Accurate 3D tracking in highly deformable scenes with occlusions and shadows can facilitate new applications in robotics, augmented reality, and generative AI. However, tracking under these conditions is extremely challenging due to the ambiguity that arises with large deformations, shadows, and occlusions. We introduce MD-Splatting, an approach for simultaneous 3D tracking and novel view synthesis, using video captures of a dynamic scene from various camera poses. MD-Splatting builds on recent advances in Gaussian splatting, a method that learns the properties of a large number of Gaussians for state-of-the-art and fast novel view synthesis. MD-Splatting learns a deformation function to project a set of Gaussians with non-metric, thus canonical, properties into metric space. The deformation function uses a neural-voxel encoding and a multilayer perceptron (MLP) to infer Gaussian position, rotation, and a shadow scalar. We enforce physics-inspired regularization terms based on local rigidity, conservation of momentum, and isometry, which leads to trajectories with smaller trajectory errors. MD-Splatting achieves high-quality 3D tracking on highly deformable scenes with shadows and occlusions. Compared to state-of-the-art, we improve 3D tracking by an average of 23.9 %, while simultaneously achieving high-quality novel view synthesis. With sufficient texture such as in scene 6, MD-Splatting achieves a median tracking error of 3.39 mm on a cloth of 1 x 1 meters in size. Project website: https://md-splatting.github.io/.

Graph auto-encoders are widely used to construct graph representations in Euclidean vector spaces. However, it has already been pointed out empirically that linear models on many tasks can outperform graph auto-encoders. In our work, we prove that the solution space induced by graph auto-encoders is a subset of the solution space of a linear map. This demonstrates that linear embedding models have at least the representational power of graph auto-encoders based on graph convolutional networks. So why are we still using nonlinear graph auto-encoders? One reason could be that actively restricting the linear solution space might introduce an inductive bias that helps improve learning and generalization. While many researchers believe that the nonlinearity of the encoder is the critical ingredient towards this end, we instead identify the node features of the graph as a more powerful inductive bias. We give theoretical insights by introducing a corresponding bias in a linear model and analyzing the change in the solution space. Our experiments are aligned with other empirical work on this question and show that the linear encoder can outperform the nonlinear encoder when using feature information.

The number of congenital syphilis cases in Japan this year has already set a new annual record high, according to data recently released by the National Institute of Infectious Diseases. As of Oct. 4, the annual count stood at 32, surpassing the previous annual record of 23 cases, set in 2019. Meanwhile, the overall number of syphilis cases in the country in 2023 came to 13,251 as of Nov. 19, topping the 2022 total of 13,228, which was the first figure above 10,000 since the current survey method was introduced in 1999. By prefecture, 3,244 cases were reported in Tokyo, 1,760 in Osaka, 829 in Fukuoka, 751 in Aichi and 607 in Hokkaido. While some people say that the current spread of syphilis is due to sexual intercourse between strangers who met through social media, the clear reason behind the spread has not yet been identified.

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics. Conventional methods, refined over decades, tackle this challenge in two steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models (LLM) in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have explored whether the same Transformer architecture can produce numerical representations for DNA sequences. Such models have shown early promise in tasks involving classification of short DNA sequences, such as the detection of coding vs non-coding regions, as well as the identification of enhancer and promoter sequences. Performance at sequence classification tasks does not, however, translate to sequence alignment, where it is necessary to conduct a genome-wide search to successfully align every read. We address this open problem by framing it as an Embed-Search-Align task. In this framework, a novel encoder model DNA-ESA generates representations of reads and fragments of the reference, which are projected into a shared vector space where the read-fragment distance is used as surrogate for alignment. In particular, DNA-ESA introduces: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. DNA-ESA is >97% accurate when aligning 250-length reads onto a human reference genome of 3 gigabases (single-haploid), far exceeds the performance of 6 recent DNA-Transformer model baselines and shows task transfer across chromosomes and species.

