Semantic segmentation of electron microscopy (EM) images of biological samples remains a challenge in the life sciences. EM data captures details of biological structures, sometimes with such complexity that even human observers can find it overwhelming. We introduce ϵ-Seg, a method based on hierarchical variational autoencoders (HVAES), employing center-region masking, sparse label contrastive learning (CL), a Gaussian mixture model (GMM) prior, and clustering-free label prediction. Center-region masking and the inpainting loss encourage the model to learn robust and representative embeddings to distinguish the desired classes, even if training labels are sparse (0.05% of the total image data or less). For optimal performance, we employ CL and a GMM prior to shape the latent space of the HVAE such that encoded input patches tend to cluster w.r.t. the semantic classes we wish to distinguish. Finally, instead of clustering latent embeddings for semantic segmentation, we propose a MLP semantic segmentation head to directly predict class labels from latent embeddings. We show empirical results of ϵ-Seg and baseline methods on 2dense EM datasets of biological tissues and demonstrate the applicability of our method also on fluorescence microscopy data. Our results show that ϵ-Seg is capable of achieving competitive sparsely-supervised segmentation results on complex biological image data, even if only limited amounts of training labels are available.

The urban environment is characterized by complex spatio-temporal dynamics arising from diverse human activities and interactions. Effectively modeling these dynamics is essential for understanding and optimizing urban systems. In this work, we introduce UrbanDiT, a foundation model for open-world urban spatiotemporal learning that successfully scales up diffusion transformers in this field.

Causal inference is essential for developing and evaluating medical interventions, yet real-world medical datasets are often difficult to access due to regulatory barriers. This makes synthetic data a potentially valuable asset that enables these medical analyses, along with the development of new inference methods themselves. Generative models can produce synthetic data that closely approximate real data distributions, yet existing methods do not consider the unique challenges that downstream causal inference tasks, and specifically those focused on treatments, pose. We establish a set of desiderata that synthetic data containing treatments should satisfy to maximise downstream utility: preservation of (i) the covariate distribution, (ii) the treatment assignment mechanism, and (iii) the outcome generation mechanism. Based on these desiderata, we propose a set of evaluation metrics to assess such synthetic data. Finally, we present STEAM: a novel method for generating Synthetic data for Treatment Effect Analysis in Medicine that mimics the data-generating process of data containing treatments and optimises for our desiderata. We empirically demonstrate that STEAM achieves state-of-the-art performance across our metrics as compared to existing generative models, particularly as the complexity of the true data-generating process increases.

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Modern tokenizers employ deterministic algorithms to map text into a single "canonical" token sequence, yet the same string can be encoded as many noncanonical tokenizations using the tokenizer vocabulary. In this work, we investigate the robustness of LMs to text encoded with non-canonical tokenizations entirely unseen during training. Surprisingly, when evaluated across 20 benchmarks, we find that instruction-tuned models retain up to 93.4% of their original performance when given a randomly sampled tokenization, and 90.8% with character-level tokenization. We see that overall stronger models tend to be more robust, and robustness diminishes as the tokenization departs farther from the canonical form. Motivated by these results, we then identify settings where non-canonical tokenization schemes can improve performance, finding that character-level segmentation improves string manipulation and code understanding tasks by up to +14%, and right-aligned digit grouping enhances large-number arithmetic by +33%. Finally, we investigate the source of this robustness, finding that it arises in the instructiontuning phase. We show that while both base and post-trained models grasp the semantics of non-canonical tokenizations (perceiving them as containing misspellings), base models try to mimic the imagined mistakes and degenerate into nonsensical output, while post-trained models are committed to fluent responses. Overall, our findings suggest that models are less tied to their tokenizer than previously believed, and demonstrate the promise of intervening on tokenization at inference time to boost performance.1

