K-Paths: Reasoning over Graph Paths for Drug Repurposing and Drug Interaction Prediction

Drug discovery is a complex and time-intensive process that requires identifying and validating new therapeutic candidates. Computational approaches using large-scale biomedical knowledge graphs (KGs) offer a promising solution to accelerate this process. However, extracting meaningful insights from large-scale KGs remains challenging due to the complexity of graph traversal. Existing subgraph-based methods are tailored to graph neural networks (GNNs), making them incompatible with other models, such as large language models (LLMs). We introduce K-Paths, a retrieval framework that extracts structured, diverse, and biologically meaningful paths from KGs. Integrating these paths enables LLMs and GNNs to effectively predict unobserved drug-drug and drug-disease interactions. Unlike traditional path-ranking approaches, K-Paths retrieves and transforms paths into a structured format that LLMs can directly process, facilitating explainable reasoning. K-Paths employs a diversity-aware adaptation of Yen's algorithm to retrieve the K shortest loopless paths between entities in an interaction query, prioritizing biologically relevant and diverse relationships. Our experiments on benchmark datasets show that K-Paths improves the zero-shot performance of Llama 8.1B's F1-score by 12.45 points on drug repurposing and 13.42 points on interaction severity prediction. We also show that Llama 70B achieves F1-score gains of 6.18 and 8.46 points, respectively. K-Paths also improves the supervised training efficiency of EmerGNN, a state-of-the-art GNN, by reducing KG size by 90% while maintaining strong predictive performance. Beyond its scalability and efficiency, K-Paths uniquely bridges the gap between KGs and LLMs, providing explainable rationales for predicted interactions. These capabilities show that K-Paths is a valuable tool for efficient data-driven drug discovery.

$100K or 100 Days: Trade-offs when Pre-Training with Academic Resources

Pre-training is notoriously compute-intensive and academic researchers are notoriously under-resourced. It is, therefore, commonly assumed that academics can't pre-train models. In this paper, we seek to clarify this assumption. We first survey academic researchers to learn about their available compute and then empirically measure the time to replicate models on such resources. We introduce a benchmark to measure the time to pre-train models on given GPUs and also identify ideal settings for maximizing training speed. We run our benchmark on a range of models and academic GPUs, spending 2,000 GPU-hours on our experiments. Our results reveal a brighter picture for academic pre-training: for example, although Pythia-1B was originally trained on 64 GPUs for 3 days, we find it is also possible to replicate this model (with the same hyper-parameters) in 3x fewer GPU-days: i.e. on 4 GPUs in 18 days. We conclude with a cost-benefit analysis to help clarify the trade-offs between price and pre-training time. We believe our benchmark will help academic researchers conduct experiments that require training larger models on more data. We fully release our codebase at: https://github.com/apoorvkh/academic-pretraining.

Planetarium: A Rigorous Benchmark for Translating Text to Structured Planning Languages

Many recent works have explored using language models for planning problems. One line of research focuses on translating natural language descriptions of planning tasks into structured planning languages, such as the planning domain definition language (PDDL). While this approach is promising, accurately measuring the quality of generated PDDL code continues to pose significant challenges. First, generated PDDL code is typically evaluated using planning validators that check whether the problem can be solved with a planner. This method is insufficient because a language model might generate valid PDDL code that does not align with the natural language description of the task. Second, existing evaluation sets often have natural language descriptions of the planning task that closely resemble the ground truth PDDL, reducing the challenge of the task. To bridge this gap, we introduce \benchmarkName, a benchmark designed to evaluate language models' ability to generate PDDL code from natural language descriptions of planning tasks. We begin by creating a PDDL equivalence algorithm that rigorously evaluates the correctness of PDDL code generated by language models by flexibly comparing it against a ground truth PDDL. Then, we present a dataset of $132,037$ text-to-PDDL pairs across 13 different tasks, with varying levels of difficulty. Finally, we evaluate several API-access and open-weight language models that reveal this task's complexity. For example, $87.6\%$ of the PDDL problem descriptions generated by GPT-4o are syntactically parseable, $82.2\%$ are valid, solve-able problems, but only $35.1\%$ are semantically correct, highlighting the need for a more rigorous benchmark for this problem.