Determining suitable low-dimensional representations of complex high-dimensional data is a challenging task in numerous applications. Whether its preprocessing biological datasets prior to their analysis (Nguyen & Holmes, 2019), the visualisation of complex structure in single-cell sequencing data (Lähnemann et al., 2020), or the comparison of different manifold representations (Barannikov et al., 2022): an understanding of structural (dis)similarities is crucial, especially in the context of datasets that are ever-increasing in size and dimensionality. The primary assumption driving such analyses is the manifold hypothesis, which assumes that data is a (noisy) subsample from some unknown manifold. Operating under this assumption, manifold learning methods have made large advances in detecting complex structures in data, but they typically use local measures of the embedding quality, which are ultimately relying on local approximations of manifolds by k-nearest neighbour graphs. However, such approximations--which require specific parameter choices and thresholds--can have a substantial negative impact on both embedding results and the interpretation of evaluation scores. Moreover, countering the increasing popularity of non-linear dimensionality reduction methods that claim to preserve local and global structures, recent work (Chari & Pachter, 2023) sheds some doubt on the assumption that'good' embeddings should also faithfully preserve distances, while raising questions of how to measure the inevitable distortions introduced by representation learning. Thus, there is a need for novel methods in representation learning, which efficiently summarise data across varying levels of similarity, eliminating the need to rely on fixed neighbourhood graphs. Motivated by these considerations, we adopt a more general perspective that does not rely on manifold approximations. To this end, we propose a novel embedding quality measure based on metric space magnitude, a recently-proposed mathematical invariant that encapsulates numerous important geometric characteristics of metric spaces.

In many real-world applications, due to recent developments in the privacy landscape, training data may be aggregated to preserve the privacy of sensitive training labels. In the learning from label proportions (LLP) framework, the dataset is partitioned into bags of feature-vectors which are available only with the sum of the labels per bag. A further restriction, which we call learning from bag aggregates (LBA) is where instead of individual feature-vectors, only the (possibly weighted) sum of the feature-vectors per bag is available. We study whether such aggregation techniques can provide privacy guarantees under the notion of label differential privacy (label-DP) previously studied in for e.g. [Chaudhuri-Hsu'11, Ghazi et al.'21, Esfandiari et al.'22]. It is easily seen that naive LBA and LLP do not provide label-DP. Our main result however, shows that weighted LBA using iid Gaussian weights with $m$ randomly sampled disjoint $k$-sized bags is in fact $(\varepsilon, \delta)$-label-DP for any $\varepsilon > 0$ with $\delta \approx \exp(-\Omega(\sqrt{k}))$ assuming a lower bound on the linear-mse regression loss. Further, the $\ell_2^2$-regressor which minimizes the loss on the aggregated dataset has a loss within $\left(1 + o(1)\right)$-factor of the optimum on the original dataset w.p. $\approx 1 - exp(-\Omega(m))$. We emphasize that no additive label noise is required. The analogous weighted-LLP does not however admit label-DP. Nevertheless, we show that if additive $N(0, 1)$ noise can be added to any constant fraction of the instance labels, then the noisy weighted-LLP admits similar label-DP guarantees without assumptions on the dataset, while preserving the utility of Lipschitz-bounded neural mse-regression tasks. Our work is the first to demonstrate that label-DP can be achieved by randomly weighted aggregation for regression tasks, using no or little additive noise.

