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Pre-trained large language models (LLMs) have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks and to be appropriately specialized to particular domains. Here, we target bioinformatics due to the amount of domain knowledge, algorithms, and data operations this discipline requires. We present BioCoder, a benchmark developed to evaluate LLMs in generating bioinformatics-specific code. BioCoder spans much of the field, covering cross-file dependencies, class declarations, and global variables. It incorporates 1,026 Python functions and 1,243 Java methods extracted from GitHub, along with 253 examples from the Rosalind Project, all pertaining to bioinformatics. Using topic modeling, we show that the overall coverage of the included code is representative of the full spectrum of bioinformatics calculations. BioCoder incorporates a fuzz-testing framework for evaluation. We have applied it to evaluate various models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, GPT-3.5, and GPT- 4. Furthermore, we fine-tuned one model (StarCoder), demonstrating that our training dataset can enhance the performance on our testing benchmark (by >15% in terms of Pass@K under certain prompt configurations and always >3%). The results highlight two key aspects of successful models: (1) Successful models accommodate a long prompt (> 2,600 tokens) with full context, including functional dependencies. (2) They contain domain-specific knowledge of bioinformatics, beyond just general coding capability. This is evident from the performance gain of GPT-3.5/4 compared to the smaller models on our benchmark (50% vs. up to 25%). Availability and implementation: Code is available at: //github.com/gersteinlab/biocoder and //biocoder-benchmark. github.io/.

Large language models (LLMs) are revolutionizing conversational recommender systems by adeptly indexing item content, understanding complex conversational contexts, and generating relevant item titles. However, controlling the distribution of recommended items remains a challenge. This leads to suboptimal performance due to the failure to capture rapidly changing data distributions, such as item popularity, on targeted conversational recommendation platforms. In conversational recommendation, LLMs recommend items by generating the titles (as multiple tokens) autoregressively, making it difficult to obtain and control the recommendations over all items. Thus, we propose a Reindex-Then-Adapt (RTA) framework, which converts multi-token item titles into single tokens within LLMs, and then adjusts the probability distributions over these single-token item titles accordingly. The RTA framework marries the benefits of both LLMs and traditional recommender systems (RecSys): understanding complex queries as LLMs do; while efficiently controlling the recommended item distributions in conversational recommendations as traditional RecSys do. Our framework demonstrates improved accuracy metrics across three different conversational recommendation datasets and two adaptation settings

By harnessing the capabilities of large language models (LLMs), recent large multimodal models (LMMs) have shown remarkable versatility in open-world multimodal understanding. Nevertheless, they are usually parameter-heavy and computation-intensive, thus hindering their applicability in resource-constrained scenarios. To this end, several lightweight LMMs have been proposed successively to maximize the capabilities under constrained scale (e.g., 3B). Despite the encouraging results achieved by these methods, most of them only focus on one or two aspects of the design space, and the key design choices that influence model capability have not yet been thoroughly investigated. In this paper, we conduct a systematic study for lightweight LMMs from the aspects of model architecture, training strategy, and training data. Based on our findings, we obtain Imp -- a family of highly capable LMMs at the 2B-4B scales. Notably, our Imp-3B model steadily outperforms all the existing lightweight LMMs of similar size, and even surpasses the state-of-the-art LMMs at the 13B scale. With low-bit quantization and resolution reduction techniques, our Imp model can be deployed on a Qualcomm Snapdragon 8Gen3 mobile chip with a high inference speed of about 13 tokens/s.

Large language models (LLMs) have exhibited a strong promise in automatically generating executable code from natural language descriptions, particularly with interactive features that allow users to engage in the code-generation process by instructing the LLM with iterative feedback. However, existing interaction paradigms often assume that users have expert knowledge to debug source code and are not optimized for non-professional programmers' use. This raises challenges in making interactive code generation more accessible for individuals with varying levels of programming expertise. To tackle these challenges, we present IntelliExplain, which offers a novel human-LLM interaction paradigm to enhance non-professional programmers' experience by enabling them to interact with source code via natural language explanations. Users interact with IntelliExplain by providing natural language corrective feedback on errors they identify from the explanations. Feedback is used by the system to revise the code, until the user is satisfied with explanations by the system of the code. Our user study demonstrates that users with IntelliExplain achieve a significantly higher success rate 11.6% and 25.3% better than with vanilla GPT-3.5, while also requiring 39.0% and 15.6% less time in Text-to-SQL and Python code generation tasks, respectively.

Large language models (LLMs) are versatile and can address many tasks, but for computational efficiency, it is often desirable to distill their capabilities into smaller student models. One way to do this for classification tasks is via dataset synthesis, which can be accomplished by generating examples of each label from the LLM. Prior approaches to synthesis use few-shot prompting, which relies on the LLM's parametric knowledge to generate usable examples. However, this leads to issues of repetition, bias towards popular entities, and stylistic differences from human text. In this work, we propose Synthesize by Retrieval and Refinement (SynthesizRR), which uses retrieval augmentation to introduce variety into the dataset synthesis process: as retrieved passages vary, the LLM is "seeded" with different content to generate its examples. We empirically study the synthesis of six datasets, covering topic classification, sentiment analysis, tone detection, and humor, requiring complex synthesis strategies. We find SynthesizRR greatly improves lexical and semantic diversity, similarity to human-written text, and distillation performance, when compared to standard 32-shot prompting and six baseline approaches.