Preference Tuning For Toxicity Mitigation Generalizes Across Languages

Detoxifying multilingual Large Language Models (LLMs) has become crucial due to their increasing global use. In this work, we explore zero-shot cross-lingual generalization of preference tuning in detoxifying LLMs. Unlike previous studies that show limited cross-lingual generalization for other safety tasks, we demonstrate that Direct Preference Optimization (DPO) training with only English data can significantly reduce toxicity in multilingual open-ended generations. For example, the probability of mGPT-1.3B generating toxic continuations drops from 46.8% to 3.9% across 17 different languages after training. Our results also extend to other multilingual LLMs, such as BLOOM, Llama3, and Aya-23. Using mechanistic interpretability tools like causal intervention and activation analysis, we identified the dual multilinguality property of MLP layers in LLMs, which explains the cross-lingual generalization of DPO. Finally, we show that bilingual sentence retrieval can predict the cross-lingual transferability of DPO preference tuning.

If CLIP Could Talk: Understanding Vision-Language Model Representations Through Their Preferred Concept Descriptions

Recent works often assume that Vision-Language Model (VLM) representations are based on visual attributes like shape. However, it is unclear to what extent VLMs prioritize this information to represent concepts. We propose Extract and Explore (EX2), a novel approach to characterize important textual features for VLMs. EX2 uses reinforcement learning to align a large language model with VLM preferences and generates descriptions that incorporate the important features for the VLM. Then, we inspect the descriptions to identify the features that contribute to VLM representations. We find that spurious descriptions have a major role in VLM representations despite providing no helpful information, e.g., Click to enlarge photo of CONCEPT. More importantly, among informative descriptions, VLMs rely significantly on non-visual attributes like habitat to represent visual concepts. Also, our analysis reveals that different VLMs prioritize different attributes in their representations. Overall, we show that VLMs do not simply match images to scene descriptions and that non-visual or even spurious descriptions significantly influence their representations.

Learning to Generate Instruction Tuning Datasets for Zero-Shot Task Adaptation

We introduce Bonito, an open-source model for conditional task generation: the task of converting unannotated text into task-specific training datasets for instruction tuning. Our goal is to enable zero-shot task adaptation of large language models on users' specialized, private data. We train Bonito on a new large-scale dataset with 1.65M examples created by remixing existing instruction tuning datasets into meta-templates. The meta-templates for a dataset produce training examples where the input is the unannotated text and the task attribute and the output consists of the instruction and the response. We use Bonito to generate synthetic tasks for seven datasets from specialized domains across three task types -- yes-no question answering, extractive question answering, and natural language inference -- and adapt language models. We show that Bonito significantly improves the average performance of pretrained and instruction tuned models over the de facto self supervised baseline. For example, adapting Mistral-Instruct-v2 and instruction tuned variants of Mistral and Llama2 with Bonito improves the strong zero-shot performance by 22.1 F1 points whereas the next word prediction objective undoes some of the benefits of instruction tuning and reduces the average performance by 0.8 F1 points. We conduct additional experiments with Bonito to understand the effects of the domain, the size of the training set, and the choice of alternative synthetic task generators. Overall, we show that learning with synthetic instruction tuning datasets is an effective way to adapt language models to new domains. The model, dataset, and code are available at https://github.com/BatsResearch/bonito.