Machine learning models -- including prominent zero-shot models -- are often trained on datasets whose labels are only a small proportion of a larger label space. Such spaces are commonly equipped with a metric that relates the labels via distances between them. We propose a simple approach to exploit this information to adapt the trained model to reliably predict new classes -- or, in the case of zero-shot prediction, to improve its performance -- without any additional training. Our technique is a drop-in replacement of the standard prediction rule, swapping argmax with the Fr\'echet mean. We provide a comprehensive theoretical analysis for this approach, studying (i) learning-theoretic results trading off label space diameter, sample complexity, and model dimension, (ii) characterizations of the full range of scenarios in which it is possible to predict any unobserved class, and (iii) an optimal active learning-like next class selection procedure to obtain optimal training classes for when it is not possible to predict the entire range of unobserved classes. Empirically, using easily-available external metrics, our proposed approach, Loki, gains up to 29.7% relative improvement over SimCLR on ImageNet and scales to hundreds of thousands of classes. When no such metric is available, Loki can use self-derived metrics from class embeddings and obtains a 10.5% improvement on pretrained zero-shot models such as CLIP.

In recent years, graph neural networks (GNNs) have become a popular tool for solving various problems over graphs. In these models, the link structure of the graph is typically exploited and nodes' embeddings are iteratively updated based on adjacent nodes. Nodes' contents are used solely in the form of feature vectors, served as nodes' first-layer embeddings. However, the filters or convolutions, applied during iterations/layers to these initial embeddings lead to their impact diminish and contribute insignificantly to the final embeddings. In order to address this issue, in this paper we propose augmenting nodes' embeddings by embeddings generating from their content, at higher GNN layers. More precisely, we propose models wherein a structural embedding using a GNN and a content embedding are computed for each node. These two are combined using a combination layer to form the embedding of a node at a given layer. We suggest methods such as using an auto-encoder or building a content graph, to generate content embeddings. In the end, by conducting experiments over several real-world datasets, we demonstrate the high accuracy and performance of our models.

The overarching objective of this paper is two-fold. First, to explore model-based approaches to characterize the primary cause of the noise. in the RE dataset TACRED Second, to identify the potentially noisy instances. Towards the first objective, we analyze predictions and performance of state-of-the-art (SOTA) models to identify the root cause of noise in the dataset. Our analysis of TACRED shows that the majority of the noise in the dataset originates from the instances labeled as no-relation which are negative examples. For the second objective, we explore two nearest-neighbor-based strategies to automatically identify potentially noisy examples for elimination and reannotation. Our first strategy, referred to as Intrinsic Strategy (IS), is based on the assumption that positive examples are clean. Thus, we have used false-negative predictions to identify noisy negative examples. Whereas, our second approach, referred to as Extrinsic Strategy, is based on using a clean subset of the dataset to identify potentially noisy negative examples. Finally, we retrained the SOTA models on the eliminated and reannotated dataset. Our empirical results based on two SOTA models trained on TACRED-E following the IS show an average 4% F1-score improvement, whereas reannotation (TACRED-R) does not improve the original results. However, following ES, SOTA models show the average F1-score improvement of 3.8% and 4.4% when trained on respective eliminated (TACRED-EN) and reannotated (TACRED-RN) datasets respectively. We further extended the ES for cleaning positive examples as well, which resulted in an average performance improvement of 5.8% and 5.6% for the eliminated (TACRED-ENP) and reannotated (TACRED-RNP) datasets respectively.

Problems involving geometric data arise in physics, chemistry, robotics, computer vision, and many other fields. Such data can take numerous forms, for instance points, direction vectors, translations, or rotations, but to date there is no single architecture that can be applied to such a wide variety of geometric types while respecting their symmetries. In this paper we introduce the Geometric Algebra Transformer (GATr), a general-purpose architecture for geometric data. GATr represents inputs, outputs, and hidden states in the projective geometric (or Clifford) algebra, which offers an efficient 16-dimensional vector-space representation of common geometric objects as well as operators acting on them. GATr is equivariant with respect to E(3), the symmetry group of 3D Euclidean space. As a Transformer, GATr is versatile, efficient, and scalable. We demonstrate GATr in problems from n-body modeling to wall-shear-stress estimation on large arterial meshes to robotic motion planning. GATr consistently outperforms both non-geometric and equivariant baselines in terms of error, data efficiency, and scalability.