifolds. To support efficient large-scale training, we introduce BEV-Warp, a high-throughput simulation environment that performs closed-loop evaluation directly in Bird's-Eye View feature space via spatial warping. RAD-2 reduces the collision rate by 56% compared with strong diffusion-based planners. Real-world deployment further demonstrates improved perceived safety and driving smoothness in complex urban traffic.

MultiPly: Reconstruction of Multiple People from Monocular Video in the Wild

We present MultiPly, a novel framework to reconstruct multiple people in 3D from monocular in-the-wild videos. Reconstructing multiple individuals moving and interacting naturally from monocular in-the-wild videos poses a challenging task. Addressing it necessitates precise pixel-level disentanglement of individuals without any prior knowledge about the subjects. Moreover, it requires recovering intricate and complete 3D human shapes from short video sequences, intensifying the level of difficulty. To tackle these challenges, we first define a layered neural representation for the entire scene, composited by individual human and background models. We learn the layered neural representation from videos via our layer-wise differentiable volume rendering. This learning process is further enhanced by our hybrid instance segmentation approach which combines the self-supervised 3D segmentation and the promptable 2D segmentation module, yielding reliable instance segmentation supervision even under close human interaction. A confidence-guided optimization formulation is introduced to optimize the human poses and shape/appearance alternately. We incorporate effective objectives to refine human poses via photometric information and impose physically plausible constraints on human dynamics, leading to temporally consistent 3D reconstructions with high fidelity. The evaluation of our method shows the superiority over prior art on publicly available datasets and in-the-wild videos.

  • 7 authors
·
Jun 3, 2024

LEXIS: LatEnt ProXimal Interaction Signatures for 3D HOI from an Image

Reconstructing 3D Human-Object Interaction from an RGB image is essential for perceptive systems. Yet, this remains challenging as it requires capturing the subtle physical coupling between the body and objects. While current methods rely on sparse, binary contact cues, these fail to model the continuous proximity and dense spatial relationships that characterize natural interactions. We address this limitation via InterFields, a representation that encodes dense, continuous proximity across the entire body and object surfaces. However, inferring these fields from single images is inherently ill-posed. To tackle this, our intuition is that interaction patterns are characteristically structured by the action and object geometry. We capture this structure in LEXIS, a novel discrete manifold of interaction signatures learned via a VQ-VAE. We then develop LEXIS-Flow, a diffusion framework that leverages LEXIS signatures to estimate human and object meshes alongside their InterFields. Notably, these InterFields help in a guided refinement that ensures physically-plausible, proximity-aware reconstructions without requiring post-hoc optimization. Evaluation on Open3DHOI and BEHAVE shows that LEXIS-Flow significantly outperforms existing SotA baselines in reconstruction, contact, and proximity quality. Our approach not only improves generalization but also yields reconstructions perceived as more realistic, moving us closer to holistic 3D scene understanding. Code & models will be public at https://anticdimi.github.io/lexis.

  • 5 authors
·
Apr 21

ppiTrim: Constructing non-redundant and up-to-date interactomes

Robust advances in interactome analysis demand comprehensive, non-redundant and consistently annotated datasets. By non-redundant, we mean that the accounting of evidence for every interaction should be faithful: each independent experimental support is counted exactly once, no more, no less. While many interactions are shared among public repositories, none of them contains the complete known interactome for any model organism. In addition, the annotations of the same experimental result by different repositories often disagree. This brings up the issue of which annotation to keep while consolidating evidences that are the same. The iRefIndex database, including interactions from most popular repositories with a standardized protein nomenclature, represents a significant advance in all aspects, especially in comprehensiveness. However, iRefIndex aims to maintain all information/annotation from original sources and requires users to perform additional processing to fully achieve the aforementioned goals. To address issues with iRefIndex and to achieve our goals, we have developed ppiTrim, a script that processes iRefIndex to produce non-redundant, consistently annotated datasets of physical interactions. Our script proceeds in three stages: mapping all interactants to gene identifiers and removing all undesired raw interactions, deflating potentially expanded complexes, and reconciling for each interaction the annotation labels among different source databases. As an illustration, we have processed the three largest organismal datasets: yeast, human and fruitfly. While ppiTrim can resolve most apparent conflicts between different labelings, we also discovered some unresolvable disagreements mostly resulting from different annotation policies among repositories. URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/ppiTrim.html

  • 2 authors
·
Jul 7, 2011

Exploring the cloud of feature interaction scores in a Rashomon set

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.

  • 4 authors
·
May 17, 2023

Are You Learning Biological Signal or Shortcuts? Auditing and Mitigating Bias in Protein-Protein Interaction Datasets

Protein-protein interaction (PPI) databases do not faithfully reflect biological realities. Instead, they are influenced by study and technical biases that distort certain protein and interaction attributes. Machine learning models can exploit these as learning shortcuts if the negative dataset is not constructed with care. So far, the shortcuts introduced during PPI dataset construction have only been examined in isolation. Here, we systematically characterize both reported and, to our knowledge, previously unreported biases in PPI datasets that lead machine learning models to learn shortcuts instead of biological signal. We analyze HIPPIE, IntAct, and STRING, dedicated PPI databases, as well as two datasets derived from 3D-structural information in the Protein Data Bank (PDB). We show that random data splitting introduces strong topological shortcuts. When train-test protein overlap is removed, the resulting datasets still retain usable shortcuts stemming from self-interactions, taxonomic identity, and functional relatedness, whose prevalence interestingly depends on the data source. We further show that sampling negatives from a set of high-confidence non-interactors, an intuitively appealing choice, can amplify the shortcut stemming from functional relatedness. To detect and mitigate these biases, we provide an open Nextflow pipeline that combines similarity-aware, data-loss-minimizing dataset splitting with bias-minimizing negative sampling, both formulated as integer linear programs. Its key concept of quantifying biases to minimize them through optimization-based negative sampling can, in principle, be extended to any machine learning problem where the pool of negative candidates is much larger than the positives and is thus of interest also beyond PPI prediction.

  • 5 authors
·
Sep 8

Predicting Unseen Scientific Interactions: Conditional Flow Models Hallucinate Non-Additive Effects

Conditional generative models are increasingly used for scientific prediction beyond the direct training support. Yet scientific questions often concern whether one intervention changes the effect of another. Such interactions can be of primary interest while explaining little of the total variation, allowing models to appear accurate overall without recovering the relevant scientific effect. It remains unclear how these models learn interactions and when these successfully extrapolate to unseen conditions. We therefore study interaction recovery in flow-matching models using a physiological time-series simulator, drug dose-response data, combinatorial cell perturbations, and molecular conformer generations, where we separate recovery from hallucinated interaction structure. In the controlled setting, individual effects are learned much earlier than interactions and models hallucinate interactions where none exist. Across settings, we find qualitatively different generalization problems, with successful prediction depending on whether condition structure continues from observed to held-out targets. When it does, interactions are recoverable. If not, models can generate plausible responses while missing the interaction. We furthermore find that hallucinations increase as targets become less identifiable, and that successful interaction recovery in output space can fail under nonlinear readouts. Finally, we show that aggregate fidelity metrics can conceal whether models learn and extrapolate interactions.

  • 3 authors
·
Oct 13