LexC-Gen: Generating Data for Extremely Low-Resource Languages with Large Language Models and Bilingual Lexicons

Data scarcity in low-resource languages can be addressed with word-to-word translations from labeled task data in high-resource languages using bilingual lexicons. However, bilingual lexicons often have limited lexical overlap with task data, which results in poor translation coverage and lexicon utilization. We propose lexicon-conditioned data generation (LexC-Gen), a method that generates low-resource-language classification task data at scale. Specifically, LexC-Gen first uses high-resource-language words from bilingual lexicons to generate lexicon-compatible task data, and then it translates them into low-resource languages with bilingual lexicons via word translation. Across 17 extremely low-resource languages, LexC-Gen generated data is competitive with expert-translated gold data, and yields on average 5.6 and 8.9 points improvement over existing lexicon-based word translation methods on sentiment analysis and topic classification tasks respectively. We show that conditioning on bilingual lexicons is the key component of LexC-Gen. LexC-Gen is also practical -- it only needs a single GPU to generate data at scale. It works well with open-access LLMs, and its cost is one-fifth of the cost of GPT4-based multilingual data generation.

Leveraging Large Language Models for Structure Learning in Prompted Weak Supervision

Prompted weak supervision (PromptedWS) applies pre-trained large language models (LLMs) as the basis for labeling functions (LFs) in a weak supervision framework to obtain large labeled datasets. We further extend the use of LLMs in the loop to address one of the key challenges in weak supervision: learning the statistical dependency structure among supervision sources. In this work, we ask the LLM how similar are these prompted LFs. We propose a Structure Refining Module, a simple yet effective first approach based on the similarities of the prompts by taking advantage of the intrinsic structure in the embedding space. At the core of Structure Refining Module are Labeling Function Removal (LaRe) and Correlation Structure Generation (CosGen). Compared to previous methods that learn the dependencies from weak labels, our method finds the dependencies which are intrinsic to the LFs and less dependent on the data. We show that our Structure Refining Module improves the PromptedWS pipeline by up to 12.7 points on the benchmark tasks. We also explore the trade-offs between efficiency and performance with comprehensive ablation experiments and analysis. Code for this project can be found in https://github.com/BatsResearch/su-bigdata23-code.

Follow-Up Differential Descriptions: Language Models Resolve Ambiguities for Image Classification

A promising approach for improving the performance of vision-language models like CLIP for image classification is to extend the class descriptions (i.e., prompts) with related attributes, e.g., using brown sparrow instead of sparrow. However, current zero-shot methods select a subset of attributes regardless of commonalities between the target classes, potentially providing no useful information that would have helped to distinguish between them. For instance, they may use color instead of bill shape to distinguish between sparrows and wrens, which are both brown. We propose Follow-up Differential Descriptions (FuDD), a zero-shot approach that tailors the class descriptions to each dataset and leads to additional attributes that better differentiate the target classes. FuDD first identifies the ambiguous classes for each image, and then uses a Large Language Model (LLM) to generate new class descriptions that differentiate between them. The new class descriptions resolve the initial ambiguity and help predict the correct label. In our experiments, FuDD consistently outperforms generic description ensembles and naive LLM-generated descriptions on 12 datasets. We show that differential descriptions are an effective tool to resolve class ambiguities, which otherwise significantly degrade the performance. We also show that high quality natural language class descriptions produced by FuDD result in comparable performance to few-shot adaptation methods.

Low-Resource Languages Jailbreak GPT-4

AI safety training and red-teaming of large language models (LLMs) are measures to mitigate the generation of unsafe content. Our work exposes the inherent cross-lingual vulnerability of these safety mechanisms, resulting from the linguistic inequality of safety training data, by successfully circumventing GPT-4's safeguard through translating unsafe English inputs into low-resource languages. On the AdvBenchmark, GPT-4 engages with the unsafe translated inputs and provides actionable items that can get the users towards their harmful goals 79% of the time, which is on par with or even surpassing state-of-the-art jailbreaking attacks. Other high-/mid-resource languages have significantly lower attack success rate, which suggests that the cross-lingual vulnerability mainly applies to low-resource languages. Previously, limited training on low-resource languages primarily affects speakers of those languages, causing technological disparities. However, our work highlights a crucial shift: this deficiency now poses a risk to all LLMs users. Publicly available translation APIs enable anyone to exploit LLMs' safety vulnerabilities. Therefore, our work calls for a more holistic red-teaming efforts to develop robust multilingual safeguards with wide language coverage.