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Publications
Interpretable deep learning architectures for improving drug response prediction performance: myth or reality?
Motivation: Recent advances in deep learning model development have enabled more accurate prediction of drug response in cancer. However, th… (see more)e black-box nature of these models still remains a hurdle in their adoption for precision cancer medicine. Recent efforts have focused on making these models interpretable by incorporating signaling pathway information in model architecture. While these models improve interpretability, it is unclear whether this higher interpretability comes at the cost of less accurate predictions, or a prediction improvement can also be obtained. Results: In this study, we comprehensively and systematically assessed four state-of-the-art interpretable models developed for drug response prediction to answer this question using three pathway collections. Our results showed that models that explicitly incorporate pathway information in the form of a latent layer perform worse compared to models that incorporate this information implicitly. Moreover, in most evaluation setups the best performance is achieved using a simple black-box model. In addition, replacing the signaling pathways with randomly generated pathways shows a comparable performance for the majority of these interpretable models. Our results suggest that new interpretable models are necessary to improve the drug response prediction performance. In addition, the current study provides different baseline models and evaluation setups necessary for such new models to demonstrate their superior prediction performance. Availability and Implementation: Implementation of all methods are provided in https://github.com/Emad-COMBINE-lab/InterpretableAI_for_DRP. Generated uniform datasets are in https://zenodo.org/record/7101665#.YzS79HbMKUk. Contact: amin.emad@mcgill.ca Supplementary Information: Online-only supplementary data is available at the journal’s website.
In this paper, we explore effective prompting techniques to enhance zero- and few-shot Visual Question Answering (VQA) performance in contem… (see more)porary Vision-Language Models (VLMs). Central to our investigation is the role of question templates in guiding VLMs to generate accurate answers. We identify that specific templates significantly influence VQA outcomes, underscoring the need for strategic template selection. Another pivotal aspect of our study is augmenting VLMs with image captions, providing them with additional visual cues alongside direct image features in VQA tasks. Surprisingly, this augmentation significantly improves the VLMs' performance in many cases, even though VLMs"see"the image directly! We explore chain-of-thought (CoT) reasoning and find that while standard CoT reasoning causes drops in performance, advanced methods like self-consistency can help recover it. Furthermore, we find that text-only few-shot examples enhance VLMs' alignment with the task format, particularly benefiting models prone to verbose zero-shot answers. Lastly, to mitigate the challenges associated with evaluating free-form open-ended VQA responses using string-matching based VQA metrics, we introduce a straightforward LLM-guided pre-processing technique to adapt the model responses to the expected ground-truth answer distribution. In summary, our research sheds light on the intricacies of prompting strategies in VLMs for VQA, emphasizing the synergistic use of captions, templates, and pre-processing to enhance model efficacy.
State space models (SSMs) have shown impressive results on tasks that require modeling long-range dependencies and efficiently scale to long… (see more) sequences owing to their subquadratic runtime complexity. Originally designed for continuous signals, SSMs have shown superior performance on a plethora of tasks, in vision and audio; however, SSMs still lag Transformer performance in Language Modeling tasks. In this work, we propose a hybrid layer named Block-State Transformer (BST), that internally combines an SSM sublayer for long-range contextualization, and a Block Transformer sublayer for short-term representation of sequences. We study three different, and completely parallelizable, variants that integrate SSMs and block-wise attention. We show that our model outperforms similar Transformer-based architectures on language modeling perplexity and generalizes to longer sequences. In addition, the Block-State Transformer demonstrates more than tenfold increase in speed at the layer level compared to the Block-Recurrent Transformer when model parallelization is employed.
Across a variety of ranking tasks, researchers use reciprocal rank to measure the effectiveness for users interested in exactly one relevant… (see more) item. Despite its widespread use, evidence suggests that reciprocal rank is brittle when discriminating between systems. This brittleness, in turn, is compounded in modern evaluation settings where current, high-precision systems may be difficult to distinguish. We address the lack of sensitivity of reciprocal rank by introducing and connecting it to the concept of best-case retrieval, an evaluation method focusing on assessing the quality of a ranking for the most satisfied possible user across possible recall requirements. This perspective allows us to generalize reciprocal rank and define a new preference-based evaluation we call lexicographic precision or lexiprecision. By mathematical construction, we ensure that lexiprecision preserves differences detected by reciprocal rank, while empirically improving sensitivity and robustness across a broad set of retrieval and recommendation tasks.
