DNA-encoded libraries (DELs) are a powerful approach for rapidly screening large numbers of diverse compounds. One of the key challenges in using DELs is library design, which involves choosing the building blocks that will be combinatorially combined to produce the final library. In this paper we consider the task of protein-protein interaction (PPI) biased DEL design. To this end, we evaluate several machine learning algorithms on the PPI modulation task and use them as a reward for the proposed GFlowNet-based generative approach. We additionally investigate the possibility of using structural information about building blocks to design a hierarchical action space for the GFlowNet. The observed results indicate that GFlowNets are a promising approach for generating diverse combinatorial library candidates.

Featurizing microscopy images for use in biological research remains a significant challenge, especially for large-scale experiments spanning millions of images. This work explores the scaling properties of weakly supervised classifiers and self-supervised masked autoencoders (MAEs) when training with increasingly larger model backbones and microscopy datasets. Our results show that ViT-based MAEs outperform weakly supervised classifiers on a variety of tasks, achieving as much as a 11.5% relative improvement when recalling known biological relationships curated from public databases. Additionally, we develop a new channel-agnostic MAE architecture (CA-MAE) that allows for inputting images of different numbers and orders of channels at inference time. We demonstrate that CA-MAEs effectively generalize by inferring and evaluating on a microscopy image dataset (JUMP-CP) generated under different experimental conditions with a different channel structure than our pretraining data (RPI-93M). Our findings motivate continued research into scaling self-supervised learning on microscopy data in order to create powerful foundation models of cellular biology that have the potential to catalyze advancements in drug discovery and beyond.

Citation Text Generation (CTG) is a task in natural language processing (NLP) that aims to produce text that accurately cites or references a cited document within a source document. In CTG, the generated text draws upon contextual cues from both the source document and the cited paper, ensuring accurate and relevant citation information is provided. Previous work in the field of citation generation is mainly based on the text summarization of documents. Following this, this paper presents a framework, and a comparative study to demonstrate the use of Large Language Models (LLMs) for the task of citation generation. Also, we have shown the improvement in the results of citation generation by incorporating the knowledge graph relations of the papers in the prompt for the LLM to better learn the relationship between the papers. To assess how well our model is performing, we have used a subset of standard S2ORC dataset, which only consists of computer science academic research papers in the English Language. Vicuna performs best for this task with 14.15 Meteor, 12.88 Rouge-1, 1.52 Rouge-2, and 10.94 Rouge-L. Also, Alpaca performs best, and improves the performance by 36.98% in Rouge-1, and 33.14% in Meteor by including knowledge graphs.

This work identifies 18 foundational challenges in assuring the alignment and safety of large language models (LLMs). These challenges are organized into three different categories: scientific understanding of LLMs, development and deployment methods, and sociotechnical challenges. Based on the identified challenges, we pose $200+$ concrete research questions.

A teacher's knowledge base consists of knowledge of mathematics content, knowledge of student epistemology, and pedagogical knowledge. It has severe implications on the understanding of student's knowledge of content, and the learning context in general. The necessity to formalize the different content knowledge in approximate senses is recognized in the education research literature. A related problem is that of coherent formalizability. Existing responsive or smart AI-based software systems do not concern themselves with meaning, and trained ones are replete with their own issues. In the present research, many issues in modeling teachers' understanding of content are identified, and a two-tier rough set-based model is proposed by the present author for the purpose of developing software that can aid the varied tasks of a teacher. The main advantage of the proposed approach is in its ability to coherently handle vagueness, granularity and multi-modality. An extended example to equational reasoning is used to demonstrate these. The paper is meant for rough set researchers intending to build logical models or develop meaning-aware AI-software to aid teachers, and education research experts.

In this paper, we study the embedded feature selection problem in linear Support Vector Machines (SVMs), in which a cardinality constraint is employed, leading to a fully explainable selection model. The problem is NP-hard due to the presence of the cardinality constraint, even though the original linear SVM amounts to a problem solvable in polynomial time. To handle the hard problem, we first introduce two mixed-integer formulations for which novel SDP relaxations are proposed. Exploiting the sparsity pattern of the relaxations, we decompose the problems and obtain equivalent relaxations in a much smaller cone, making the conic approaches scalable. To make the best usage of the decomposed relaxations, we propose heuristics using the information of its optimal solution. Moreover, an exact procedure is proposed by solving a sequence of mixed-integer decomposed SDPs. Numerical results on classical benchmarking datasets are reported, showing the efficiency and effectiveness of our approach.

