Daily Papers

Comprehensively characterizing cellular diversity is critical for understanding tissue development, identifying disease-associated populations and investigating gene programmes linked to specialized functions. Advances in single-cell profiling reveal additional cell-specific transcripts and molecular associations, yet many foundation models represent only a restricted portion of this increasingly rich molecular information. Here we present CellNet, which enables panoramic modelling of single-cell transcriptomes by integrating DNA-derived gene identities and measured RNA expression in a shared image representation. Pretrained on 231 million cell profiles spanning 40 species, CellNet improves rare-population and condition-associated state recognition in evaluated cohorts while retaining competitive general cell representations. It predicts withheld coding-gene expression and selected non-coding targets in total-RNA data, and recovers lineage-specific expression patterns in spatial measurements. Prediction also extends across species, including to targets without expression-pretraining exposure. Its gene representations retrieve known non-coding modules and developmental or neural programmes, including from sparsely detected RNA queries. Together, these results establish CellNet as a scalable framework for interpreting cellular diversity through increasingly comprehensive transcriptomic measurements.

NeMo (Neural Modules) is a Python framework-agnostic toolkit for creating AI applications through re-usability, abstraction, and composition. NeMo is built around neural modules, conceptual blocks of neural networks that take typed inputs and produce typed outputs. Such modules typically represent data layers, encoders, decoders, language models, loss functions, or methods of combining activations. NeMo makes it easy to combine and re-use these building blocks while providing a level of semantic correctness checking via its neural type system. The toolkit comes with extendable collections of pre-built modules for automatic speech recognition and natural language processing. Furthermore, NeMo provides built-in support for distributed training and mixed precision on latest NVIDIA GPUs. NeMo is open-source https://github.com/NVIDIA/NeMo

Natural language-driven no-code development allows users to specify software functionality using natural language (NL) instead of editing source code, promising increased productivity and democratized development. Large language models (LLMs) show potential in enabling this paradigm. In this context, software documentation acts as an NL specification for functionality. This work introduces NoCode-bench, a benchmark designed to evaluate LLMs on real-world NL-driven feature addition tasks, consisting of 634 tasks across 10 projects and 114k code changes. Each task pairs documentation updates with corresponding code implementations, validated by developer-written test cases. A subset of 114 high-quality, human-verified instances, NoCode-bench Verified, ensures reliable evaluation. Our experiments reveal that, despite high token usage, the best LLMs achieve a task success rate of only 28.07%, highlighting challenges in cross-file editing, codebase understanding, and tool calling. These findings indicate that LLMs are not yet ready for fully NL-driven no-code development. NoCode-bench lays the foundation for future advances in this area.

Neural Module Networks, originally proposed for the task of visual question answering, are a class of neural network architectures that involve human-specified neural modules, each designed for a specific form of reasoning. In current formulations of such networks only the parameters of the neural modules and/or the order of their execution is learned. In this work, we further expand this approach and also learn the underlying internal structure of modules in terms of the ordering and combination of simple and elementary arithmetic operators. Our results show that one is indeed able to simultaneously learn both internal module structure and module sequencing without extra supervisory signals for module execution sequencing. With this approach, we report performance comparable to models using hand-designed modules.

Large Language Models (LLMs) have significantly advanced the automation of software engineering tasks. One prominent example is code generation, where an LLM produces code in a specified programming language based on a natural language description. Most research in this area has focused on high-resource languages, such as Python or Java, which benefit from abundant training data. A smaller body of work has explored low-resource languages, which are underrepresented in training corpora. In contrast, no-resource languages for which LLMs have seen virtually no training data remain largely unstudied. These languages often emerge in industry, where organizations develop proprietary or domain-specific languages unsupported by commercial tools like GitHub Copilot. This results in the need for companies to deploy their own in-house code recommenders. To investigate possible solutions in this context, we build and release three code generation benchmarks for no-resource languages, based on two recently proposed programming languages for which very little training data is available. Using these benchmarks, we experiment several solutions to teach LLMs about no-resource languages, including prompt-based techniques as well as pre-training and fine-tuning exploiting the little data available. While further pre-training gives the largest performance gains for no-resource languages, applying it directly to instruction-tuned models harms their ability to follow instructions. To address this, we start from a base model, further pre-training it on the target language, and then inject instruction-following capabilities via weight diff transfer from an instruction model. Such an approach significantly improves code generation capabilities in no-resource settings, allowing companies to cheaply deploy a specialized instruct model without dealing with the computational cost of instruction fine-tuning.