Estimating heterogeneous treatment effects (HTEs) is crucial for personalized decision-making. However, this task is challenging in survival analysis, which includes time-to-event data with censored outcomes (e.g., due to study dropout). In this paper, we propose a toolbox of orthogonal survival learners to estimate HTEs from time-to-event data under censoring. Our learners have three main advantages: (i) we show that learners from our toolbox are guaranteed to be orthogonal and thus robust with respect to nuisance estimation errors; (ii) our toolbox allows for incorporating a custom weighting function, which can lead to robustness against different types of low overlap, and (iii) our learners are modelagnostic (i.e., they can be combined with arbitrary machine learning models). We instantiate the learners from our toolbox using several weighting functions and, as a result, propose various neural orthogonal survival learners. Some of these coincide with existing survival learners (including survival versions of the DRand R-learner), while others are novel and further robust w.r.t.

Autonomous vehicles rely on detailed and accurate environmental information to operate safely. High definition (HD) maps offer a promising solution, but their high maintenance cost poses a significant barrier to scalable deployment. This challenge is addressed by online HD map construction methods, which generate local HD maps from live sensor data. However, these methods are inherently limited by the short perception range of onboard sensors. To overcome this limitation and improve general performance, recent approaches have explored the use of standard definition (SD) maps as prior, which are significantly easier to maintain.

Despite the success of Vision-Language Models (VLMs) like CLIP in aligning vision and language, their proficiency in detailed, fine-grained visual comprehension remains a key challenge. We present CLIP-IN, a novel framework that bolsters CLIP's fine-grained perception through two core innovations. Firstly, we leverage instruction-editing datasets, originally designed for image manipulation, as a unique source of hard negative image-text pairs. Coupled with a symmetric hard negative contrastive loss, this enables the model to effectively distinguish subtle visual-semantic differences. Secondly, CLIP-IN incorporates long descriptive captions, utilizing rotary positional encodings to capture rich semantic context often missed by standard CLIP. Our experiments demonstrate that CLIP-IN achieves substantial gains on the MMVP benchmark and various fine-grained visual recognition tasks, without compromising robust zero-shot performance on broader classification and retrieval tasks. Critically, integrating CLIP-IN's visual representations into Multimodal Large Language Models significantly reduces visual hallucinations and enhances reasoning abilities. This work underscores the considerable potential of synergizing targeted, instruction-based contrastive learning with comprehensive descriptive information to elevate the fine-grained understanding of VLMs.

Current text-to-image diffusion generation typically employs complete-text conditioning. Due to the intricate syntax, diffusion transformers (DiTs) inherently suffer from a comprehension defect of complete-text captions. One-fly complete-text input either overlooks critical semantic details or causes semantic confusion by simultaneously modeling diverse semantic primitive types. To mitigate this defect of DiTs, we propose a novel split-text conditioning framework named DiT-ST. This framework converts a complete-text caption into a split-text caption, a collection of simplified sentences, to explicitly express various semantic primitives and their interconnections. The split-text caption is then injected into different denoising stages of DiT-ST in a hierarchical and incremental manner.

Recent interest in building foundation models for knowledge graphs has highlighted a fundamental challenge: knowledge graph data is scarce. The best-known knowledge graphs are primarily human-labeled, created by pattern-matching, or extracted using early NLP techniques. While human-generated knowledge graphs are in short supply, automatically extracted ones are of questionable quality. We present KGGen, a novel text-to-knowledge-graph generator that uses language models to extract high-quality graphs from plain text with a novel entity resolution approach that clusters related entities, significantly reducing the sparsity problem that plagues existing extractors. Unlike other KG generators, KGGen clusters and de-duplicates related entities to reduce sparsity in extracted KGs. Along with KGGen, we release Measure of Information in Nodes and Edges (MINE), the first benchmark to test an extractor's ability to produce a useful KG from plain text. We benchmark our new tool against leading existing generators such as Microsoft's GraphRAG; we achieve comparable retrieval accuracy on the generated graphs and better information retention.