Large-scale biological discovery requires integrating massive, heterogeneous datasets like those from the JUMP Cell Painting consortium, but technical batch effects and a lack of generalizable models remain critical roadblocks. To address this, we introduce CellPainTR, a Transformer-based architecture designed to learn foundational representations of cellular morphology that are robust to batch effects. Unlike traditional methods that require retraining on new data, CellPainTR's design, featuring source-specific context tokens, allows for effective out-of-distribution (OOD) generalization to entirely unseen datasets without fine-tuning. We validate CellPainTR on the large-scale JUMP dataset, where it outperforms established methods like ComBat and Harmony in both batch integration and biological signal preservation. Critically, we demonstrate its robustness through a challenging OOD task on the unseen Bray et al. dataset, where it maintains high performance despite significant domain and feature shifts. Our work represents a significant step towards creating truly foundational models for image-based profiling, enabling more reliable and scalable cross-study biological analysis.

Large language models (LLMs) have showcased impressive multilingual machine translation ability. However, unlike encoder-decoder style models, decoder-only LLMs lack an explicit alignment between source and target contexts. Analyzing contribution scores during generation processes revealed that LLMs can be biased towards previously generated tokens over corresponding source tokens, leading to unfaithful translations. To address this issue, we propose to encourage LLMs to pay more attention to the source context from both source and target perspectives in zeroshot prompting: 1) adjust source context attention weights; 2) suppress irrelevant target prefix influence; Additionally, we propose 3) avoiding over-reliance on the target prefix in instruction tuning. Experimental results from both human-collected unfaithfulness test sets focusing on LLM-generated unfaithful translations and general test sets, verify our methods' effectiveness across multiple language pairs. Further human evaluation shows our method's efficacy in reducing hallucinatory translations and facilitating faithful translation generation.

Standard context-aware neural machine translation (NMT) typically relies on parallel document-level data, exploiting both source and target contexts. Concatenation-based approaches in particular, still a strong baseline for document-level NMT, prepend source and/or target context sentences to the sentences to be translated, with model variants that exploit equal amounts of source and target data on each side achieving state-of-the-art results. In this work, we investigate whether target data should be further promoted within standard concatenation-based approaches, as most document-level phenomena rely on information that is present on the target language side. We evaluate novel concatenation-based variants where the target context is prepended to the source language, either in isolation or in combination with the source context. Experimental results in English-Russian and Basque-Spanish show that including target context in the source leads to large improvements on target language phenomena. On source-dependent phenomena, using only target language context in the source achieves parity with state-of-the-art concatenation approaches, or slightly underperforms, whereas combining source and target context on the source side leads to significant gains across the board.

Recent studies show that deep reinforcement learning (DRL) agents tend to overfit to the task on which they were trained and fail to adapt to minor environment changes. To expedite learning when transferring to unseen tasks, we propose a novel approach to representing the current task using reward machines (RMs), state machine abstractions that induce subtasks based on the current task's rewards and dynamics. Our method provides agents with symbolic representations of optimal transitions from their current abstract state and rewards them for achieving these transitions. These representations are shared across tasks, allowing agents to exploit knowledge of previously encountered symbols and transitions, thus enhancing transfer. Empirical results show that our representations improve sample efficiency and few-shot transfer in a variety of domains.

Large language models (LLMs) with billions of parameters and pretrained on massive amounts of data are now capable of near or better than state-of-the-art performance in a variety of downstream natural language processing tasks. Neural machine translation (NMT) is one such task that LLMs have been applied to with great success. However, little research has focused on applying LLMs to the more difficult subset of NMT called simultaneous translation (SimulMT), where translation begins before the entire source context is available to the model. In this paper, we address key challenges facing LLMs fine-tuned for SimulMT, validate classical SimulMT concepts and practices in the context of LLMs, explore adapting LLMs that are fine-tuned for NMT to the task of SimulMT, and introduce Simul-LLM, the first open-source fine-tuning and evaluation pipeline development framework for LLMs focused on SimulMT.

Humans learn about objects via interaction and using multiple perceptions, such as vision, sound, and touch. While vision can provide information about an object's appearance, non-visual sensors, such as audio and haptics, can provide information about its intrinsic properties, such as weight, temperature, hardness, and the object's sound. Using tools to interact with objects can reveal additional object properties that are otherwise hidden (e.g., knives and spoons can be used to examine the properties of food, including its texture and consistency). Robots can use tools to interact with objects and gather information about their implicit properties via non-visual sensors. However, a robot's model for recognizing objects using a tool-mediated behavior does not generalize to a new tool or behavior due to differing observed data distributions. To address this challenge, we propose a framework to enable robots to transfer implicit knowledge about granular objects across different tools and behaviors. The proposed approach learns a shared latent space from multiple robots' contexts produced by respective sensory data while interacting with objects using tools. We collected a dataset using a UR5 robot that performed 5,400 interactions using 6 tools and 6 behaviors on 15 granular objects and tested our method on cross-tool and cross-behavioral transfer tasks. Our results show the less experienced target robot can benefit from the experience gained from the source robot and perform recognition on a set of novel objects. We have released the code, datasets, and additional results: https://github.com/gtatiya/Tool-Knowledge-Transfer.

Internet links enable users to deepen their understanding of a topic by providing convenient access to related information. However, the majority of links are unanchored -- they link to a target webpage as a whole, and readers may expend considerable effort localizing the specific parts of the target webpage that enrich their understanding of the link's source context. To help readers effectively find information in linked webpages, we introduce the task of anchor prediction, where the goal is to identify the specific part of the linked target webpage that is most related to the source linking context. We release the AuthorAnchors dataset, a collection of 34K naturally-occurring anchored links, which reflect relevance judgments by the authors of the source article. To model reader relevance judgments, we annotate and release ReaderAnchors, an evaluation set of anchors that readers find useful. Our analysis shows that effective anchor prediction often requires jointly reasoning over lengthy source and target webpages to determine their implicit relations and identify parts of the target webpage that are related but not redundant. We benchmark a performant T5-based ranking approach to establish baseline performance on the task, finding ample room for improvement.

Context-aware neural machine translation aims to use the document-level context to improve translation quality. However, not all words in the context are helpful. The irrelevant or trivial words may bring some noise and distract the model from learning the relationship between the current sentence and the auxiliary context. To mitigate this problem, we propose a novel end-to-end encoder-decoder model with a layer-wise selection mechanism to sift and refine the long document context. To verify the effectiveness of our method, extensive experiments and extra quantitative analysis are conducted on four document-level machine translation benchmarks. The experimental results demonstrate that our model significantly outperforms previous models on all datasets via the soft selection mechanism.