As the rapidly advancing domain of natural language processing (NLP), large language models (LLMs) have emerged as powerful tools for interpreting human commands and generating text across various tasks. Nonetheless, the resilience of LLMs to handle text containing inherent errors, stemming from human interactions and collaborative systems, has not been thoroughly explored. Our study investigates the resilience of LLMs against five common types of disruptions including 1) ASR (Automatic Speech Recognition) errors, 2) OCR (Optical Character Recognition) errors, 3) grammatical mistakes, 4) typographical errors, and 5) distractive content. We aim to investigate how these models react by deliberately embedding these errors into instructions. Our findings reveal that while some LLMs show a degree of resistance to certain types of noise, their overall performance significantly suffers. This emphasizes the importance of further investigation into enhancing model resilience. In response to the observed decline in performance, our study also evaluates a "re-pass" strategy, designed to purify the instructions of noise before the LLMs process them. Our analysis indicates that correcting noisy instructions, particularly for open-source LLMs, presents significant challenges.

During inference for transformer-based large language models (LLM), prefilling is the computation of the key-value (KV) cache for input tokens in the prompt prior to autoregressive generation. For longer input prompt lengths, prefilling will incur a significant overhead on decoding time. In this work, we highlight the following pitfall of prefilling: for batches containing high-varying prompt lengths, significant computation is wasted by the standard practice of padding sequences to the maximum length. As LLMs increasingly support longer context lengths, potentially up to 10 million tokens, variations in prompt lengths within a batch become more pronounced. To address this, we propose prepacking, a simple yet effective method to optimize prefilling computation. To avoid redundant computation on pad tokens, prepacking combines prompts of varying lengths into a sequence and packs multiple sequences into a compact batch using a bin-packing algorithm. It then modifies the attention mask and positional encoding to compute multiple prefilled KV-caches for multiple prompts within a single sequence. On standard curated dataset containing prompts with varying lengths, we obtain a significant speed and memory efficiency improvements as compared to the default padding-based prefilling computation within Huggingface across a range of base model configurations and inference serving scenarios.

Cancer is one of the leading causes of death globally, and early diagnosis is crucial for patient survival. Deep learning algorithms have great potential for automatic cancer analysis. Artificial intelligence has achieved high performance in recognizing and segmenting single lesions. However, diagnosing multiple lesions remains a challenge. This study examines and compares various neural network architectures and training strategies for automatically segmentation of cancer lesions using PET/CT images from the head, neck, and whole body. The authors analyzed datasets from the AutoPET and HECKTOR challenges, exploring popular single-step segmentation architectures and presenting a two-step approach. The results indicate that the V-Net and nnU-Net models were the most effective for their respective datasets. The results for the HECKTOR dataset ranged from 0.75 to 0.76 for the aggregated Dice coefficient. Eliminating cancer-free cases from the AutoPET dataset was found to improve the performance of most models. In the case of AutoPET data, the average segmentation efficiency after training only on images containing cancer lesions increased from 0.55 to 0.66 for the classic Dice coefficient and from 0.65 to 0.73 for the aggregated Dice coefficient. The research demonstrates the potential of artificial intelligence in precise oncological diagnostics and may contribute to the development of more targeted and effective cancer assessment techniques.

Robotic arms built from stiffness-adjustable, continuously bending segments serially connected with revolute joints have the ability to change their mechanical architecture and workspace, thus allowing high flexibility and adaptation to different tasks with less than six degrees of freedom, a concept that we call malleable robots. Known stiffening mechanisms may be used to implement suitable links for these novel robotic manipulators; however, these solutions usually show a reduced performance when bending due to structural deformation. By including an inner support structure this deformation can be minimised, resulting in an increased stiffening performance. This paper presents a new multi-material spine-inspired flexible structure for providing support in stiffness-controllable layer-jamming-based robotic links of large diameter. The proposed spine mechanism is highly movable with type and range of motions that match those of a robotic link using solely layer jamming, whilst maintaining a hollow and light structure. The mechanics and design of the flexible spine are explored, and a prototype of a link utilising it is developed and compared with limb segments based on granular jamming and layer jamming without support structure. Results of experiments verify the advantages of the proposed design, demonstrating that it maintains a constant central diameter across bending angles and presents an improvement of more than 203% of resisting force at 180 degrees.