Neural Module Network (NMN) is a machine learning model for solving the visual question answering tasks. NMN uses programs to encode modules' structures, and its modularized architecture enables it to solve logical problems more reasonably. However, because of the non-differentiable procedure of module selection, NMN is hard to be trained end-to-end. To overcome this problem, existing work either included ground-truth program into training data or applied reinforcement learning to explore the program. However, both of these methods still have weaknesses. In consideration of this, we proposed a new learning framework for NMN. Graph-based Heuristic Search is the algorithm we proposed to discover the optimal program through a heuristic search on the data structure named Program Graph. Our experiments on FigureQA and CLEVR dataset show that our methods can realize the training of NMN without ground-truth programs and achieve superior efficiency over existing reinforcement learning methods in program exploration.

Non-local (NL) block is a popular module that demonstrates the capability to model global contexts. However, NL block generally has heavy computation and memory costs, so it is impractical to apply the block to high-resolution feature maps. In this paper, to investigate the efficacy of NL block, we empirically analyze if the magnitude and direction of input feature vectors properly affect the attention between vectors. The results show the inefficacy of softmax operation which is generally used to normalize the attention map of the NL block. Attention maps normalized with softmax operation highly rely upon magnitude of key vectors, and performance is degenerated if the magnitude information is removed. By replacing softmax operation with the scaling factor, we demonstrate improved performance on CIFAR-10, CIFAR-100, and Tiny-ImageNet. In Addition, our method shows robustness to embedding channel reduction and embedding weight initialization. Notably, our method makes multi-head attention employable without additional computational cost.

Large Language Models (LLMs) have showcased impressive capabilities in handling straightforward programming tasks. However, their performance tends to falter when confronted with more challenging programming problems. We observe that conventional models often generate solutions as monolithic code blocks, restricting their effectiveness in tackling intricate questions. To overcome this limitation, we present Modular-of-Thought Coder (MoTCoder). We introduce a pioneering framework for MoT instruction tuning, designed to promote the decomposition of tasks into logical sub-tasks and sub-modules. Our investigations reveal that, through the cultivation and utilization of sub-modules, MoTCoder significantly improves both the modularity and correctness of the generated solutions, leading to substantial relative pass@1 improvements of 12.9% on APPS and 9.43% on CodeContests. Our codes are available at https://github.com/dvlab-research/MoTCoder.

Deep representations have shown promising performance when transferred to downstream tasks in a black-box manner. Yet, their inherent lack of interpretability remains a significant challenge, as these features are often opaque to human understanding. In this paper, we propose Non-negative Contrastive Learning (NCL), a renaissance of Non-negative Matrix Factorization (NMF) aimed at deriving interpretable features. The power of NCL lies in its enforcement of non-negativity constraints on features, reminiscent of NMF's capability to extract features that align closely with sample clusters. NCL not only aligns mathematically well with an NMF objective but also preserves NMF's interpretability attributes, resulting in a more sparse and disentangled representation compared to standard contrastive learning (CL). Theoretically, we establish guarantees on the identifiability and downstream generalization of NCL. Empirically, we show that these advantages enable NCL to outperform CL significantly on feature disentanglement, feature selection, as well as downstream classification tasks. At last, we show that NCL can be easily extended to other learning scenarios and benefit supervised learning as well. Code is available at https://github.com/PKU-ML/non_neg.

Though LLMs are capable of generating plausible programs, it's challenging to interact with the LLMs further to revise the program, especially if the user's specific requirements are different from the initial proposal. In this paper, we introduce ANPL, an interactive programming system that ensures users can always refine the generated code towards their specific programmatic intents via structured decompositions. Borrowing the paradigm of sketching from program synthesis, an ANPL program consists of a set of input-outputs that it must satisfy, a ``sketch'' -- control/data flow expressed in precise code (e.g. Python), and ``holes'' -- sub-modules to be implemented by the LLM specified with natural language. The user revises an ANPL program by either modifying the sketch, changing the language used to describe the holes, or providing additional input-outputs to a particular hole, turning it into a sub-ANPL program that can be solved recursively. This workflow allows the users to offload programming burdens to the LLM as much as possible while retaining the ability to pinpoint and resolve bugs locally, without exposing the rest of the program to the LLM. We deploy ANPL on the Abstraction and Reasoning Corpus (ARC), a set of unique tasks that are challenging for state-of-the-art AI systems, showing it outperforms baseline programming systems that (a) without the ability to decompose tasks interactively and (b) without the guarantee that the modules can be correctly composed together. Additional evaluations on APPS, HumanEval, and real-world programming tasks have validated that the ANPL framework is applicable to multiple programming domains. We release the ANPL solutions to the ARC tasks as a dataset, providing insights into how humans decompose novel tasks programmatically. See our code at https://iprc-dip.github.io/ANPL/.