Retrieval-Augmented Language Modeling (RALM) by integrating large language models (LLM) with relevant documents from an external corpus is a proven method for enabling the LLM to generate information beyond the scope of its pre-training corpus. Previous work using utilizing retrieved content by simply prepending retrieved contents to the input poses a high runtime issue, which degrades the inference efficiency of the LLMs because they fail to use the Key-Value (KV) cache efficiently. In this paper, we propose \textsc{FlashBack}, a modular RALM designed to improve the inference efficiency of RALM with appending context pattern while maintaining decent performance after specific fine-tuning without heavily destruct the knowledge integrity of the LLM. \textsc{FlashBack} appends retrieved documents at the end of the context for efficiently utilizing the KV cache instead of prepending them. Our experiment shows that the inference speed of \textsc{FlashBack} is up to $4\times$ faster than the prepending method on a 7B LLM (Llama 2). Via bypassing unnecessary re-computation, it demonstrates an advancement by achieving significantly faster inference speed, and this heightened efficiency will substantially reduce inferential cost. Our code will be publicly available.

Large language models (LLMs) with retrieval augmented-generation (RAG) have been the optimal choice for scalable generative AI solutions in the recent past. However, the choice of use-cases that incorporate RAG with LLMs have been either generic or extremely domain specific, thereby questioning the scalability and generalizability of RAG-LLM approaches. In this work, we propose a unique LLM-based system where multiple LLMs can be invoked to enable data authentication, user query routing, data retrieval and custom prompting for question answering capabilities from data tables that are highly varying and large in size. Our system is tuned to extract information from Enterprise-level data products and furnish real time responses under 10 seconds. One prompt manages user-to-data authentication followed by three prompts to route, fetch data and generate a customizable prompt natural language responses. Additionally, we propose a five metric scoring module that detects and reports hallucinations in the LLM responses. Our proposed system and scoring metrics achieve >90% confidence scores across hundreds of user queries in the sustainability, financial health and social media domains. Extensions to the proposed extreme RAG architectures can enable heterogeneous source querying using LLMs.

Transformer-based large language models (LLM) have been widely used in language processing applications. However, most of them restrict the context window that permits the model to attend to every token in the inputs. Previous works in recurrent models can memorize past tokens to enable unlimited context and maintain effectiveness. However, they have "flat" memory architectures, which have limitations in selecting and filtering information. Since humans are good at learning and self-adjustment, we speculate that imitating brain memory hierarchy is beneficial for model memorization. We propose the Hierarchical Memory Transformer (HMT), a novel framework that enables and improves models' long-context processing ability by imitating human memorization behavior. Leveraging memory-augmented segment-level recurrence, we organize the memory hierarchy by preserving tokens from early input token segments, passing memory embeddings along the sequence, and recalling relevant information from history. Evaluating general language modeling (Wikitext-103, PG-19) and question-answering tasks (PubMedQA), we show that HMT steadily improves the long-context processing ability of context-constrained and long-context models. With an additional 0.5% - 2% of parameters, HMT can easily plug in and augment future LLMs to handle long context effectively. Our code is open-sourced on Github: //github.com/OswaldHe/HMT-pytorch.

Transformer-based large language models (LLMs) are now deployed to hundreds of millions of users. LLM inference is commonly performed on batches of sequences that share a prefix, such as few-shot examples or a chatbot system prompt. Decoding in this large-batch setting can be bottlenecked by the attention operation, which reads large key-value (KV) caches from memory and computes inefficient matrix-vector products for every sequence in the batch. In this work, we introduce Hydragen, a hardware-aware exact implementation of attention with shared prefixes. Hydragen computes attention over the shared prefix and unique suffixes separately. This decomposition enables efficient prefix attention by batching queries together across sequences, reducing redundant memory reads and enabling the use of hardware-friendly matrix multiplications. Our method can improve end-to-end CodeLlama-13b throughput by up to 32x against competitive baselines, with speedup growing with the batch size and shared prefix length. Hydragen also enables the use of very long shared contexts: with a large batch size, increasing the prefix length from 1K to 16K tokens decreases Hydragen throughput by less than 15%, while the throughput of baselines drops by over 90%. Hydragen generalizes beyond simple prefix-suffix decomposition and can be applied to tree-based prompt sharing patterns, allowing us to further reduce inference time on competitive programming problems by 55%.

The emergence of large language models (LLMs) has substantially influenced natural language processing, demonstrating exceptional results across various tasks. In this study, we employ ``Introspective Tips" to facilitate LLMs in self-optimizing their decision-making. By introspectively examining trajectories, LLM refines its policy by generating succinct and valuable tips. Our method enhances the agent's performance in both few-shot and zero-shot learning situations by considering three essential scenarios: learning from the agent's past experiences, integrating expert demonstrations, and generalizing across diverse games. Importantly, we accomplish these improvements without fine-tuning the LLM parameters; rather, we adjust the prompt to generalize insights from the three aforementioned situations. Our framework not only supports but also emphasizes the advantage of employing LLM in in-contxt decision-making. Experiments involving over 100 games in TextWorld illustrate the superior performance of our approach.