We do not speak word by word from scratch; our brain quickly structures a pattern like sth do sth at someplace and then fill in the detailed descriptions. To render existing encoder-decoder image captioners such human-like reasoning, we propose a novel framework: learning to Collocate Neural Modules (CNM), to generate the `inner pattern' connecting visual encoder and language decoder. Unlike the widely-used neural module networks in visual Q\&A, where the language (ie, question) is fully observable, CNM for captioning is more challenging as the language is being generated and thus is partially observable. To this end, we make the following technical contributions for CNM training: 1) compact module design --- one for function words and three for visual content words (eg, noun, adjective, and verb), 2) soft module fusion and multi-step module execution, robustifying the visual reasoning in partial observation, 3) a linguistic loss for module controller being faithful to part-of-speech collocations (eg, adjective is before noun). Extensive experiments on the challenging MS-COCO image captioning benchmark validate the effectiveness of our CNM image captioner. In particular, CNM achieves a new state-of-the-art 127.9 CIDEr-D on Karpathy split and a single-model 126.0 c40 on the official server. CNM is also robust to few training samples, eg, by training only one sentence per image, CNM can halve the performance loss compared to a strong baseline.

Chat-based language models are designed to be helpful, yet they should not comply with every user request. While most existing work primarily focuses on refusal of "unsafe" queries, we posit that the scope of noncompliance should be broadened. We introduce a comprehensive taxonomy of contextual noncompliance describing when and how models should not comply with user requests. Our taxonomy spans a wide range of categories including incomplete, unsupported, indeterminate, and humanizing requests (in addition to unsafe requests). To test noncompliance capabilities of language models, we use this taxonomy to develop a new evaluation suite of 1000 noncompliance prompts. We find that most existing models show significantly high compliance rates in certain previously understudied categories with models like GPT-4 incorrectly complying with as many as 30% of requests. To address these gaps, we explore different training strategies using a synthetically-generated training set of requests and expected noncompliant responses. Our experiments demonstrate that while direct finetuning of instruction-tuned models can lead to both over-refusal and a decline in general capabilities, using parameter efficient methods like low rank adapters helps to strike a good balance between appropriate noncompliance and other capabilities.

Out-of-distribution (OOD) detection refers to training the model on an in-distribution (ID) dataset to classify whether the input images come from unknown classes. Considerable effort has been invested in designing various OOD detection methods based on either convolutional neural networks or transformers. However, zero-shot OOD detection methods driven by CLIP, which only require class names for ID, have received less attention. This paper presents a novel method, namely CLIP saying no (CLIPN), which empowers the logic of saying no within CLIP. Our key motivation is to equip CLIP with the capability of distinguishing OOD and ID samples using positive-semantic prompts and negation-semantic prompts. Specifically, we design a novel learnable no prompt and a no text encoder to capture negation semantics within images. Subsequently, we introduce two loss functions: the image-text binary-opposite loss and the text semantic-opposite loss, which we use to teach CLIPN to associate images with no prompts, thereby enabling it to identify unknown samples. Furthermore, we propose two threshold-free inference algorithms to perform OOD detection by utilizing negation semantics from no prompts and the text encoder. Experimental results on 9 benchmark datasets (3 ID datasets and 6 OOD datasets) for the OOD detection task demonstrate that CLIPN, based on ViT-B-16, outperforms 7 well-used algorithms by at least 2.34% and 11.64% in terms of AUROC and FPR95 for zero-shot OOD detection on ImageNet-1K. Our CLIPN can serve as a solid foundation for effectively leveraging CLIP in downstream OOD tasks. The code is available on https://github.com/xmed-lab/CLIPN.

Recent works have shown that Large Language Models (LLMs) could empower traditional neuro-symbolic models via programming capabilities to translate language into module descriptions, thus achieving strong visual reasoning results while maintaining the model's transparency and efficiency. However, these models usually exhaustively generate the entire code snippet given each new instance of a task, which is extremely ineffective. We propose generative neuro-symbolic visual reasoning by growing and reusing modules. Specifically, our model consists of three unique stages, module initialization, module generation, and module execution. First, given a vision-language task, we adopt LLMs to examine whether we could reuse and grow over established modules to handle this new task. If not, we initialize a new module needed by the task and specify the inputs and outputs of this new module. After that, the new module is created by querying LLMs to generate corresponding code snippets that match the requirements. In order to get a better sense of the new module's ability, we treat few-shot training examples as test cases to see if our new module could pass these cases. If yes, the new module is added to the module library for future reuse. Finally, we evaluate the performance of our model on the testing set by executing the parsed programs with the newly made visual modules to get the results. We find the proposed model possesses several advantages. First, it performs competitively on standard tasks like visual question answering and referring expression comprehension; Second, the modules learned from one task can be seamlessly transferred to new tasks; Last but not least, it is able to adapt to new visual reasoning tasks by observing a few training examples and reusing modules.